Hi Jianqing, On Sep 19, 2013, at 2:48 PM, "Xu, Jianqing" <x...@medimmune.com> wrote: > Say I have a local desktop having 16 cores. If I just want to run jobs on one > computer or a single node (but multiple cores), I understand that I don't > have to install and use OpenMPI, as Gromacs has its own thread-MPI included > already and it should be good enough to run jobs on one machine. However, for > some reasons, OpenMPI has already been installed on my machine, and I > compiled Gromacs with it by using the flag: "-DGMX_MPI=ON". My questions are: > > > 1. Can I still use this executable (mdrun_mpi, built with OpenMPI > library) to run multi-core jobs on my local desktop? Or the default > Thread-MPI is actually a better option for a single computer or single node > (but multi-cores) for whatever reasons? You can either use OpenMPI or Gromacs build-in thread MPI library. If you only want to run on a single machine, I would recommend recompiling with thread-MPI, because this is in many cases a bit faster.
> 2. Assuming I can still use this executable, let's say I want to use > half of the cores (8 cores) on my machine to run a job, > > mpirun -np 8 mdrun_mpi -v -deffnm md > > a). Since I am not using all the cores, do I still need to "lock" the > physical cores to use for better performance? Something like "-nt" for > Thread-MPI? Or it is not necessary? Depends on whether you get good scaling or not. Compare to a run on 1 core, for large systems the 4 or 8 core parallel runs should be (nearly) 4 or 8 times as fast. If that is the case, you do not need to worry about pinning. > > b). For running jobs on a local desktop, or single node having ... say 16 > cores, or even 64 cores, should I turn off the "separate PME nodes" (-npme > 0)? Or it is better to leave as is? You may want to check with g_tune_pme. Note that the optimum will depend on your system, and for each MD system you should find that out. > > 3. If I want to run two different projects on my local desktop, say one > project takes 8 cores, the other takes 4 cores (assuming I have enough > memory), I just submit the jobs twice on my desktop: > > nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 >& log1& > > nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 >& log2 & > > Will this be acceptable ? Will two jobs be competing the resource and > eventually affect the performance? Make some quick test runs (over a couple of minutes). Then you can check the performance of your 8 core run with and without another simulation running. Best, Carsten > > Sorry for so many detailed questions, but your help on this will be highly > appreciated! > > Thanks a lot, > > Jianqing > > > > To the extent this electronic communication or any of its attachments contain > information that is not in the public domain, such information is considered > by MedImmune to be confidential and proprietary. This communication is > expected to be read and/or used only by the individual(s) for whom it is > intended. If you have received this electronic communication in error, please > reply to the sender advising of the error in transmission and delete the > original message and any accompanying documents from your system immediately, > without copying, reviewing or otherwise using them for any purpose. Thank you > for your cooperation. > -- > 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 -- 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://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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
