Training: Difference between revisions
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| Center for Simulational Physics || | | Center for Simulational Physics || Out-Reach (CSP Seminar Talk 20170831) || [[media: Introduction on HPC Resources at the GACRC.pdf]] | ||
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| Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]] | | Computational Physics - Spring 2017 || On-class (PHYS4601/6601) || [[media: phys4601.pdf]] | ||
Revision as of 13:55, 14 August 2017
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 | 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 |
Zcluster Decommissioning Awareness Sessions
The GACRC will host three awareness sessions in August. We will help to answer your questions related to the zcluster decommissioning.
| Title | Date/Time |
|---|---|
| Session 1 | August 15th, Tuesday, 14:00 PM - 15:30 PM |
| Session 2 | August 17th, Thursday, 14:00 PM - 15:30 PM |
| Session 3 | August 22nd, Tuesday, 14:00 PM - 15:30 PM |
Please Note: A Sapelo user account will not be granted by only attending awareness sessions. To obtain a Sapelo user account, you are required to attend either (1) a zcluster-Sapelo migrating training session to be scheduled in September and October, or (2) a regular Introduction to HPC Using Sapelo Cluster at GACRC session, hosted weekly.
More information about these training sessions will be posted on the GACRC’s training web page, at gacrc.uga.edu/training as well as on the GACRC's wiki, at wiki.gacrc.uga.edu/wiki/Training .
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 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.
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
| Dept./Center/Institute | Type | Workshop PDF |
|---|---|---|
| Center for Simulational Physics | 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 | 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.