URSA.gsu.edu - basic info

URSA is a 576 processor Super Computer based on the Power5+ processor and IBM’s P series architecture. ( More details.) The system has 18 TB user disk storage with backups.

URSA has 36 nodes each with 8 dual core processors. Each node has 32 GB RAM with one node configured with maximum memory of 256 GB and one node with 64 GB. Within each node we have SMP options available and between the nodes we have a Brocade high speed interconnect (IBM pSeries High Performance Switch). Also implemented is IBM’s Parallel Environment (an MPI utility designed for the pSeries architecture with features like remote memory access).

Attached to the nodes is a 18 TB SAN (Storage Area Network) via a fiber SAN switch. The SAN is implemented using IBM GPFS (General Parallel File System http://www-03.ibm.com/systems/clusters/software/gpfs.html) and is accessed via a DS4800 raid controller. The SAN environment is made up of 16 300GB 100k rpm fiber channel disks behind redundant 2GB/s controllers. “Large Page” support is currently turned on in the SAN and can be configured in a number of ways to meet fast data access needs.

System Administration

• AIX 5.3.2
• Job scheduler: LoadLeveler
• Location: Technology Operations Center (TOC)
• Backups, UPS power, HVAC, 24 hr attended operation

Accessing URSA

Users access URSA either directly via SSH and SFTP or via ResearchComputingPortal.

Researchers

Biology, Chemistry, Physics &Astronomy, Math & Statistics, Computer Science, Risk Management & Insurance, Finance, Political Science and SURAgrid users under agreement with SURA - Southeastern Universities Research Association (http://www.sura.org).

Case Study from IBM

Applications:

Amber8 - http://amber.scripps.edu/

• Molecular force dynamics simulation on bio-molecules (50 various program modules)
• Sander: "main" program used for molecular dynamics simulations.
• Simulated annealing with NMR-derived energy restraints
• Also used for replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations
• pmemd: extensively-modified version (by Bob Duke) of sander, limited to periodic, PME simulations. Faster, and scales better on parallel machines, than sander. Program of choice for "standard" periodic simulations
• LEaP? : X-windows-based program for basic model building.

Gaussian03 - http://www.gaussian.com/

• Electronic structure program to study molecules and reactions under a wide range of conditions
• Based on quantum mechanics, Gaussian predicts the energies, molecular structures, properties, and vibration frequencies of molecular system
• Enables study of compounds that are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures

SAS - http://www.sas.com/

-- JaroKlc - 19 Jun 2008