Research Computing Center Wiki - User contributions [en]

Training

2019-09-26T19:39:39Z

Pakala: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==
In '''October''' 2019, the GACRC hosts nine regular training sessions (Sapelo2 cluster new user training, Linux basics, and Python basics).

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || October 4th, Friday, 10 AM - 12 PM
|-
| Using Sapelo2 Cluster at the GACRC || October 9th, Wednesday, 1 PM - 3 PM
|-
| Using Sapelo2 Cluster at the GACRC || October 18th, Friday, 1 PM - 3 PM
|-
| Using Sapelo2 Cluster at the GACRC || October 23rd, Wednesday, 1 PM - 3 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || September 27th, Friday, 1 PM - 3 PM
|-
| Use Linux on Cluster || October 2nd, Wednesday, 1 PM - 3 PM
|-
| Use Linux on Cluster || October 11th, Friday, 10 AM - 12 PM
|-
| Use Linux on Cluster || October 18th, Friday, 10 AM - 12 PM
|-
| Use Linux on Cluster || October 25th, Friday, 1 PM - 3 PM
|-
|}

===Python Basics ===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python basics || October 11th, Friday, 1 PM - 3 PM
|-
|}

==How to Register==

If you would like to attend, please send us a request using the GACRC Training Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25852 . In your request, please tell us which session(s) you want to attend.

'''Please note''', training workshops '''Using Sapelo2 Cluster at the GACRC''' and '''Use Linux on Cluster''' are ONLY offered for new users who need computing user accounts on the GACRC Sapelo2 cluster. If you want to have a user account on the Sapelo2 cluster, please ask your group PI to send us a request using the GACRC User Account Request form at https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 HPC cluster and computational batch job submission workflow

Cluster's storage environment

Computational queues on cluster

Software environment

How to submit computational batch jobs

Other tips and guidelines for users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common commands, filesystem, and shell

Linux shell scripting basics

Common Linux utilities, e.g., grep, sed, find, sort, and awk, etc.

Linux Hands-on practice

Title: '''Python Basics I, II'''

Focus of I: Python language overview, scientific modules and distributions

Python general lexical conventions

Basic built-in data types, like string, list, tuple, dictionary, etc.

Focus of II: Programming structures: control flow and loop

Function: procedural programming with examples, lambda expression, factory function and generator

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Install Python packages/modules in a user's home directory on Sapelo2 cluster

Python versions installed on Sapelo2

Python environment details on Sapelo2

How to know a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly!'''

Focus: Use conda to create and configure your own python virtual environments; Activate your environments to run python apps from your home directory on Sapelo2

What is Conda and its environment

Conda on Sapelo2

Use conda to create and configure your own python virtual environments

Activate your environments to run python apps from your home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Basic Graphs in R'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Description: This course will assume little to no background knowledge in R

Understand fundamentals of graph plotting in R; Know how to how to load data in R; Learn how to draw a variety of univariate and bivariate graphs, such as histograms, bar charts, and scatter plots

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v6.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver3.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04252019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Using conda on the GACRC Sapelo2 Cluster.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Department of Linguistics - Fall2019 || On-class (LING6570) || [[media: GACRC Teaching cluster new user training workshop LING6570 Part2.pdf]]
|-
| The Center for Simulational Physics - Fall2019 || Out-Reach (Seminar Talk 20190820) || [[media: Introduction to GACRC Computing Facility - Sapelo2 Cluster CSP-Fall2019.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer2018 || Out-Reach (Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer2017 || Out-Reach (Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

File:Linux Training For New Users Of Cluster Suchi 04252019.pdf

2019-04-24T20:28:33Z

Pakala: Pakala uploaded a new version of File:Linux Training For New Users Of Cluster Suchi 04252019.pdf

Training

2019-04-24T20:24:14Z

Pakala: /* Linux Training for New Cluster Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''May''' 2019, the GACRC is going to host eight regular training sessions (Sapelo2 cluster new user training, Linux basics, Python) and one topical session on using Conda environment on Sapelo2 cluster.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python (1 session)

4. Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly! (1 session)

Brief introduction: Conda is an open source package management system and environment management system that you can use to quickly install, run and update Python packages and their dependencies. Since Conda easily creates, saves, loads and switches between environments in your home directory on the Sapelo2 cluster, it will become very easy for you to create and maintain your own software environment for your research needs on the Sapelo2 cluster.

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || May 14th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || May 20th, Monday, 1:00 PM - 3:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || May 30th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || May 13th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || May 23rd, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || May 28th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Basics || May 21st, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' Regular Sapelo2 users who have user account on the Sapelo2 cluster

'''Training Goal:'''

1. Understand what is Conda and its virtual environment

2. Know how to use conda to create and configure your own python virtual environments

3. Know how to activate your environments to run python apps from your home directory on Sapelo2

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly! || May 16th, Thursday, 1:45 PM - 3:30 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 HPC cluster and computational batch job submission workflow

Cluster's storage environment

Computational queues on cluster

Software environment

How to submit computational batch jobs

Other tips and guidelines for users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common commands, filesystem, and shell

Linux shell scripting basics

Common Linux utilities, e.g., grep, sed, find, sort, and awk, etc.

Linux Hands-on practice

Title: '''Python Basics I, II'''

Focus of I: Python language overview, scientific modules and distributions

Python general lexical conventions

Basic built-in data types, like string, list, tuple, dictionary, etc.

Focus of II: Programming structures: control flow and loop

Function: procedural programming with examples, lambda expression, factory function and generator

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Install Python packages/modules in a user's home directory on Sapelo2 cluster

Python versions installed on Sapelo2

Python environment details on Sapelo2

How to know a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''Do It Yourself: Using Conda to create and run python environments to suit your computing needs effortlessly!'''

Focus: Use conda to create and configure your own python virtual environments; Activate your environments to run python apps from your home directory on Sapelo2

What is Conda and its environment

Conda on Sapelo2

Use conda to create and configure your own python virtual environments

Activate your environments to run python apps from your home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04252019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Conda on Sapelo2.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

File:Linux Training For New Users Of Cluster Suchi 04252019.pdf

2019-04-24T20:23:39Z

Pakala:

Training

2019-04-10T18:15:29Z

Pakala: /* Linux Training for Linux-inexperienced Cluster New Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April''' 2019, the GACRC is going to host twelve regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics, Perl basics) and one topical session on Conda basics.

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Perl basics (1 session)

4. Conda basics (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || April 4th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || April 8th, Monday, 1:00 PM - 3:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || April 16th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || April 25th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || April 2nd, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 11th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 15th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 23rd, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || April 9th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics II || April 18th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics I===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand Perl general scripting style

2. Know how to make a simple perl script and run it on perl command line

3. Understand Perl language fundamentals, e.g., scalar data and variable, list data and array, scalar and list context

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || April 22nd, Monday, 1:00 PM - 3:00 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' Regular Sapelo2 users who have user account on the Sapelo2 cluster

'''Training Goal:'''

1. Conda environment on Sapelo2

2. How to use conda for configuring your own Python environment on the cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Conda Basics on Sapelo2 || April 29th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 02202019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Conda on Sapelo2.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2019-04-10T18:15:15Z

Pakala: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April''' 2019, the GACRC is going to host twelve regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics, Perl basics) and one topical session on Conda basics.

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Perl basics (1 session)

4. Conda basics (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || April 4th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || April 8th, Monday, 1:00 PM - 3:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || April 16th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || April 25th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || March 26th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 2nd, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 11th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 15th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 23rd, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || April 9th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics II || April 18th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics I===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand Perl general scripting style

2. Know how to make a simple perl script and run it on perl command line

3. Understand Perl language fundamentals, e.g., scalar data and variable, list data and array, scalar and list context

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || April 22nd, Monday, 1:00 PM - 3:00 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' Regular Sapelo2 users who have user account on the Sapelo2 cluster

'''Training Goal:'''

1. Conda environment on Sapelo2

2. How to use conda for configuring your own Python environment on the cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Conda Basics on Sapelo2 || April 29th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 02202019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Conda on Sapelo2.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2019-02-20T18:41:53Z

Pakala: /* Linux Training for New Cluster Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2019, the GACRC is going to host nine regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics) and one topical session on basic programming in R language.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Basic Programming in R (1 two-hour session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || February 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 4th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 21st, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' Linux basics

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || February 11th, Monday, 1:00 PM - 3:00 PM
|-
| Python Language Basics II || February 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Use probability functions in R

2. Make a function for simple computational tasks

3. Understand R programming structures of loops and branching statements

4. Optimize a function

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Basic Programming in R || February 18th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 02202019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2019-02-15T21:15:13Z

Pakala: /* Python Basics I/II */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2019, the GACRC is going to host nine regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics) and one topical session on basic programming in R language.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Basic Programming in R (1 two-hour session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || February 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 4th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 21st, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' Linux basics

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || February 11th, Monday, 1:00 PM - 3:00 PM
|-
| Python Language Basics II || February 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Use probability functions in R

2. Make a function for simple computational tasks

3. Understand R programming structures of loops and branching statements

4. Optimize a function

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Basic Programming in R || February 18th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 02152019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2019-02-15T20:27:20Z

Pakala: /* Linux Training for New Cluster Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2019, the GACRC is going to host nine regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics) and one topical session on basic programming in R language.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Basic Programming in R (1 two-hour session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || February 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 4th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 21st, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' Linux basics

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || January 31st, Thursday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || February 11th, Monday, 1:00 PM - 3:00 PM
|-
| Python Language Basics II || February 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Use probability functions in R

2. Make a function for simple computational tasks

3. Understand R programming structures of loops and branching statements

4. Optimize a function

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Basic Programming in R || February 18th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 02152019.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2019-01-30T13:43:38Z

Pakala: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend a Sapelo2 cluster introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2019, the GACRC is going to host nine regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics) and one topical session on basic programming in R language.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Basic Programming in R (1 two-hour session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===
'''Prerequisite:''' Linux basics. A Linux-inexperienced user must complete a prerequisite Linux training for Linux-inexperienced cluster new users.

'''Training Goal:'''

1. Know how to log on to cluster in or off campus

2. Understand cluster storage and software environment

3. Know how to submit a computational batch job following Sapelo2 cluster general workflow

4. Know how to find support from the GACRC support team when you have any issues running on cluster

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || February 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Understand fundamental concepts of Linux working environment (filesystem hierarchy, path, PATH, etc.)

2. Know how to use Linux common commands (ls, cd, pwd, cat, more, nano, mkdir, rm, cp, mv, etc.)

3. Understand what is Linux bash shell and know how to make a simple Linux script and run it in Linux environment

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 4th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 21st, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===
'''Prerequisite:''' Linux basics

'''Training Goal:'''

1. Understand fundamental concepts of Python (interpreter, module, package, distribution, 3rd-party-modules like numpy, scipy, etc.)

2. Know how to run python interactively and how to make a simple python script and run it on python command line

3. Understand Python language fundamentals, e.g., built-in data types (list, tuple, string, etc.), functions, built-in modules (os, sys, re, csv, etc.)

4. Know how to define a function and call it for basic text/csv file I/O

5. Understand Python object-oriented programming (OOP) fundamentals using class, inheritance and polymorphism (Python-II)

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || January 31st, Thursday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || February 11th, Monday, 1:00 PM - 3:00 PM
|-
| Python Language Basics II || February 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===
'''Prerequisite:''' No prerequisites

'''Training Goal:'''

1. Use probability functions in R

2. Make a function for simple computational tasks

3. Understand R programming structures of loops and branching statements

4. Optimize a function

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Basic Programming in R || February 18th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 11272018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2019-01-25T16:13:17Z

Pakala: /* Linux Training for Linux-inexperienced Cluster New Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2019, the GACRC is going to host nine regular training sessions (Sapelo2 cluster new user training, Linux basics, Python basics) and one topical session on basic programming in R language.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Basic Programming in R (1 two-hour session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || January 28th, Monday, 1:00 PM - 3:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using Sapelo2 Cluster at the GACRC || February 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 4th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 21st, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics I/II===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || January 31st, Thursday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || February 11th, Monday, 1:00 PM - 3:00 PM
|-
| Python Language Basics II || February 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Basic Programming in R || February 18th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 11272018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || On-Class (PHYS4601/6601) || [[media:GACRC Teaching cluster new user training workshop-phys4601.pdf]] [[media:Gacrc handout2019 phys4601.pdf]]
|-
| The Center for Simulational Physics || On-Class (PHYS8602) || [[media:GACRC Teaching cluster new user training workshop-phys8602.pdf]] [[media:Gacrc handout2019 phys8602.pdf]]
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2019]]

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-12-04T19:28:09Z

Pakala: /* Topical Sessions */

Training

2018-12-04T19:25:36Z

Pakala: /* Linux Training for Linux-inexperienced Cluster New Users */

Training

2018-12-04T19:24:31Z

Pakala: /* Sapelo2 Cluster New User Training */

Training

2018-12-04T19:23:13Z

Pakala: /* Regular Training Announcement */

Training

2018-12-04T19:22:52Z

Pakala: /* Regular Training Announcement */

Transferring Files

2018-12-03T19:39:42Z

Pakala: /* Using FileZilla */

[[Category:Zcluster]][[Category:Sapelo2]][[Category:Teaching]]

===The File Transfer nodes (xfer.gacrc.uga.edu)===

Users can transfer files between their local machines and GACRC storage using various programs, such as (a) Filezilla, (b) WinSCP, (c) a secure copy (scp), and (d) an SSH secure File Transfer software (SSH file transfer). To transfer files, you must have a file transfer program installed on your local machine and a connection to the UGA campus network.

All Sapelo2 users, as well as all GACRC PIs, can access the xfer nodes using the hostname '''xfer.gacrc.uga.edu''' and using their UGA MyID (not the 810 or 811 number) and the MyID password to authenticate. Two-factor authentication using Archpass Duo is also necessary. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo].

For connecting from off-campus, please first connect to the UGA VPN and then connect to xfer.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN].

To transfer files using scp (or SSH file transfer) you must have scp (or SSH) on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

The GACRC file transfer nodes (xfer) are configured to facilitate file transfer. These nodes, which have a hostname of '''xfer.gacrc.uga.edu''', are connected via a higher-bandwidth network connection. Hence, maximum transfer speed between a user's local machine and the GACRC systems can be achieved by transferring files to/from the host xfer.gacrc.uga.edu (instead of the login nodes of the clusters).

Note that a user's home directory on the xfer nodes is the same as the user's Sapelo2 home directory, which is '''not''' the same as the user's home directory on the teaching cluster.

The xfer node can access the following file systems using the full path:

1. Your home directory on an xfer node is the same as your Sapelo2 home directory, and the path is /home/username

2. The zcluster home directory: /panfs/pstor.storage/home/groupname/username '''(for former zcluster users only)'''

3. The zcluster escratch4 directory: /escratch4/username '''(for former zcluster users only)'''

4. The Sapelo2 scratch directory: /scratch/username

5. The Sapelo2 work directory: /work/groupname

6. The project file system for the lab: /project/groupname

'''Note:''' Starting Nov. 16th, the old /lustre1 file system was replaced by a /scratch file system. All files that were present in /lustre1 on Nov. 16th have been copied to /scratch. When submitting new jobs, please use /scratch and do not use /lustre1 anymore.

===Transferring Files from your local storage device to Sapelo2 or vice-versa===

To transfer files from your local storage device to Sapelo2 or from Sapelo2 to your local storage device, please connect to xfer.gacrc.uga.edu (use your UGA MyID, the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

====Using FileZilla====

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and Sapelo2, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://xfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

Once the connection is established you can upload files from your local machine to Sapelo2 or download files from Sapelo2 to your local machine.

Here is the PDF to check step-by-step screen shots:
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[ media:Xfer Filezilla 12032018.pdf]]
|-
|}

====Using WinSCP====

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and Sapelo2, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: xfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, kept the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.

====Using SSH Secure File Transfer====

In order to use the SSH Secure File Transfer software that is installed as part of SSH (Secure Shell Utilities for Windows) available on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page, users need to start the Secure File Transfer application and open a connection to host xfer.gacrc.uga.edu. You will have to enter your UGA MyID as the username, but other fields (port number, etc) can be left empty (or leave the default value, if any). You will be prompted for your MyID password and after that you will be prompted to enter DUO two factor authentication code. Please choose one of the options like DUO push, Phone call or SMS passcodes. Once the connection is established, you can upload or download files.

Here is the PDF to check step-by-step screen shots:
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[ media:Xfer SSH File Transfer Nov292018.pdf]]
|-
|}

====Using scp====

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to Sapelo2:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your Sapelo2 home directory to which files are being transferred. You will then be asked to enter your UGA MyID password. You will also be prompted for two-factor authentication with Archpass Duo.

(Note: yourUGAMyID@ can be omitted if your username on Sapelo2 is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer (e.g. all files with .dat extension):

<pre class="gcommand">
scp *.dat yourUGAMyID@xfer.gacrc.uga.edu:subdirectory
</pre>

A directory and all its contents can be transferred using the scp option '''-r''', for recursive file transferring. For example, to transfer a directory on your local machine called programs and all files in it to your Sapelo2 home directory, use:

<pre class="gcommand">
scp -r programs yourUGAMyID@xfer.gacrc.uga.edu:
</pre>

You can also use the scp option '''-p''' to preserve the file features, such as last modification time, file permissions, etc.

To transfer files directly to your Sapelo2 /scratch area (such as /scratch/johndoe/):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/scratch/johndoe/subdirectory
</pre>

To transfer files directly to your Sapelo2 work directory:

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/work/groupname/subdirname
</pre>

To transfer files directly to your lab's project file system (such as /project/groupname):

<pre class="gcommand">
scp filename yourUGAMyID@xfer.gacrc.uga.edu:/project/groupname
</pre>

To transfer files from the decommissioned zcluster home dir to your local machine

From your local machine, issue the command:

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:/panfs/pstor.storage/home/groupname/username/subdirectory/filename ./
</pre>

The transferred file will be at your working directory. (Note: yourUGAMyID@ can be omitted if your username on Sapelo2 is the same as on your local machine)

Wildcards can be used for multiple file transfer (e.g. all files with .dat extension in your Sapelo2 home dir, in a subdirectory called subdir):

<pre class="gcommand">
scp yourUGAMyID@xfer.gacrc.uga.edu:subdir/\*.dat ./
</pre>

(Note the backslash “ \ ” preceeding * in the last example.)

====Download directly from internet to Sapelo2====

Here is an example on how to download [http://hannonlab.cshl.edu/fastx_toolkit/index.html FastaX] software from internet directly to Sapelo2

<pre class="gcommand">
wget https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>

Some websites use indirect connections, it could be downloaded as
<pre class="gcommand">
curl -OL https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
</pre>



===Transferring Files from the decommissioned zcluster to Sapelo2===

Use ssh to login to xfer.gacrc.uga.edu using your UGA MyID username and MyID password. You will also be prompted for two-factor authentication with Archpass Duo. This file transfer node has the following file systems mounted:

* zcluster /escratch4 file system. To access it, use e.g.
<pre class="gcommand">
cd /escratch4/username
</pre>

* zcluster home file systems. To access your zcluster home directory, use the following
<pre class="gcommand">
cd /panfs/pstor.storage/home/groupname/username
</pre>

For example, if your group is named abclab and your username is jsmith use
<pre class="gcommand">
cd /panfs/pstor.storage/home/abclab/jsmith
</pre>

* Sapelo2 home file systems. To access your Sapelo2 home directory, use the following
<pre class="gcommand">
cd /home/username
</pre>

* Sapelo2 scratch file system on the Lustre file system. To access your /scratch space use the following
<pre class="gcommand">
cd /scratch/username
</pre>

* Sapelo2 work file system on the Lustre file system. To access your group's /work space use the following
<pre class="gcommand">
cd /work/abclab
</pre>

* /project file system. To access your group's /project space use the following (please note that this file system is mounted when it is first accessed, so you need to access it with the full path):
<pre class="gcommand">
cd /project/abclab
</pre>

Because the xfer node mounts all these file systems, users can ssh into an xfer node and use '''cp''' or '''rsync''' to copy the files between any two of these file systems. Users can also copy files from their zcluster home dirs or /escratch4 to their project file system (/project/groupname).

===Transferring Files between two file systems on Sapelo2===

Use ssh to login to xfer.gacrc.uga.edu using your UGA MyID username and password (and two-factor authentication via Archpass Duo) to transfer files between different file systems on Sapelo2, including the project area.



===The File Transfer node for the teaching cluster (txfer.gacrc.uga.edu)===

Users can transfer files between their local machines and the teaching cluster using (a) Filezilla, (b) a secure copy (scp), or (c) an SSH secure File Transfer software (SSH file transfer). To transfer files using scp (or SSH file transfer) you must have scp (or SSH) on your local machine and a connection to the UGA campus network. An scp software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure File Transfer Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

Access to txfer.gacrc.uga.edu requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

===Transferring Files from your local storage device to the teaching cluster===

To transfer files from your local storage device to the teaching cluster, please connect to txfer.gacrc.uga.edu (use your UGA MyID and the MyID password to authenticate). You will also be prompted for two-factor authentication with Archpass Duo.

====Using FileZilla====

In order to use [http://filezilla-project.org/ FileZilla] to transfer files between a local machine and the teaching cluster, users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these steps:

1. Go to File -> Site Manager

2. Add a New Site with the following configuration.

In the '''General''' tab select

<pre class="gcomment">

Protocol: SFTP - SSH File Transfer Protocol

Host: sftp://txfer.gacrc.uga.edu

Port: 22

Logon Type: Interactive

User: [your UGA MyID]
</pre>

In the '''Transfer Settings''' tab, check the box for "Limit number of simultaneous connections" and set "Maximum number of connections" to 1.

If this step is omitted, then you will need to enter your password and Duo authentication for each file that you upload or download. By limiting the number of simultaneous connections to 1, you only need to enter your password and Duo authentication once per session.

With the above settings saved, you should be able to transfer files to txfer using filezilla. When you open the connection, you will be prompted for your MyID password (unless you use key based ssh). If the password authenticates successfully, then another pop-up window will prompt for Duo. Note that the Duo window looks very similar to the password window, but the text in the box will describe the options you can use for Duo (for example, a push, enter a passcode, etc).

====Using WinSCP====

In order to use [http://winscp.net/ WinSCP] to transfer files between a local Windows machine and the teaching cluster, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcut button, Login window pops up, in that you select new site and enter the following information to start the new session:

<pre class="gcomment">

Session:

File Protocol: SFTP

Host name: txfer.gacrc.uga.edu

Port number: 22

Username: [your UGA MyID]

Password: [your MyID password]

</pre>

If the password authenticates successfully, then another pop-up window will prompt for Duo two-factor authentication. It says, Using Keyboard-interactive authentication and lists the Duo options you can choose from: Duo push, Phone Call, or SMS passcode, etc. Once the connection is established you can upload or download files from Local Machine to Cluster or vice-versa. Note: Under Advanced, kept the "Default" option for Transfer settings Rule. With this default option, you will be able to transfer multiple files or folders during the session.

====Using SSH Secure File Transfer====

In order to use the SSH Secure File Transfer software that is installed as part of SSH (Secure Shell Utilities for Windows) available on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page, users need to start the Secure File Transfer application and open a connection to host txfer.gacrc.uga.edu. You will have to enter your UGA MyID as the username, but other fields (port number, etc) can be left empty (or leave the default value, if any). You will be prompted for your MyID password and after that you will be prompted to enter DUO two factor authentication code. Please choose one of the options like DUO push, Phone call or SMS passcodes. Once the connection is established, you can upload or download files.

Here is the PDF to check step-by-step screen shots:
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[ media: Txfer SSH File Transfer Nov302018.pdf]]
|-
|}

====Using scp====

Sample commands to transfer files from your local Unix/Linux/Mac OS X machine to the teaching cluster:

Open a terminal in your local machine, change directory (cd) to where the files are located in your local machine, and at the command prompt type:

<pre class="gcommand">
scp filename yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

where ''filename'' is the name of the file to be transferred, ''yourUGAMyID'' is your UGA MyID, and ''subdirectory'' is the subdirectory in your teaching cluster home directory to which files are being transferred. You will then be asked to enter your UGA MyID password.

(Note: username@ can be omitted if your username on the teaching cluster is the same as on your local machine). Multiple files (e.g. file1, file2, and file3) can be transferred with a single command:

<pre class="gcommand">
scp file1 file2 file3 yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

Wildcards can be used for multiple file transfer (e.g. all files with .dat extension):

<pre class="gcommand">
scp *.dat yourUGAMyID@txfer.gacrc.uga.edu:subdirectory
</pre>

===Transferring Files between your Sapelo2 directories and the teaching cluster===

To transfer files between your Sapelo2 directories (e.g. your Sapelo2 home directory or /lustre1 directory) and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to copy files to/from your home directory at txfer.gacrc.uga.edu.

For example, to transfer a directory called subdir2 in your /lustre1 directory to your teaching cluster home directory. On xfer.gacrc.uga.edu issue the command:
<pre class="gcommand">
scp -r -p /lustre1/yourUGAMyID/subdir2 yourUGAMyID@txfer.gacrc.uga.edu:

UGA DUO authentication is required for SSH/SCP access to
GACRC systems.

UGA DUO is a two-factor authentication service which
requires a password (one factor) and a code, phone,
or device (second factor) to successfully authenticate.

If you are not enrolled in the UGA DUO service please
visit the UGA DUO service self-service portal to enroll
and configure or manage your DUO enabled devices.

https://eits.uga.edu/access_and_security/infosec/tools/duo/portal/

For additional help with UGA DUO authentication or to
report an issue please visit:

https://eits.uga.edu/access_and_security/infosec/tools/archpass/

Password:

Duo two-factor login for yourUGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>
When you enter your password, you will be prompted for the two-factor authentication step. Once you enter a passcode or select an option, the file transfer will start.

===Transferring Files between your project area and the teaching cluster===

To transfer files between your /project area and your teaching cluster home directory, please first use ssh to login into xfer.gacrc.uga.edu. Then use the scp command to e.g. copy files from /project to your home directory at txfer.gacrc.uga.edu (or to copy files from your home directory at txfer.gacrc.uga.edu to your /project area).

For example, to copy a file called species.fa from your teaching cluster home directory to a subdirectory called binf1234 in your /project area, use the following command on xfer.gacrc.uga.edu:

<pre class="gcommand">
scp txfer.gacrc.uga.edu:species.fa /project/abclab/binf1234
</pre>
where ''abclab'' needs to be changed to the name of your group.

File:Xfer Filezilla 12032018.pdf

2018-12-03T19:39:12Z

Pakala:

Training

2018-11-27T20:48:21Z

Pakala: /* Linux Training for New Cluster Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''December''' 2018, the GACRC is going to host eight regular training sessions. These sessions will cover Sapelo2 cluster new user training, Linux basics, Python basics.

We offer:

1. Sapelo2 cluster new user training (3 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python basics (2 sessions)

In '''November''' 2018, the GACRC is going to host eleven regular training sessions. These sessions will cover Sapelo2 cluster new user training, Linux basics, Python/Perl basics, and Python resources on Sapelo2 cluster (we will talk about, e.g., Python environment, packages, how to install packages in user's space, etc.).

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python basics (2 sessions)

4. Perl basics (1 session)

4. Python on GACRC Sapelo2 cluster (1 session; topical)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || November 29th, Thursday, 10:00 AM - 12:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || December 6th, Thursday, 10:00 AM - 12:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || December 14th, Friday, 10:00 AM - 12:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || December 18th, Tuesday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || November 27th, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || December 4th, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || December 13th, Thursday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || December 20th, Thursday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || December 7th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || December 7th, Friday, 11:30 AM - 1:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 Cluster || November 30th, Friday, 10:00 AM - 12:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop v5.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 11272018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Food Science - Fall 2018 || On-Class (FYOS1001) || [[media:High Performance Computing (HPC) on Sapelo2 Cluster at GACRC.pdf]]
|-
|The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-09-24T16:01:04Z

Pakala: /* Out-Reach/On-Class Talk */

Training

2018-09-24T12:47:05Z

Pakala: /* Out-Reach/On-Class Talk */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''September''' 2018, the GACRC is going to host nine regular training sessions and one topical session. These sessions will cover new user training on Sapelo2 cluster, Linux basics, Python basics, and Python resources on Sapelo2 cluster (we will talk about, e.g., Python environment, packages, how to install packages in user's space, etc.).

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python basics (2 sessions)

4. Python on GACRC Sapelo2 cluster (1 session; topical)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using Sapelo2 Cluster at the GACRC || September 7th, Friday, 10:00 AM - 12:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || September 13th, Thursday, 10:00 AM - 12:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || September 18th, Tuesday, 10:00 AM - 12:00 PM
|-
| Using Sapelo2 Cluster at the GACRC || September 27th, Thursday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || September 6th, Thursday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || September 11th, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || September 20th, Thursday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 14th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || September 14th, Friday, 11:30 AM - 1:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 Cluster || September 25th, Tuesday, 10:00 AM - 12:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Using Sapelo2 Cluster at the GACRC'''

Focus: Sapelo2 cluster and batch job workflow

Cluster's storage environment

Computing queues on cluster

Software environment

Batch job workflow, how to submit a computational batch job

Other tips and guidelines for Sapelo2 users

Title: '''Use Linux on Cluster'''

Focus: Linux OS fundamentals

Linux common command, filesystem, and shell

Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Linux Hands-on practice

Title: '''Python Language Basics I, II'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Title: '''Python on GACRC Sapelo2 Cluster'''

Focus: Installation of Python packages/modules on Sapelo2 cluster

How to know Python versions installed on Sapelo2

How to know Python environment details on Sapelo2

How to know if a Python package is installed or not on Sapelo2

How to install a Python package in user's home directory on Sapelo2

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''Perl Language Basics I, II'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop ver3.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop ver2.pdf]]
|-
|}

====Linux Training for New Cluster Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 07092018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Dr. Arnold On-Class Fall 2018 || On-Class (GENE4220) || [[GACRC Teaching Cluster new user training workshop 09242018.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-09-04T18:37:22Z

Pakala: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''September''' 2018, the GACRC is going to host nine regular training sessions and one topical session. These sessions will cover new user training on Sapelo2 cluster, Linux basics, Python basics, and Python resources on Sapelo2 cluster (we will talk about, e.g., Python environment, packages, how to install packages in user's space, etc.).

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python basics (2 sessions)

4. Python on GACRC Sapelo2 cluster (1 session; topical)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || September 7th, Friday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || September 13th, Thursday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || September 18th, Tuesday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || September 27th, Thursday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || September 6th, Thursday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || September 11th, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || September 20th, Thursday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 14th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || September 14th, Friday, 11:30 AM - 1:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 Cluster || September 25th, Tuesday, 10:00 AM - 12:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Teaching Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Teaching cluster new user training workshop.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 07092018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics - Summer 2018 || Out-Reach (CSP Seminar Talk 20180821) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-08-08T13:50:40Z

Pakala: /* Python Basics I/II */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August''' 2018, the GACRC is going to host ten regular training sessions. These sessions will cover new user training on Sapelo2 cluster, Linux basics, and Python basics.

We will also host two topical sessions. One is on Python resources on Sapelo2 cluster (we will talk about, e.g., Python environment, packages, how to install packages in user's space, etc.); the other one is a special 3-hour session giving an introduction on R language.

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Python on GACRC Sapelo2 cluster (1 session; topical)

5. An Introduction to R Language (1 sessions; 3-hour topical)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || August 10th, Friday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || August 16th, Thursday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || August 23rd, Thursday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || August 31st, Friday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || August 9th, Thursday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || August 14th, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || August 21st, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || August 30th, Thursday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || August 17th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || August 17th, Friday, 11:30 AM - 1:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 Cluster || August 28th, Tuesday, 10:00 AM - 12:00 PM
|-
| An Introduction on R Language || August 24th, Friday, 10:00 AM - 1:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 07092018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-08-07T14:59:08Z

Pakala: /* Linux Training for Linux-inexperienced Cluster New Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''August''' 2018, the GACRC is going to host ten regular training sessions. These sessions will cover new user training on Sapelo2 cluster, Linux basics, and Python basics.

We will also host two topical sessions. One is on Python resources on Sapelo2 cluster (we will talk about, e.g., Python environment, packages, how to install packages in user's space, etc.); the other one is a special 3-hour session giving an introduction on R language.

We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (4 sessions)

3. Python basics (2 sessions)

4. Python on GACRC Sapelo2 cluster (1 session; topical)

5. An Introduction to R Language (1 sessions; 3-hour topical)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || August 10th, Friday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || August 16th, Thursday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || August 23rd, Thursday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || August 31st, Friday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || August 9th, Thursday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || August 14th, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || August 21st, Tuesday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || August 30th, Thursday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || August 17th, Friday, 10:00 AM - 11:30 PM
|-
| Python Language Basics II || August 17th, Friday, 11:30 AM - 1:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 Cluster || August 28th, Tuesday, 10:00 AM - 12:00 PM
|-
| An Introduction on R Language || August 24th, Friday, 10:00 AM - 1:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 07092018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-07-09T17:27:22Z

Pakala: /* Linux Training For New Users Of Cluster */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''July''' 2018, the GACRC is going to host thirteen training sessions. These sessions will provide new user training on Sapelo2 cluster, Linux basics, and Python/Perl basics, etc.. We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (5 sessions)

3. Python and Perl basics (3 sessions)

4. Python on GACRC Sapelo2 cluster (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || July 12th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || July 16th, Monday, 1:00 PM - 3:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || July 24th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || July 30th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || July 10th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || July 16th, Monday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || July 23rd, Monday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || July 26th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || July 31st, Tuesday, 1:45 PM - 3:30 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || July 9th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || July 9th, Monday, 1:00 PM - 3:00 PM
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || July 19th, Thursday, 1:45 PM - 3:30 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 Cluster || July 30th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 07092018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-06-12T20:13:39Z

Pakala: /* Linux Training for Linux-inexperienced Cluster New Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''June''' 2018, the GACRC is going to host eleven training sessions. These sessions will provide new user training on Sapelo2 cluster, Linux basics, and Python/Perl basics, etc.. We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python and Perl basics (3 sessions)

4. Python on GACRC Sapelo2 cluster (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || June 5th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || June 11th, Monday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || June 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || June 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || June 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || June 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || June 25th, Monday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || June 4th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || June 4th, Monday, 1:00 PM - 3:00 PM
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || June 11th, Monday, 1:00 PM - 3:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 cluster || June 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04022018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-06-12T20:12:51Z

Pakala: /* Sapelo2 Cluster New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''June''' 2018, the GACRC is going to host eleven training sessions. These sessions will provide new user training on Sapelo2 cluster, Linux basics, and Python/Perl basics, etc.. We offer:

1. Sapelo2 cluster new user training (4 sessions)

2. Linux training for Linux-inexperienced cluster new users (3 sessions)

3. Python and Perl basics (3 sessions)

4. Python on GACRC Sapelo2 cluster (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || June 5th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || June 11th, Monday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || June 14th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || June 25th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || May 29th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || June 7th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || June 12th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || June 25th, Monday, 10:00 AM - 12:00 PM
|-
|}

====Python Basics I/II====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || June 4th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || June 4th, Monday, 1:00 PM - 3:00 PM
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || June 11th, Monday, 1:00 PM - 3:00 PM
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Sapelo2 cluster || June 28th, Thursday, 1:45 PM - 3:30 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04022018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Miller plant science - Summer 2018 || Out-Reach (jlmlab) || [[media: Introduction to GACRC Sapelo2 cluster.pdf]]
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-04-03T20:27:27Z

Pakala: /* Linux Training for New Users of Cluster */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April''' 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of new user training on the GACRC Sapelo clustsr and new user training on Sapelo2 cluster, Linux basics, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Sapelo2 cluster new user training (4 sessions)

4. Linux training for Linux-inexperienced cluster new users (5 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Perl Basics I (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo Cluster New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 5th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 16th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo Cluster New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 12th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 23rd, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || April 9th, Monday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 17th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 26th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 30th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || April 3rd, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 9th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 19th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 23rd, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 30th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || April 10th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || April 24th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || April 16th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Sapelo Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Level1-2 ver1.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Linux Training For New Users Of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04022018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-04-03T20:26:47Z

Pakala: /* Linux Training for cluster New Users */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April''' 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of new user training on the GACRC Sapelo clustsr and new user training on Sapelo2 cluster, Linux basics, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Sapelo2 cluster new user training (4 sessions)

4. Linux training for Linux-inexperienced cluster new users (5 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Perl Basics I (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo Cluster New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 5th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 16th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo Cluster New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 12th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 23rd, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || April 9th, Monday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 17th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 26th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 30th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || April 3rd, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 9th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 19th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 23rd, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 30th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || April 10th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || April 24th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || April 16th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Sapelo Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Level1-2 ver1.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Linux Training for New Users of Cluster====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04022018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-04-03T20:26:04Z

Pakala: /* Linux Basics and Hands-on */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April''' 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of new user training on the GACRC Sapelo clustsr and new user training on Sapelo2 cluster, Linux basics, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Sapelo2 cluster new user training (4 sessions)

4. Linux training for Linux-inexperienced cluster new users (5 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Perl Basics I (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo Cluster New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 5th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 16th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo Cluster New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 12th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 23rd, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || April 9th, Monday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 17th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 26th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 30th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || April 3rd, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 9th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 19th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 23rd, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 30th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || April 10th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || April 24th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || April 16th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Sapelo Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Level1-2 ver1.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Linux Training for cluster New Users====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04022018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-04-03T20:24:45Z

Pakala: /* Linux Basics and Hands-on */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''April''' 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of new user training on the GACRC Sapelo clustsr and new user training on Sapelo2 cluster, Linux basics, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Sapelo2 cluster new user training (4 sessions)

4. Linux training for Linux-inexperienced cluster new users (5 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Perl Basics I (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo Cluster New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 5th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 16th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo Cluster New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 12th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || April 23rd, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Using the Sapelo2 Cluster at the GACRC || April 9th, Monday, 10:00 AM - 12:00 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 17th, Tuesday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 26th, Thursday, 1:45 PM - 3:30 PM
|-
| Using the Sapelo2 Cluster at the GACRC || April 30th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || April 3rd, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 9th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 19th, Thursday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || April 23rd, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || April 30th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics II || April 10th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics I || April 24th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || April 16th, Monday, 1:00 PM - 3:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Sapelo2 cluster new user training workshop.pdf]]
|-
| [[media: GACRC Sapelo2 cluster new user training hands-out.pdf]]
|-
|}

====Sapelo Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Level1-2 ver1.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Linux Training For New Users Of Cluster Suchi 04022018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-03-19T19:34:55Z

Pakala:

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''March''' 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of introductions to the GACRC Linux HPC clusters (Sapelo and Sapelo2), Linux basics, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (3 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (3 sessions) for cluster-experienced new users

3. Sapelo cluster new user training (2 sessions)

4. Linux training for Linux-inexperienced cluster new users (3 sessions)

5. Linux Basics I (1 session) and II (1 sessions)

6. Python Basics I (1 session) and II (1 session)

6. Perl Basics I (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo Cluster New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 8th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Sapelo Cluster New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 6th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 15th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 19th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Sapelo2 Cluster New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo2 Cluster at GACRC || March 13th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo2 Cluster at GACRC || March 26th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || March 5th, Monday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || March 12th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || March 20th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || March 26th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || March 19th, Monday, 1:00 PM - 3:00 PM
|-
| Introduction to Linux Basics II and Hands-on || March 29th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Basics I || March 12th, Monday, 10:00 AM - 12:00 PM
|-
| Python Basics II || March 27th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || March 1st, Thursday, 1:45 PM - 3:30 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo2 Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo2 Cluster at GACRC Level1-2 ver1.pdf]]
|-
|}

====Sapelo Cluster Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Level1-2 ver1.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 02202018.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi Feb202018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-02-26T18:00:27Z

Pakala: /* How to Register */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''March''' 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (4 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (3 sessions) for cluster-experienced new users

3. Linux training for Linux-inexperienced cluster new users (4 sessions)

4. Linux Basics I (1 session) and II (1 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Perl Basics I (1 session)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 8th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 13th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 22nd, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 26th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Sapelo New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 6th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 15th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || March 19th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || March 5th, Monday, 10:00 AM - 12:00 PM
|-
| Use Linux on Cluster || March 12th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || March 20th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || March 26th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || March 19th, Monday, 1:00 PM - 3:00 PM
|-
| Introduction to Linux Basics II and Hands-on || March 29th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || March 12th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || March 27th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || March 1st, Thursday, 1:45 PM - 3:30 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Level1-2 ver1.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 02202018.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi Feb202018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Biochemistry and Molecular Biology - Spring 2018 || On-Class (BCMB8330) ||[[media: GACRC zcluster Class Training BCMB8330 Spring 2018.pdf]]
|-
| The Center for Simulational Physics - Summer 2017 || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-02-01T21:11:18Z

Pakala: /* Linux Basics and Hands-on */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2018, the GACRC is going to host fifteen training sessions. These sessions will provide two levels of introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, regression modeling in R language, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Linux training for Linux-inexperienced cluster new users (3 sessions)

4. Linux Basics I (1 session) and II (2 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Three topical sessions: Regression modeling in R Language, Python on GACRC computing resources, and How to submit and run jobs efficiently and correctly on Sapelo

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 15th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 27th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Sapelo New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 8th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 19th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 5th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 13th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics II and Hands-on || February 6th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || February 20th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || February 22nd, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || February 12th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || February 12th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Regression Modeling in R || February 5th, Monday, 10:00 AM - 12:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || February 19th, Monday, 1:00 AM - 3:00 PM
|-
| Python on GACRC Computing Resources || February 26th, Monday, 10:00 AM - 12:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 02202018.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi Feb202018.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-02-01T20:18:23Z

Pakala: /* Linux Basics and Hands-on */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2018, the GACRC is going to host fifteen training sessions. These sessions will provide two levels of introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, regression modeling in R language, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Linux training for Linux-inexperienced cluster new users (3 sessions)

4. Linux Basics I (1 session) and II (2 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Three topical sessions: Regression modeling in R Language, Python on GACRC computing resources, and How to submit and run jobs efficiently and correctly on Sapelo

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 15th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 27th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Sapelo New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 8th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 19th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 5th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 13th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics II and Hands-on || February 6th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || February 20th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || February 22nd, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || February 12th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || February 12th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Regression Modeling in R || February 5th, Monday, 10:00 AM - 12:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || February 19th, Monday, 1:00 AM - 3:00 PM
|-
| Python on GACRC Computing Resources || February 26th, Monday, 10:00 AM - 12:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 02202018.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-01-30T20:39:14Z

Pakala: /* Regular Training Announcement */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''February''' 2018, the GACRC is going to host fifteen training sessions. These sessions will provide two levels of introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, regression modeling in R language, Python and Perl language basics, etc.. We offer:

1. Sapelo cluster new user training, Level 1 (2 sessions) for cluster-inexperienced new users

2. Sapelo cluster new user training, Level 2 (2 sessions) for cluster-experienced new users

3. Linux training for Linux-inexperienced cluster new users (3 sessions)

4. Linux Basics I (1 session) and II (2 sessions)

5. Python Basics I (1 session) and II (1 session)

6. Three topical sessions: Regression modeling in R Language, Python on GACRC computing resources, and How to submit and run jobs efficiently and correctly on Sapelo

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training Level 1===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 15th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 27th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Sapelo New User Training Level 2===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 8th, Thursday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || February 19th, Monday, 10:00 AM - 12:00 PM
|-
|}

===Linux Training for Linux-inexperienced Cluster New Users===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Use Linux on Cluster || February 5th, Monday, 1:00 PM - 3:00 PM
|-
| Use Linux on Cluster || February 13th, Tuesday, 1:45 PM - 3:30 PM
|-
| Use Linux on Cluster || February 26th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics II and Hands-on || February 6th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || February 20th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || February 22nd, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || February 12th, Monday, 10:00 AM - 12:00 PM
|-
| Python Language Basics II || February 12th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Regression Modeling in R || February 5th, Monday, 10:00 AM - 12:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || February 19th, Monday, 1:00 AM - 3:00 PM
|-
| Python on GACRC Computing Resources || February 26th, Monday, 10:00 AM - 12:00 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2018]]

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2018-01-10T18:19:16Z

Pakala: /* Topic Introduction */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''January''' 2018, the GACRC is going to host ten regular training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo2 cluster), Linux basics, and language basics of Python. We offer:

1. Three Introduction to HPC Using Sapelo2 Cluster at GACRC training sessions (mandatory for new user account creation)

2. Two Linux-I introductory sessions and One Linux-II introductory sessions (each combined with a hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. One topical session on Python resources at GACRC

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || January 16th, Tuesday, 1:45 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || January 22nd, Monday, 10:00 AM - 12:00 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || January 29th, Monday, 1:00 PM - 3:00 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || January 22nd, Monday, 1:00 PM - 3:00 PM
|-
| Introduction to Linux Basics II and Hands-on || January 29th, Monday, 10:00 AM - 12:00 PM
|-
| Introduction to Linux Basics I and Hands-on || January 30th, Tuesday, 1:45 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || January 9th, Tuesday, 1:45 PM - 3:30 PM
|-
| Python Language Basics II || January 11th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || January 25th, Thursday, 1:45 PM - 3:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python on GACRC Computing Resources || January 18th, Thursday, 1:45 PM - 3:30 PM
|-
|}

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo2'''

Focus: Sapelo2 cluster general workflow and correct computing resource requesting

Overview of Sapelo2 cluster with reference tables and operational diagrams

Sapelo2 batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo2 cluster guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-26T19:10:51Z

Pakala: /* Sapelo New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''November''' 2017, the GACRC is going to host nineteen regular training sessions and one Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Four Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. One Zcluster-Sapelo migrating training sessions

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 7th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 17th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 21st, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 30th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 2nd, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 2nd, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 9th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 9th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 14th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 14th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 28th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 28th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || November 10th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || November 10th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
| Perl Language Basics I || November 21st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 7th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || November 16th, Thursday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 17th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 30th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 13 || November 16th, Thursday, 11:00 PM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop ver16.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-26T16:33:18Z

Pakala: /* Sapelo New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''November''' 2017, the GACRC is going to host nineteen regular training sessions and one Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Four Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. One Zcluster-Sapelo migrating training sessions

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 7th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 17th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 21st, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 30th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 2nd, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 2nd, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 9th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 9th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 14th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 14th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 28th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 28th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || November 10th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || November 10th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
| Perl Language Basics I || November 21st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 7th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || November 16th, Thursday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 17th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 30th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 13 || November 16th, Thursday, 11:00 PM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Pakala 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-25T19:02:36Z

Pakala: /* Sapelo New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''November''' 2017, the GACRC is going to host nineteen regular training sessions and one Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Four Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. One Zcluster-Sapelo migrating training sessions

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 7th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 17th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 21st, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 30th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 2nd, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 2nd, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 9th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 9th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 14th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 14th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 28th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 28th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || November 10th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || November 10th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
| Perl Language Basics I || November 21st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 7th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || November 16th, Thursday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 17th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 30th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 13 || November 16th, Thursday, 11:00 PM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 10252017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-23T19:18:32Z

Pakala: /* Zcluster-Sapelo Migrating Training Sessions */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''November''' 2017, the GACRC is going to host nineteen regular training sessions and one Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Four Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. One Zcluster-Sapelo migrating training sessions

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 7th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 17th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 21st, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || November 30th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 2nd, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 2nd, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 9th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 9th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 14th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 14th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || November 28th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || November 28th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || November 10th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || November 10th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
| Perl Language Basics I || November 21st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 7th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || November 16th, Thursday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 17th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || November 30th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 13 || November 16th, Thursday, 11:00 PM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-20T17:19:51Z

Pakala: /* Python Basics */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || October 13th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || October 13th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 8 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
| Session 9 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 10 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 11 || October 20th, Friday, 10:00 AM - 11:30 AM
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-20T17:19:10Z

Pakala: /* Topical Sessions */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 28th, Thursday, 11:00 AM - 12:30 PM
|-
| Python Language Basics II || September 28th, Thursday, 2:00 PM - 3:30 PM
|-
| Python Language Basics I || October 13th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || October 13th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 8 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
| Session 9 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 10 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 11 || October 20th, Friday, 10:00 AM - 11:30 AM
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-20T17:17:01Z

Pakala: /* Linux Basics and Hands-on */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 28th, Thursday, 11:00 AM - 12:30 PM
|-
| Python Language Basics II || September 28th, Thursday, 2:00 PM - 3:30 PM
|-
| Python Language Basics I || October 13th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || October 13th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| NCBI Blast application on Sapelo cluster || September 26th, Tuesday, 11:00 AM - 12:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 6th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 10th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || October 17th, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 8 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
| Session 9 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 10 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 11 || October 20th, Friday, 10:00 AM - 11:30 AM
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-20T17:16:05Z

Pakala: /* Sapelo New User Training */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 3rd, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || October 5th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || October 12th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || October 19th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || October 19th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 28th, Thursday, 11:00 AM - 12:30 PM
|-
| Python Language Basics II || September 28th, Thursday, 2:00 PM - 3:30 PM
|-
| Python Language Basics I || October 13th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || October 13th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| NCBI Blast application on Sapelo cluster || September 26th, Tuesday, 11:00 AM - 12:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 6th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 10th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || October 17th, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 8 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
| Session 9 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 10 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 11 || October 20th, Friday, 10:00 AM - 11:30 AM
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-10-20T17:14:14Z

Pakala: /* Zcluster-Sapelo Migrating Training Sessions */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''October''' 2017, the GACRC is going to host '''seventeen''' regular training sessions and '''four''' Zcluster-Sapelo migrating training sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python and Perl, Python on GACRC computing resources. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Four Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of Python resources at the Sapelo

6. Four Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 29th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 6th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 10th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 17th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || October 31st, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || October 3rd, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || October 5th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || October 12th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || October 19th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || October 19th, Thursday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || October 24th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 28th, Thursday, 11:00 AM - 12:30 PM
|-
| Python Language Basics II || September 28th, Thursday, 2:00 PM - 3:30 PM
|-
| Python Language Basics I || October 13th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || October 13th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || October 26th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| NCBI Blast application on Sapelo cluster || September 26th, Tuesday, 11:00 AM - 12:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 6th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 10th, Tuesday, 2:00 PM - 3:30 PM
|-
| Python on GACRC Computing Resources || October 17th, Tuesday, 2:00 PM - 3:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || October 31st, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 8 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
| Session 9 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 10 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 11 || October 20th, Friday, 10:00 AM - 11:30 AM
|-
| Session 12 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

NCBI Connection

2017-10-11T18:45:11Z

Pakala:

Please contact us to get permission if you need to connect to NCBI on GACRC clusters. Please specify your path of scripts, the block of code on how to connect to NCBI and command to test your script in the request.

NCBI's main mission is to provide interactive web access. Fetching data directly from www.ncbi.nlm.nih.gov is blocked at GACRC.

To fetch data from NCBI, i.e. fasta, fastq, sra etc. There is a scripting API available users to avoid intensive visit of NCBI web URLs. The API is called e-utilities and you must use this for all your
scripts. There is no advantage or functionality that this scraping of the web pages can offer that the API cannot. Please refer to:

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework&part=eutils

http://www.ncbi.nlm.nih.gov/books/NBK25501

If you feel you must write a script in order to download data please follow policy:

- If you are searching PubMed or Entrez, please use the E-utilities if you have not already done so (http://www.ncbi.nlm.nih.gov/books/NBK25497).

- Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI web address.

- Use the &email= and the &tool= field so that we can track your project and contact you if there is a problem.

- For all scripts, do not send requests more than 3 per second. http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.General_Usage_Guidelines

- Only one job one thread at a time. No multi-thread / multiple jobs to run the query at same time

- If you are sending unique identifiers (GI's, Accession numbers, Gene IDsetc.) you can send multiple UIDs per requests (up 500 per requests) rather than one per request. Or use the webenv and retmax fields for batches of records (http://www.ncbi.nlm.nih.gov/books/NBK1058/#eutils_esayers-5-4-3).

- Limit all scripts to the off peak hours of 9 PM to 5 AM Eastern Standard Time (USA).

Please note that abstracts in PubMed may incorporate material that may be protected by U.S. and foreign copyright laws. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. Transmission or reproduction of protected items beyond that allowed by fair use (PDF) as defined in the copyright laws requires the written permission of the copyright owners. If you wish to do a large scale data mining project on PubMed, the raw data, MEDLINE, is you can enter into a licensing agreement and lease the data. For more information on this please see http://www.nlm.nih.gov/databases/leased.html

[[#top|Back to Top]]

Training

2017-09-18T16:17:19Z

Pakala: /* Zcluster-Sapelo Migrating Training Sessions */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''September''' 2017, the GACRC is going to host '''fifteen''' regular training sessions. '''five''' Zcluster-Sapelo migrating training sessions, and '''two''' collaborative R introduction sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python, Perl, and R, and NCBI Blast application on Sapelo. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Three Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Three topical sessions on:

(1) Two sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of NCBI Blast application on Sapelo

6. Two collaborative R sessions

7. Five Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 25th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 5th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 15th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 19th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 29th, Friday, 10:00 AM - 11:30 AM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || September 5th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || September 12th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || September 14th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || September 21th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || September 21th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 28th, Thursday, 11:00 AM - 12:30 PM
|-
| Python Language Basics II || September 28th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM
|-
|-
| Perl Language Basics I || September 19th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || September 15th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || September 29th, Friday, 11:30 AM - 1:00 PM
|-
| NCBI Blast application on Sapelo cluster || September 26th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===R Introduction Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| R language Introduction I || September 7th, Thursday, 11:00 AM - 12:30 PM
|-
| R language Introduction II || September 7th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Five''' Zcluster-Sapelo migrating training sessions in '''September''' and the other '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 1 || September 8th, Friday, 10:00 AM - 12:00 PM
|-
| Session 2 || September 12th, Tuesday, 11:00 PM - 12:30 PM
|-
| Session 3 || September 14th, Thursday, 2:00 PM - 3:30 PM
|-
| Session 4 || September 22nd, Friday, 10:00 AM - 12:00 PM
|-
| Session 5 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

For users' convenience, '''four''' Zcluster-Sapelo migrating training sessions in '''October''' are scheduled as follows:

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 1 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 2 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 3 || October 20th, Friday, 10:00 AM - 12:00 PM
|-
| Session 4 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Zcluster-Sapelo Migrating Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: GACRC Zcluster-Sapelo Migrating Training.pdf]]
|-
|}

====Sapelo New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Perl Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Perl Language Basics I Workshop v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-08-30T17:15:40Z

Pakala: /* Perl Basics */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

In '''September''' 2017, the GACRC is going to host '''fifteen''' regular training sessions. '''five''' Zcluster-Sapelo migrating training sessions, and '''two''' collaborative R introduction sessions. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, language basics of Python, Perl, and R, and NCBI Blast application on Sapelo. We offer:

1. Four Introduction to HPC Using Sapelo Cluster at GACRC training sessions (mandatory for new user account creation)

2. Three Linux-I introductory sessions and Two Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Three topical sessions on:

(1) Two sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of NCBI Blast application on Sapelo

6. Two collaborative R sessions

7. Five Zcluster-Sapelo migrating training sessions

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 25th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 5th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 15th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 19th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || September 29th, Friday, 10:00 AM - 11:30 AM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || September 5th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics I and Hands-on || September 12th, Tuesday, 2:00 PM - 3:30 PM
|-
| Introduction to Linux Basics II and Hands-on || September 14th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || September 21th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || September 21th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || September 28th, Thursday, 11:00 AM - 12:30 PM
|-
| Python Language Basics II || September 28th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM
|-
|-
| Perl Language Basics I || September 19th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| How to submit and run jobs efficiently and correctly on Sapelo || September 15th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || September 29th, Friday, 11:30 AM - 1:00 PM
|-
| NCBI Blast application on Sapelo cluster || September 26th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

===R Introduction Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| R language Introduction I || September 7th, Thursday, 11:00 AM - 12:30 PM
|-
| R language Introduction II || September 7th, Thursday, 2:00 PM - 3:30 PM
|-
|}

===Zcluster-Sapelo Migrating Training Sessions===

The GACRC will host '''Five''' Zcluster-Sapelo migrating training sessions in '''September''' and the other '''Four''' sessions in '''October'''.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 1 || September 8th, Friday, 10:00 AM - 12:00 PM
|-
| Session 2 || September 12th, Tuesday, 11:00 PM - 12:30 PM
|-
| Session 3 || September 14th, Thursday, 2:00 PM - 3:30 PM
|-
| Session 4 || September 22nd, Friday, 10:00 AM - 12:00 PM
|-
| Session 5 || September 26th, Tuesday, 2:00 PM - 3:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will be granted by attending a Zcluster-Sapelo migrating training session.]]

To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.

For users' convenience, '''four''' Zcluster-Sapelo migrating training sessions in '''October''' are scheduled as follows:

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 1 || October 3rd, Tuesday, 11:00 AM - 12:30 PM
|-
| Session 2 || October 12th, Thursday, 11:00 PM - 12:30 PM
|-
| Session 3 || October 21st, Friday, 10:00 AM - 12:00 PM
|-
| Session 4 || October 24th, Tuesday, 11:00 AM - 12:30 PM
|-
|}

More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training.

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

Title: '''Perl Language Basics I, II, and III'''

Focus of I: Overview of Perl language,

Perl general scripting style

Perl fundamental data types

Focus of II: Program structure: control flow and loop

Perl subroutine

Perl I/O

Focus of III: Perl regular expression (PRE)

Text processing using PRE

==Download==

====Sapelo and zcluster New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf]]
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02132017.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| The Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach ((CSP Seminar Talk 20160906) || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
|-
| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
|-
| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
|-
| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
|-
| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
|-
| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]

Training

2017-08-07T19:42:32Z

Pakala: /* Topic Introduction */

==GACRC Training==

The GACRC regularly hosts training sessions on a number of subjects relevant to the use of our computational and storage resources. Scheduled trainings will be announced through the GACRC mailing list.

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.'''

==Regular Training Announcement==

The GACRC is going to host '''seventeen''' regular training sessions and '''three''' interactive Question-and-Answer sessions in '''August''' 2017. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, Python language basics, Perl language basics, and NCBI Blast application on Sapelo.

We offer:

1. Four Sapelo cluster new user training sessions (mandatory for new user account creation)

2. Three Linux-I introductory sessions and Three Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of NCBI Blast application on Sapelo

6. Three interactive Question-and-Answer sessions (Bring your questions to us for a discussion. No registration is needed. We are looking forward to seeing you in the classroom with your questions to us!)

====Training Location:====

Davison Life Sciences Complex (Life Science Building), Room C128

120 East Green Street, Athens, GA 30602

==Event Schedule==

===Sapelo New User Training===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 1st, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 11th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 15th, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to HPC Using Sapelo Cluster at GACRC || August 25th, Friday, 10:00 AM - 11:30 AM
|-
|}

===Linux Basics and Hands-on===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Introduction to Linux Basics I and Hands-on || August 4th, Friday, 10:00 AM - 11:30 AM
|-
| Introduction to Linux Basics II and Hands-on || August 4th, Friday, 11:30 AM - 1:00 PM
|-
| Introduction to Linux Basics I and Hands-on || August 10th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || August 17th, Thursday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics I and Hands-on || August 22nd, Tuesday, 11:00 AM - 12:30 PM
|-
| Introduction to Linux Basics II and Hands-on || August 24th, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Python Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Python Language Basics I || August 18th, Friday, 10:00 AM - 11:30 AM
|-
| Python Language Basics II || August 18th, Friday, 11:30 AM - 1:00 PM
|-
|}

===Perl Basics===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Perl Language Basics I || August 31st, Thursday, 11:00 AM - 12:30 PM
|-
|}

===Topical Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 3rd, Thursday, 11:00 AM - 12:30 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 11th, Friday, 11:30 AM - 1:00 PM
|-
| How to submit and run jobs efficiently and correctly on Sapelo || August 25th, Friday, 11:30 AM - 1:00 PM
|-
| NCBI Blast application on Sapelo cluster || August 29th, Tuesday, 11:00 AM - 12:30 PM
|}

===Interactive Question-and-Answer Sessions===

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Question-and-Answer || August 1st, Tuesday, 14:00 PM - 15:30 PM
|-
| Question-and-Answer || August 3rd, Thursday, 14:00 PM - 15:30 PM
|-
| Question-and-Answer || August 10th, Thursday, 14:00 PM - 15:30 PM
|-
|}

===Zcluster Decommissioning Awareness Sessions===

The GACRC will host '''three''' awareness sessions in '''August'''. We will help to answer your questions related to the zcluster decommissioning.

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Title
! scope="col" | Date/Time
|-
| Session 1 || August 15th, Tuesday, 14:00 PM - 15:30 PM
|-
| Session 2 || August 17th, Thursday, 14:00 PM - 15:30 PM
|-
| Session 3 || August 22nd, Tuesday, 14:00 PM - 15:30 PM
|-
|}

'''Please Note:''' [[A Sapelo user account will not be granted by only attending awareness sessions.]] To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session to be scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, host weekly.

More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training .

==How to Register==

If you would like to attend, please respond by email to: '''pakala@uga.edu'''. Also please tell us which session(s) you want to attend. You don't have to register the interactive Question-and-Answer sessions.

We have '''25''' seats in the lab room, so we have a 25 user/workshop limit. Please respond at your earliest convenience to register to guarantee your seat. You are welcome and encouraged to attend those workshops to learn about how to work with the HPC clusters at the GACRC.

The GACRC is going to host other training workshops and seminars covering various HPC topics, including HPC fundamental introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications on Sapelo cluster, Perl, R, C/C++/Fortran programming, etc., in the near future. We will announce those events when they are scheduled.

The GACRC Web Training page can be found at http://gacrc.uga.edu/help/training/ and the GACRC Wiki Training page can be found at https://wiki.gacrc.uga.edu/wiki/Training, from which you can find detailed information about upcoming and past training sessions from GACRC and download training materials.

==Topic Introduction==

Title: '''Introduction to HPC Using Sapelo Cluster at GACRC'''

Focus: What's the Sapelo cluster at GACRC

Sapelo cluster's computing resources

Sapelo cluster's software environment

How to operate with Sapelo cluster and batch job submission workflows

How to work with Sapelo cluster, e.g., how to run interactive jobs; how to run batch jobs; how to make job submission scripts and request computing resources; how to check job status, etc.

Title: '''Introduction to HPC Using zcluster at GACRC'''

Focus: What's zcluster at GACRC

zcluster current computing resources

zcluster software environment

How to work with zcluster, e.g., how to run interactive jobs; how to run batch jobs and request computing resources; how to make job submission scripts; how to check job status, etc.

Title: '''Introduction to Linux Basics I and II'''

Focus of I: Linux OS and brief history

Linux command, filesystem, and shell

Linux common commands, etc.

Focus of II: Linux shell

Common practices on Linux shell scripting

Common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Title: '''Linux Hands-on Practice Session (Basic Linux knowledge required)'''

Focus: Hands-on practice on Linux common commands and shell scripting with common Linux utilities, e.g., sort, find, grep, awk, and sed etc.

Hands-on practice on the work flow of job submission on zcluster with make_escratch, qsub, qstat,and qdel etc.

Title: '''Python Language Basics I, II, and III'''

Focus of I: Overview of Python language, scientific modules and distributions

General Lexical conventions

Basic built-in data types

Focus of II: Program structure: control flow and loop

Function: procedural and functional programming with examples

Python Class

Focus of III: Python modules and importing

Python Package and usage

Title: '''Python on GACRC Computing Resources'''

Focus: Python and Python packages/modules installed on zcluster and Sapelo

Python Overview

Python on Clusters

Python Packages on Clusters

Run Python Interactively on Clusters

Run Python Batch Job on Clusters

Title: '''How to submit and run jobs efficiently and correctly on Sapelo'''

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo batch job submission workflow taking global scratch as job working space

How to request computing resources correctly

How to run pipeline tasks and what are advantages/disadvantages of different options

Sapelo guideline and practical tips

Title: '''GACRC Storage Environment'''

Focus: Overview of Linux common commands related to file and folder operations

Overview of the storage enviornment of zcluster and Sapelo cluster at GACRC

How to transfer data between local and GACRC storage

New file transfer node xfer2 and how to use it to transfer data between zcluster and the new cluster

GACRC suggestions on good practices on GACRC storage, etc;

Title: '''Software installation on zcluster'''

Focus: Current status of software on zcluster; What GACRC have now and what should users install

How to obtain, install, organize software by users; What about databases

How to validate the software installation

How to trouble shoot installation, software errors, script errors, data errors, format errors, etc.

How to get help from GACRC and Common problems/mistakes

Title: '''NCBI Blast application on sapelo'''

Focus: Introduction to BLAST

BLAST job submission to sapelo

Advantages & Disadvantages: NCBI website vs run at sapelo.

Understand BLAST output

Troubleshooting the BLAST results

Title: '''NGS application overview at GACRC'''

Focus: Overview of Bioinformatics software available on HPC clusters at GACRC

It’s a brave new world – NGS and its Applications

Hardware, Software, Databases available at GACRC

NGS project: Logistics and resource considerations

Best practices, common mistakes, troubleshooting and getting help from GACRC

Title: '''R Language Introduction'''

Presenter: Dr. James Monogan (Department of Political Science, University of Georgia)

Focus: Common general topics about R language

Description:This short course will introduce users to the program R and how to use it for data analysis.

Topics covered in the 3 hour session will include data management, drawing graphs, and some basic statistics.

Please download a reference book suggested by the presenter ahead of time (free if downloaded on the university network) from: http://link.springer.com/book/10.1007/978-3-319-23446-5.

==Download==

====Sapelo and zcluster New User Training====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf]]
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf]]
|-
| [[media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02132017.pdf]]
|-
| [[media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.pdf ]]
|-
|}

====Linux Basics and Hands-on====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Introduction to Linux Basics Part-I Workshop20160113 v3.pdf]]
|-
| [[media: Introduction to Linux Basics Part-II Workshop20151130 v2.pdf]]
|-
| [[media: Linux Hands-on Practice 20160120.pdf]]
|-
| [[media: Introduction to Linux Basics Part1 Suchi 05222017.pdf]]
|-
| [[media: Introduction to Linux Basics Part2 Suchi May242017.pdf]]
|-
|}

====Python Basics====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python Language Basics I Workshop20160328 v4.pdf]]
|-
| [[media: Python Language Basics II Workshop20160425 v1.pdf]]
|-
|}

====Topical Sessions====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
| [[media: Python on GACRC Computing Resources v1.pdf]]
|-
| [[media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf]]
|-
| [[media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf]]
|-
| [[media: High Performance Computing (HPC) on Cluster.pdf]]
|-
| [[media: Software installation on zcluster.pdf]]
|-
| [[media: Blast Workshop GACRC 02012017.pdf]]
|-
|-
| [[media: Next-Generation Sequencing Applications at GACRC 10282016.pdf ]]
|-
|}

====Out-Reach/On-Class Talk====

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Dept./Center/Institute
! scope="col" | Type
! scope="col" | Workshop PDF
|-
| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]]
|-
| Computational Physics - Spring 2017 || On-class (PHYS8602) || [[media: phys8602.pdf]]
|-
| The Institute of Bioinformatics and the Quantitative Biology Consulting Group || Out-Reach || [[media: Introduction to HPC Resources at GACRC BBB Talk 20151014.pdf]]
|-
| The Center for Simulational Physics || Out-Reach || [[media: Introduction to Sapelo Computing Resources at GACRC Workshop20160906.pdf]]
|-
| Microbiology || On-Class (MIBO8150) || [[media: Introduction to HPC Resources at GACRC MIBO8150 20160926.pdf]]
|-
| Statistics || On-Class (STAT8060) || [[media: Introduction to HPC Using zcluster at GACRC Workshop STAT8060 20150826.pdf]]
|-
| Biochemistry and Molecular Biology || On-Class (BCMB8211) || [[media: Introduction to HPC Using zcluster at GACRC BCMB8211 20160114.pdf]]
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| Plant Biology || On-Class (PBIO/BINF8350) || [[media: Introduction to HPC Using zcluster at GACRC PBIO-BINF8350 20160115.pdf]]
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| Biochemistry and Molecular Biology || On-Class (BCMB8330) ||[[media: Introduction to HPC Using zcluster at GACRC BCMB8330 20160209 v2.pdf]]
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| Plant Biology - Bioinformatics Applications Fall 2016 || On-Class (PBIO4550) || [[media:Introduction to HPC Using zcluster at GACRC PBIO 4550 08182016.pdf]]
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| Bioinformatics - Essential Computing Skills for Biologists Fall 2016 || On-Class (BINF4005) || [[media:Introduction to HPC Using zcluster at GACRC BINF 4005 08312016.pdf]]
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| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:Introduction to HPC Using zcluster at GACRC GENE 4220 10192016.pdf]]
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| Statistics - Advanced Applications and Computing in R Fall 2016 || On-Class (STAT8330) || [[media: Introduction to HPC Using zcluster at GACRC STAT8330 11022016.pdf]]
|}

'''NOTE:''' The slides may become outdated and you should always check GACRC Wiki for up to date information.

==Past Sessions==

[[Past Sessions in 2017]]

[[Past Sessions in 2016]]

[[Past Sessions in 2015]]