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| Computers in Experimental Genetics Fall 2016 || On-Class (GENE4220) || [[media:]] | |||
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Revision as of 09:31, 19 October 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 sixteen training sessions in October 2016. These sessions will provide introductions to the GACRC Linux HPC clusters, Linux basics, Python language basics and GACRC Python computing resources, NCBI Blast, and NGS data processing tools. We offer:
1. Four Sapelo and two zcluster new user training sessions (mandatory for new user account creation)
2. Two Linux-I and two Linux-II introductory sessions
3. Two Python sessions (I and II)
4. One topical session on NCBI Blast application on zcluster
5. One topical session on NGS application overview (new topic)
6. One topical session on How to submit and run jobs efficiently and correctly on Sapelo
7. One topical session on Python on GACRC Computing Resources (new topic)
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 Sapelo Cluster at GACRC | October 4th, Tuesday, 2:00 PM - 3:30 PM |
| Introduction to HPC Using zcluster at GACRC | October 6th, Thursday, 2:00 PM - 3:30 PM |
| Introduction to HPC Using Sapelo Cluster at GACRC | October 14th, Friday, 10:00 AM - 11:30 AM |
| Introduction to HPC Using Sapelo Cluster at GACRC | October 18th, Tuesday, 2:00 PM - 3:30 PM |
| Introduction to HPC Using zcluster at GACRC | October 20th, Thursday, 2:00 PM - 3:30 PM |
| Introduction to HPC Using Sapelo Cluster at GACRC | October 27th, Thursday, 2:00 PM - 3:30 PM |
Linux Basics and Hands-on
| Title | Date/Time |
|---|---|
| Introduction to Linux Basics I | October 7th, Friday, 10:00 AM - 11:30 AM |
| Introduction to Linux Basics II | October 7th, Friday, 11:30 AM - 1:00 PM |
| Introduction to Linux Basics I | October 13th, Thursday, 2:00 PM - 3:30 PM |
| Introduction to Linux Basics II | October 25th, Tuesday, 2:00 PM - 3:30 PM |
Python Basics
| Title | Date/Time |
|---|---|
| Python Language Basics I | October 21st, Friday, 10:00 AM - 11:30 AM |
| Python Language Basics II | October 21st, Friday, 11:30 AM - 1:00 PM |
Topical Sessions
| Title | Date/Time |
|---|---|
| How to submit and run jobs efficiently and correctly on Sapelo | October 11th, Tuesday, 11:00 AM - 12:30 PM |
| How to run NCBI Blast on zcluster at GACRC | October 14th, Friday, 11:30 AM - 1:00 PM |
| NGS application overview | October 28th, Friday, 10:00 AM - 11:30 AM |
| Python on GACRC Computing Resources | October 28th, Friday, 11:30 PM - 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: 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 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 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: 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: 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: 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
Focus: Overview of Bioinformatics software's available on HPC clusters at GACRC
Closer look at NGS tools
Examples of NGS applications and pipelines
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
Linux Basics and Hands-on
Python Basics
| media: Python Language Basics I Workshop20160328 v4.pdf |
| media: Python Language Basics II Workshop20160425 v1.pdf |
Topical Sessions
Out-Reach/On-Class Talk
NOTE: The slides may become outdated and you should always check GACRC Wiki for up to date information.