Gromacs
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.
Benchmark data for running Gromacs on Cheaha follows:
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