Gromacs

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Revision as of 18:56, 26 January 2011 by Jpr@uab.edu (talk | contribs) (moved Gromacs Benchmark to Gromacs: This page will be an introduction and overview to the application. Its focus should be on Gromacs in general with sub pages linking to more specific content. For an example see the NIH's Biowulf page on G...)
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Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/


Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

Gromacs is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids.

Benchmarking

2011 Hardware

Benchmark data for running Gromacs on Cheaha will be developed leveraging the benchmark foundation of the NIH's Biowulf cluster Gromacs testing suite combined with local work flow characteristics.

2007 Hardware and Gromacs 3.x

Note: The Gromacs 3.x code base was severely limited in spanning multiple compute nodes. The limit for 1GigE network fabrics was 4 nodes. The following performance data is provided for historical reference only and does not reflect performance of the Gromacs 4.x code base currently install on Cheaha.

Two identical 4 CPU Gromacs runs and the jobs spread out as follows based on current queue load (the new nodes are using Infiniband, the old TCP for message passing):

Dell Blades: 4 cpu job running on 4 compute nodes

Job ID:    71566
Submitted: 14:11:40
Completed: 17:06:03
Wall Clock: 02:54:23
              NODE (s)   Real (s)      (%)
      Time:  10462.000  10462.000    100.0
                      2h54:22
              (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    238.044     16.164      4.129      5.812

Verari: 4 cpu job running on 2 compute nodes

Job ID:    71567
Submitted: 14:11:44
Completed: 23:13:01
Wall Clock: 09:01:17
              NODE (s)   Real (s)      (%)
      Time:  32473.000  32473.000    100.0
                      9h01:13
              (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     76.705      5.208      1.330     18.040