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Revision as of 13:09, 15 August 2016

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 eight training sessions from August 15th to August 31st 2016. These sessions will provide introductions to the GACRC Linux HPC clusters, Linux basics, and Python language basics. We offer:

1. Three zcluster and Sapelo new user training sessions

2. Two Linux introductory sessions (I and II)

3. One Linux Hands-on session

4. Two Python sessions (I and II)


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 the New Cluster (Sapelo) at GACRC August 16th, Tuesday, 2:00 PM - 3:30 PM
Introduction to HPC Using zcluster at GACRC August 23rd, Tuesday, 2:00 PM - 3:30 PM
Introduction to HPC Using the New Cluster (Sapelo) at GACRC August 25th, Thursday, 2:00 PM - 3:30 PM


Linux Basics and Hands-on

Title Date/Time
Introduction to Linux Basics I August 18th, Thursday, 2:00 PM - 3:30 PM
Introduction to Linux Basics II August 26th, Friday, 10:00 AM - 11:30 AM
Linux Hands-on session August 26th, Friday, 11:30 AM - 1:00 PM


Python Basics

Title Date/Time
Python Language Basics I August 19th, Friday, 10:00 AM - 11:30 AM
Python Language Basics II August 19th, Friday, 11:30 AM - 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: 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 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 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: 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


Download

Sapelo and zcluster New User Training

media: Introduction to HPC Using the New Cluster at GACRC Workshop v10.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 07282016.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

Python Basics

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

Topical Sessions

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 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