Training

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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.


Event Announcement

The GACRC is going to host thirteen regular training sessions in September 2016. These sessions will provide introductions to the GACRC Linux HPC clusters, Linux basics, NCBI Blast, and Python language basics. We are also going to co-host one long session (3 hours) on R language introduction with Dr. James Monogan from the Department of Political Science at the UGA. We offer:

1. Four Sapelo and one zcluster new user training sessions

2. Two Linux-I and two Linux-II introductory sessions

3. Two Python sessions (I and II)

4. One topical session on NCBI Blast

5. One topical session on how to submit and run jobs efficiently and correctly on Sapelo (new topical session)

6. One long session (3 hours) on R language introduction (topic introduction: https://wiki.gacrc.uga.edu/wiki/Training#Topic_Introduction)


The GACRC is going to host sixteen training sessions in October 2016. These sessions will provide introductions to the GACRC Linux HPC clusters, Linux basics, Python language basics and GACRC Python computing resources, NCBI Blast, and NGS data processing tools. We offer:

1. Four Sapelo and two zcluster new user training sessions (mandatory for new user account creation)

2. Two Linux-I and two Linux-II introductory sessions

3. Two Python sessions (I and II)

4. One topical session on NCBI Blast application on zcluster

5. One topical session on NGS application overview (new topic)

6. One topical session on How to submit and run jobs efficiently and correctly on Sapelo

7. One topical session on Python on GACRC Computing Resources (new topic)


Training Location:

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

120 East Green Street, Athens, GA 30602


Event Schedule

Sapelo and zcluster New User Training

Title Date/Time
Introduction to HPC Using Sapelo Cluster at GACRC September 27th, Tuesday, 2:00 PM - 3:30 PM
Introduction to HPC Using Sapelo Cluster at GACRC October 4th, Tuesday, 2:00 PM - 3:30 PM
Introduction to HPC Using zcluster at GACRC October 6th, Thursday, 2:00 PM - 3:30 PM
Introduction to HPC Using Sapelo Cluster at GACRC October 14th, Friday, 10:00 AM - 11:30 AM
Introduction to HPC Using Sapelo Cluster at GACRC October 18th, Tuesday, 2:00 PM - 3:30 PM
Introduction to HPC Using zcluster at GACRC October 20th, Thursday, 2:00 PM - 3:30 PM
Introduction to HPC Using Sapelo Cluster at GACRC October 27th, Thursday, 2:00 PM - 3:30 PM

Linux Basics and Hands-on

Title Date/Time
Introduction to Linux Basics II September 29th, Thursday, 2:00 PM - 3:30 PM
Introduction to Linux Basics I October 7th, Friday, 10:00 AM - 11:30 AM
Introduction to Linux Basics II October 7th, Friday, 11:30 AM - 1:00 PM
Introduction to Linux Basics I October 13th, Thursday, 2:00 PM - 3:30 PM
Introduction to Linux Basics II October 25th, Tuesday, 2:00 PM - 3:30 PM

Python Basics

Title Date/Time
Python Language Basics I October 21st, Friday, 10:00 AM - 11:30 AM
Python Language Basics II October 21st, Friday, 11:30 AM - 1:00 PM

Topical Sessions

Title Date/Time
How to submit and run jobs efficiently and correctly on Sapelo September 30th, Friday, 10:00 AM - 11:30 AM
How to submit and run jobs efficiently and correctly on Sapelo October 11th, Tuesday, 11:00 AM - 12:30 PM
How to run NCBI Blast on zcluster at GACRC October 14th, Friday, 11:30 AM - 1:00 PM
NGS application overview October 28th, Friday, 10:00 AM - 11:30 AM
Python on GACRC Computing Resources October 28th, Friday, 11:30 PM - 1:00 PM


Who Should Attend: GACRC new cluster Sapelo users and zcluster users, or researchers who are interested in learning about the GACRC computing resources, Linux basics (Linux OS, file system, shell, common commands, Linux scripting), and scientific programming (Python, C/C++, Fortran, Perl) etc..

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 introduction, Linux introductory III (Linux working environment and utilities), Bioinfomatics applications, Python language III, Python on GACRC computing resources, 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 new cluster at GACRC

New cluster's current computing resources

New cluster software environment

How to operate with the new cluster

How to work with the new 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: GACRC Storage Environment

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

Overview of the storage enviornment of zcluster and the new 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 zcluster

Focus: Introduction to BLAST

BLAST job submission to zcluster

Advantages & Disadvantages: NCBI website vs run at zcluster.

Understand BLAST output

Troubleshooting the BLAST results


Title: NGS application overview

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

Closer look at NGS tools

Examples of NGS applications and pipelines

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

media: Introduction to HPC Using the New Cluster at GACRC Workshop v12.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 09152016.pdf

Linux Basics and Hands-on

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 09062016.pdf
media: Introduction to Linux Basics Part2 09092016.pdf

Python Basics

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

Topical Sessions

media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf
media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf
media: Software installation on zcluster.pdf
media: Blast Workshop GACRC 02292016.pdf

Out-Reach/On-Class Talk

Dept./Center/Institute Type Workshop 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
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

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

Past Sessions

Past Sessions in 2016

Past Sessions in 2015