On Thu, Sep 19, 2013 at 2:48 PM, Xu, Jianqing <x...@medimmune.com> wrote: > > Dear all, > > I am learning the parallelization issues from the instructions on Gromacs > website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But > I hope to get some advice about a correct way to run jobs. > > 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?
Yes > Or the default Thread-MPI is actually a better option for a single computer > or single node (but multi-cores) for whatever reasons? Yes - lower overhead. > 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? You will see improved performance if you set the thread affinity. There is no advantage in allowing the threads to move. > 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? Depends, but usually best to use separate PME nodes. Try g_tune_pme, as Carsten suggests. > 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? Depends how many cores you have. If you want to share a node between mdruns, you should specify how many (real- or thread-) MPI ranks for each run, and how many OpenMP threads per rank, arrange for one thread per core, and use mdrun -pin and mdrun -pinoffset suitably. You should expect near linear scaling of each job when you are doing it right - but learn the behaviour of running one job per node first! Mark > 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 -- 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
