Hi Albert, On Aug 25, 2012, at 7:37 AM, Albert <mailmd2...@gmail.com> wrote:
> Dear: > > Our institute got a IBM Power 775 cluster and it claimed to be very good. > However, it doesn't support g_tune_pme. Are you shure that it is not supported? Maybe you just need the right syntax. > I use the following script for job submission: > > > > #@ job_name = gromacs_job > #@ output = gromacs.out > #@ error = gromacs.err > #@ class = kdm > #@ node = 4 > #@ tasks_per_node = 32 > #@ wall_clock_limit = 01:00:00 > #@ network.MPI = sn_all,not_shared,US,HIGH > #@ notification = never > #@ environment = COPY_ALL > #@ job_type = parallel > #@ queue > mpiexec -n 128 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr > > it is only 7 ns/day. > > However, in another cluster with the same system, Core number and parameters, > I can get up to 30 ns/day. > > Does anybody have any advices for this issue? On a Power6 machine, I have successfully used the following job file: # @ shell=/bin/ksh # # Sample script for LoadLeveler # # @ error = run_1.err.$(jobid) # @ output = run_1.out.$(jobid) # @ job_type = parallel # @ environment= COPY_ALL # @ node_usage= not_shared # @ node = 1 # @ tasks_per_node = 4 # @ resources = ConsumableCpus(1) # @ network.MPI = sn_all,not_shared,us # @ wall_clock_limit = 0:05:00 # @ notification = complete # @ queue # # run the program # export MDRUN=/path/to/gromacs-4.5.1/bin/mdrun_mpi export MPIRUN=poe #no poe here! /path/to/g_tune_pme -np 4 \ -npstring none -s ./ap.tpr -resetstep 1 -steps 10 Hope that helps, Carsten > > thank you very much > Albert > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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