Getting Started with URSA

•1. What is URSA?

URSA is a 576 processor Super Computer based on the Power5+ processor and IBM's P series architecture. The system has 18TB user disk storage with backups. URSA has 36 nodes, each with 8 dual-core processors. The nodes have 32GB memory with one node configured with maximum memory of 256GB and one node with 64GB.

•2. What types of things can URSA do?

People can run their own applications such as AMMP. However, there are also applications that are on the system such as Amber and SAS. Below is a little information on some of them.

AMMP

• § AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. (Developed by Dr. Robert W. Harrison, Professor Computer Science, Georgia State University)
• § More info ( http://www.cs.gsu.edu/~cscrwh/ )

Amber8

• § Molecular force dynamics simulation on bio-molecules (50 various program modules)
• • • Sander: "main" program used for molecular dynamics simulations.
    • More info ( http://www.gsu.edu/ist/acs/24805.html )
    • More detail about Amber8 ( http://ambermd.org/ )

Gaussian03

• • • Linda (parallel gaussian)
    • Electronic structure program to study molecules and reactions under a wide range of conditions
    • More info ( http://www.gsu.edu/ist/acs/24805.html )
    • More detail about Gaussian03 ( http://www.gaussian.com/ )

SAS

• § SAS is an application for data analysis with tools for information storage and retrieval, data modification, report writing, file handling, and statistical functions.

• § More info can contact: Dr. Jaro Klc 404-413-4744 or Help@gsu.edu

Compilers

• § Compilers are available on URSA including C and Fortran

•3. How do I create an account on URSA at Georgia State University?

Use your web browser to link to to Account Requests:

http://www.gsu.edu/ist/acs/account_requests.html, follow the instructions to fill in the blank request form and then click the Submit Account Request button.

You will receive a welcome message once the account is created. For instance, see

http://www.gsu.edu/ist/acs/24749.html.

You may also send a request to the Help Desk for an account via phone, 404-413-4357, or email, help@gsu.edu.

•4. How do I submit a job?

When you create an account on URSA, you may use the EnginFrame Portal, http://janus.gsu.edu:8080/enginframe/gsu/rcp.xml, to login to URSA. You may also submit jobs to URSA by using LoadLeveler. LoadLeveler is a batch job scheduling application and program, http://www.gsu.edu/ist/acs/24750.html, a product of IBM. Your welcome message explains how to use ssh to login directly to URSA.

Basic Loadleveler Commands:

llsubmit - submits a job to Loadleveler

llcancel - cancels a submitted job

llq - queries the status of jobs in the job queue

llstatus - queries the status of machines in the cluster

llq example:

v01n08:/u/skoviraj $ llsubmit mybasic.cmd

llsubmit: The job "v01n08.vendor.pok.ibm.com.205" has been submitted

v01n08:/u/skoviraj $ llq

Id Owner Submitted ST PRI Class Running On

v01. skoviraj 11/11 22:29 R 50 No_Class v01n02

v01. skoviraj 11/11 22:30 R 50 No_Class v01n02

v01. skoviraj 11/11 22:28 I 50 No_class

3 job steps in queue, 1 waiting, 0 pending, 2 running, 0 held

More info at http://pyxis.gsu.edu/twiki/bin/view/ResearchComputing/LoadLeveler

•5. What other resources are available to me?

• § FAQ, http://www.gsu.edu/ist/acs/26146.html
• § You may visit our website for information at http://www.gsu.edu/ist/acs/
• § You may email the Help Desk at help@gsu.edu with questions and someone will get back to you or schedule a meeting if necessary.

-- LingfeiOuyang - 12 Feb 2009