Re: [gmx-users] how to optimize performance of IBM Power 775?
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 listgmx-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 listgmx-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
[gmx-users] how to optimize performance of IBM Power 775?
Dear: Our institute got a IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme. 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? thank you very much Albert -- gmx-users mailing listgmx-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
[gmx-users] how to optimize performance of IBM Power 775?
Beyond optimizing your number of cores and npme (by hand I guess in your case), you can try hyperthreading (talk to your sysadmins if you can not simply run 2N threads, where N is the number of cores. I found on a power 6 that if you have N cores, it is optimal to run 2N-1 threads, rather than 2N threads. Nevertheless, I have found that the IBM power 5 and power 6 machines run gromacs significantly slower than, for example, a Nehalem. I don't know if it's a lack of gromacs hardware-specific optimization or simply a function of the lower power consumption of the IBM power series. A number of years ago, I posted a few emails to this list on how to optimize compilation on the power machines (flags, etc). You should be able to find those by searching. Good luck, Chris. -- original message -- Our institute got a IBM Power 775 cluster and it claimed to be very good. However, it doesn't support g_tune_pme. 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? thank you very much Albert -- gmx-users mailing listgmx-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
