Gromacs: Difference between revisions
Jpr@uab.edu (talk | contribs) (Added initial performance metrics from uabgrid-dev discussion 2009-11-11) |
Jpr@uab.edu (talk | contribs) (Link to Biowulf for reference and qualify benchmark numbers for older Gromacs and older Cheaha hardware) |
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[http://www.gromacs.org/ Gromacs] is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. | [http://www.gromacs.org/ 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 [http://biowulf.nih.gov/apps/gromacs 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 The following performance data is provided for historical reference only and does not reflect performance of the Gromacs 4.x code base currently install on Cheaha.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): | 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): | ||
Revision as of 18:51, 26 January 2011
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 The following performance data is provided for historical reference only and does not reflect performance of the Gromacs 4.x code base currently install on Cheaha.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