Skip to end of metadata
Go to start of metadata

Mission

The SSG has access to at least two clusters that can be used to speed up the different types of simulations and analyses our section does. This hands on workshop is aimed at enabling SSGers to use the cluster computing resources and help them advance their science in an efficient manner.

Schedule

Location

RPHB 4th floor computer lab

Date

Friday, October 19th, 2007

Agenda

Time

Topic

Notes

10:15 - 10:30 AM

Attendees settle in and connect to the cluster.

Attendees should make sure that they have their cluster login and password and an SOPH account to login to lab computers.

10:30 - 10:40 AM

Basic cluster concepts

Please review your notes from the 2007 HPC bootcamp. It may be helpful to look at the videos and the cluster wiki page.

10:40 - 11:10 AM

How to submit a job to the cluster: A C/C++ example

Hands on session for attendees to learn and submit jobs to the cluster. Basic workflow will be covered. Links to related documentation.

11:10 - 11:40 AM

How to submit a job on the cluster: An R example

Hands on session for attendees to learn and submit jobs to the cluster. Basic workflow will be covered. Links to related documentation.

11:40 - 12:00 PM

Q/A

Attendees continue to practice submitting jobs. We will be happy to answer to any questions and help the attendees with their jobs.

NOTE

  • This bootcamp is hands-on and will be conducted in a computer lab within RPHB.
  • Attendees are requested to make sure their account is active on the cluster. If you do not have an account yet OR your existing account is not working, please contact the cluster team support through http://etlab.eng.uab.edu/ . We recommend attendees to have their account setup on both cheaha and coosa clusters.
  • As both cheaha and coosa have the same job scheduling system (SGE - Sun Grid Engine), the job submission procedure is the same across these clusters.

Documentation

UAB HPC Resource

HPC Clusters : http://me.eng.uab.edu/wiki/index.php?title=HPC_-_High_Performance_Computing#Clusters

Queuing Systems on UAB Clusters : http://me.eng.uab.edu/wiki/index.php?title=Queuing_Systems

Library / Language

Notes / Documentation

Level

R

Running 'R' jobs on the cluster

User Level Information

 

swdev:Installing add-on 'R' packages

User Level Information

Structure / STRAT

Running Structure / STRAT programs on the cluster

User Level Information

C / C++

Compiling & Running C/C++ jobs on the cluster

User Level Information

PHASE

Running PHASE jobs on the cluster

User Level Information

Advance Topics

 Job Arrays in SGE : http://wiki.gridengine.info/wiki/index.php/Simple-Job-Array-Howto

Things to address

  • Benchmarking jobs
    • Recording intermediate results for independent permuation/iteration based jobs. At times of cluster down-time, this step will ensure the previous computations have not gone for waste.
  • Submitting embarrassingly parallel batch jobs.
  • Ways to interact with the cluster support team.
Labels
  • None