[gmx-users] Increasing performance of siumulation in cluster
mark.j.abraham at gmail.com
Fri May 31 23:59:01 CEST 2013
On Fri, May 31, 2013 at 11:30 AM, Sainitin Donakonda <saigro16 at gmail.com>wrote:
> Hi Mark,
> I forgot to mention about simulation it is protein ligand simulation which
> contains one protein and ligand with 20000 solute molecules..
So assuming you mean "solvent", about 60K atoms.
> and regarding
> hardware of cluster which is in my university as follows
> CPUs AMD Opteron 6274 number of cores 5888 th. peak performance 51.8
> TFlops compute nodes 4-way nodes *Saxonid* with 64 cores nodes with 64
> GB RAM 48 nodes with 128 GB RAM 24 nodes with 256 GB RAM 12 nodes
> with 512 GB RAM 8
Links are better than copy-and-paste...
> Can you now suggest some methods which i can use to optimize to increase
Your hardware is quite useful. You should be getting better performance.
Exactly how to do that depends on the simulation (e.g. PME or not, group or
Verlet kernels). You should start with
experiment with the balance of MPI processes and OpenMP threads per node of
your hardware. Look at the timing breakdown at the end of the .log file,
and pay attention to all the information grompp and mdrun writes!
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