Training: Difference between revisions

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| Using Sapelo2 Cluster at the GACRC || March 25th, Monday, 1:00 PM - 3:00 PM
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| Using Sapelo2 Cluster at the GACRC || April 4th, Thursday, 1:45 PM - 3:30 PM
| Using Sapelo2 Cluster at the GACRC || April 4th, Thursday, 1:45 PM - 3:30 PM

Revision as of 14:15, 10 April 2019

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

Title 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

Title 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)

Title 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

Title 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

Title 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

media: GACRC Sapelo2 cluster new user training workshop v5.1.pdf

Teaching Cluster Training

media: GACRC Teaching cluster new user training workshop ver2.pdf

Linux Training for New Cluster Users

media: Linux Training For New Users Of Cluster Suchi 02202019.pdf

Python Basics

media: Python Language Basics I Workshop20160328 v4.pdf
media: Python Language Basics II Workshop20160425 v1.pdf

Perl Basics

media: Perl Language Basics I Workshop v1.pdf

Topical Sessions

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

Dept./Center/Institute Type 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