Training
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
Sapelo and zcluster New User Training
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
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 |
Python Basics
April Schedule
| Title | Date/Time |
|---|---|
| Python Language Basics II | April 25th, Monday, 1:00 PM - 2:30 PM |
Topical Sessions
April Schedule
| Title | Date/Time |
|---|---|
| How to run NCBI Blast on zcluster at GACRC | April 13th, Wednesday, 3:00 PM - 4:30 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: Python Language Basics I and II
Focus of I:
Overview of Python language, scientific modules and distributions
General Lexical conventions
Basic built-in data types
Program structure: control flow and loop
Function: procedural and functional programming with examples
Focus of II:
Python Class
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
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
Sapelo and zcluster New User Training
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 v2.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
NOTE: The slides may become outdated and you should always check GACRC Wiki for up to date information.