On Fri, May 31, 2013 at 11:30 AM, Sainitin Donakonda <saigr...@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... https://doc.zih.tu-dresden.de/hpc-wiki/bin/view/Compendium/HardwareAtlas > Can you now suggest some methods which i can use to optimize to increase > performance > 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 http://www.gromacs.org/Documentation/Acceleration_and_parallelization and 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! Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
