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

The GACRC is going to host seventeen regular training sessions and three interactive Question-and-Answer sessions in August 2017. These sessions will provide introductions to the GACRC Linux HPC cluster (Sapelo), Linux basics, Python language basics, Perl language basics, and NCBI Blast application on Sapelo.

We offer:

1. Four Sapelo cluster new user training sessions (mandatory for new user account creation)

2. Three Linux-I introductory sessions and Three Linux-II introductory sessions (each combined with a Linux hands-on practice session)

3. One Python language basics I session and One Python basics II session

4. One Perl language basics I session

5. Four topical sessions on:

(1) Three sessions of How to submit and run jobs efficiently and correctly on Sapelo (strongly suggested for Sapelo users)

(2) One session of NCBI Blast application on Sapelo

6. Three interactive Question-and-Answer sessions (Bring your questions to us for a discussion. No registration is needed. We are looking forward to seeing you in the classroom with your questions to us!)


Training Location:

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

120 East Green Street, Athens, GA 30602


Event Schedule

Sapelo New User Training

Title Date/Time
Introduction to HPC Using Sapelo Cluster at GACRC August 1st, Tuesday, 11:00 AM - 12:30 PM
Introduction to HPC Using Sapelo Cluster at GACRC August 11th, Friday, 10:00 AM - 11:30 AM
Introduction to HPC Using Sapelo Cluster at GACRC August 15th, Tuesday, 11:00 AM - 12:30 PM
Introduction to HPC Using Sapelo Cluster at GACRC August 25th, Friday, 10:00 AM - 11:30 AM

Linux Basics and Hands-on

Title Date/Time
Introduction to Linux Basics I and Hands-on July 26th, Wednesday, 10:00 AM - 12:00 PM
Introduction to Linux Basics II and Hands-on July 26th, Wednesday, 1:00 PM - 3:00 PM
Introduction to Linux Basics I and Hands-on August 4th, Friday, 10:00 AM - 11:30 AM
Introduction to Linux Basics II and Hands-on August 4th, Friday, 11:30 AM - 1:00 PM
Introduction to Linux Basics I and Hands-on August 10th, Thursday, 11:00 AM - 12:30 PM
Introduction to Linux Basics II and Hands-on August 17th, Thursday, 11:00 AM - 12:30 PM
Introduction to Linux Basics I and Hands-on August 22nd, Tuesday, 11:00 AM - 12:30 PM
Introduction to Linux Basics II and Hands-on August 24th, Thursday, 11:00 AM - 12:30 PM

Python Basics

Title Date/Time
Python Language Basics I August 18th, Friday, 10:00 AM - 11:30 AM
Python Language Basics II August 18th, Friday, 11:30 AM - 1:00 PM


Perl Basics

Title Date/Time
Perl Language Basics I August 31st, Thursday, 11:00 AM - 12:30 PM


Topical Sessions

Title Date/Time
How to submit and run jobs efficiently and correctly on Sapelo August 3rd, Thursday, 11:00 AM - 12:30 PM
How to submit and run jobs efficiently and correctly on Sapelo August 11th, Friday, 11:30 AM - 1:00 PM
How to submit and run jobs efficiently and correctly on Sapelo August 25th, Friday, 11:30 AM - 1:00 PM
NCBI Blast application on Sapelo cluster August 29th, Tuesday, 11:00 AM - 12:30 PM

Interactive Question-and-Answer Sessions

Title Date/Time
Question-and-Answer August 1st, Tuesday, 14:00 PM - 15:30 PM
Question-and-Answer August 3rd, Thursday, 14:00 PM - 15:30 PM
Question-and-Answer August 10th, Thursday, 14:00 PM - 15:30 PM


Who Should Attend: GACRC Sapelo cluster 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, Perl, R, C/C++, Fortran) 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. You don't have to register the interactive Question-and-Answer sessions.

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 Sapelo

Focus: Sapelo general workflow and correct computing resource requesting

Overview of Sapelo cluster with reference tables and operational diagrams

Sapelo 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

Sapelo 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 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 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.


Download

Sapelo and zcluster New User Training

media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop v15.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop v8.pdf
media: Introduction to HPC Using zcluster at GACRC Workshop Pakala 02132017.pdf
media: Introduction to HPC Using Sapelo Cluster at GACRC Workshop Suchi 06262017.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 Suchi 05222017.pdf
media: Introduction to Linux Basics Part2 Suchi May242017.pdf

Python Basics

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

Topical Sessions

media: Python on GACRC Computing Resources v1.pdf
media: Submit and Run Jobs Efficiently and Correctly on Sapelo v1.pdf
media: Introduction to GACRC Storage Environment Workshop20160427 v3.pdf
media: High Performance Computing (HPC) on Cluster.pdf
media: Software installation on zcluster.pdf
media: Blast Workshop GACRC 02012017.pdf
media: Next-Generation Sequencing Applications at GACRC 10282016.pdf

Out-Reach/On-Class Talk

Dept./Center/Institute Type Workshop 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 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
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 2017

Past Sessions in 2016

Past Sessions in 2015