Training
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 March 2018, the GACRC is going to host sixteen training sessions. These sessions will provide two levels of introductions to the GACRC Linux HPC clusters (Sapelo and Sapelo2), Linux basics, Python and Perl language basics, etc.. We offer:
1. Sapelo cluster new user training, Level 1 (3 sessions) for cluster-inexperienced new users
2. Sapelo cluster new user training, Level 2 (3 sessions) for cluster-experienced new users
3. Sapelo cluster new user training (2 sessions)
4. Linux training for Linux-inexperienced cluster new users (3 sessions)
5. Linux Basics I (1 session) and II (1 sessions)
6. 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 | March 8th, Thursday, 1:45 PM - 3:30 PM |
Sapelo Cluster New User Training Level 2
| Title | Date/Time |
|---|---|
| Introduction to HPC Using Sapelo Cluster at GACRC | March 6th, Tuesday, 1:45 PM - 3:30 PM |
| Introduction to HPC Using Sapelo Cluster at GACRC | March 15th, Thursday, 1:45 PM - 3:30 PM |
| Introduction to HPC Using Sapelo Cluster at GACRC | March 19th, Monday, 10:00 AM - 12:00 PM |
Sapelo2 Cluster New User Training
| Title | Date/Time |
|---|---|
| Introduction to HPC Using Sapelo2 Cluster at GACRC | March 13th, Tuesday, 1:45 PM - 3:30 PM |
| Introduction to HPC Using Sapelo2 Cluster at GACRC | March 26th, Monday, 1:00 PM - 3:00 PM |
Linux Training for Linux-inexperienced Cluster New Users
| Title | Date/Time |
|---|---|
| Use Linux on Cluster | March 5th, Monday, 10:00 AM - 12:00 PM |
| Use Linux on Cluster | March 12th, Monday, 1:00 PM - 3:00 PM |
| Use Linux on Cluster | March 20th, Tuesday, 1:45 PM - 3:30 PM |
| Use Linux on Cluster | March 26th, Monday, 10:00 AM - 12:00 PM |
Linux Basics and Hands-on
| Title | Date/Time |
|---|---|
| Introduction to Linux Basics I and Hands-on | March 19th, Monday, 1:00 PM - 3:00 PM |
| Introduction to Linux Basics II and Hands-on | March 29th, Thursday, 1:45 PM - 3:30 PM |
Python Basics
| Title | Date/Time |
|---|---|
| Python Basics I | March 12th, Monday, 10:00 AM - 12:00 PM |
| Python Basics II | March 27th, Tuesday, 1:45 PM - 3:30 PM |
Perl Basics
| Title | Date/Time |
|---|---|
| Perl Language Basics I | March 1st, Thursday, 1:45 PM - 3:30 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 |
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 Basics and Hands-on
| media: Introduction to Linux Basics Part1 Suchi 02202018.pdf |
| media: Introduction to Linux Basics Part2 Suchi Feb202018.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
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.