Training

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Training Sessions

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 twelve training sessions in April at Davison Life Sciences Complex (Life Sciences Building), Room C128. These workshops will provide an introduction to the GACRC Linux high performance computing (HPC) clusters, the Linux basics (including hands-on sessions), NCBI Blast application, and scientific Python basics on GACRC clusters, etc.. We offer:

1. Four regular zcluster and Sapelo new user training sessions

2. Three Linux introductory sessions (I and II)

3. Two Linux hands-on practice sessions for GACRC users to obtain Linux hands-on working experiences

4. Three topical sessions focusing on GACRC Storage environment, NCBI Blast application on zcluster, and scientific Python basics on GACRC clusters II

Training Location

Davison Life Sciences Complex (Life Science Building), Room C128, 120 East Green St, Athens, GA 30602

Regular New User Training

March Schedule
Title Date/Time
Introduction to HPC Using zcluster at GACRC March 30th, Wednesday, 3:00 PM - 4:30 PM
April Schedule
Title Date/Time
Introduction to HPC Using the New Cluster at GACRC April 4th, Monday, 10:00 AM - 11:30 AM
Introduction to HPC Using zcluster at GACRC April 6th, Wednesday, 3:00 PM - 4:30 PM
Introduction to HPC Using zcluster at GACRC April 18th, Monday, 10:00 AM - 11:30 AM
Introduction to HPC Using the New Cluster at GACRC April 20th, Wednesday, 3:00 PM - 4:30 PM

Linux Basics and Hands-on

March Schedule
Title Date/Time
Linux Hands-on Practice Session (Basic Linux knowledge required) March 28th, Monday, 10:00 AM - 11:30 AM
April Schedule
Title Date/Time
Introduction to Linux Basics II April 4th, Monday, 1:00 PM - 2:30 PM
Introduction to Linux Basics I April 11th, Monday, 10:00 AM - 11:30 AM
Linux Hands-on Practice Session (Basic Linux knowledge required) April 11th, Monday, 1:00 PM - 2:30 PM
Linux Hands-on Practice Session (Basic Linux knowledge required) April 18th, Monday, 1:00 PM - 2:30 PM
Introduction to Linux Basics II April 25th, Monday, 10:00 AM - 11:30 AM

Topical Sessions

March Schedule
Title Date/Time
Scientific Python Basics on GACRC Clusters I March 28th, 2016, Monday, 1:00 PM - 2:30 PM
April Schedule
Title Date/Time
How to run NCBI Blast on zcluster at GACRC April 13th, Wednesday, 3:00 PM - 4:30 PM
Scientific Python Basics on GACRC Clusters II April 25th, Monday, 1:00 PM - 2:30 PM
GACRC Storage Environment April 27th, Wednesday, 3:00 PM - 4:30 PM

Who Should Attend: New HPC cluster and zcluster users, or researchers who are interested in learning about the GACRC computing resources and Linux basics (Linux OS, Linux filesystem, shell, and common commands, scripting, etc.).


Topic Introduction

Title: Introduction to HPC Using the New 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: 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


How to Register

If you would like to attend, please respond by email to: zhuofei@uga.edu or pakala@uga.edu. Also please tell us which session 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 working environment and utilities (Linux Part III), Bioinfomatics applications, scientific 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.


Download

New User Training Sessions

media: Introduction to HPC Using the New Cluster at GACRC Workshop20160202 v7.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop20160201 v6.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02102016.pdf

Linux Sessions

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

Python Sessions

media: Scientific Python Basics on the GACRC Clusters I Workshop20160328 v1.pdf

Topical Sessions

media: Software installation on zcluster.pdf
media: Blast Workshop GACRC 02292016.pdf
media: Introduction to GACRC Storage Environment Workshop20151109 v2.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 HPC Using the New Cluster at GACRC Workshop CSP20150915 v2.pdf
Microbiology On-Class (MIBO8150) media: Introduction to HPC Resources at GACRC MIBO8150 20151007.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
Bioinformatics - Applied Genome Analysis On-Class (BINF8940) media:Introduction to HPC Using zcluster at GACRC BINF8940 20160128.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