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.


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

Title 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

Title 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

Title 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

Title 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

Title 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

Title 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

media: GACRC Sapelo2 cluster new user training workshop.pdf
media: GACRC Sapelo2 cluster new user training hands-out.pdf

Sapelo Cluster Training

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

media: GACRC Zcluster-Sapelo Migrating Training.pdf

Linux Training for cluster New Users

media: Linux Training For New Users Of Cluster Suchi 04022018.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: 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

Dept./Center/Institute Type 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