Dear Szilárd Páll, Thanks for the response. My PBS script to launch the run is:
#! /bin/bash #PBS -l cput=5000:00:00 #PBS -l select=2:ncpus=16:ngpus=2 #PBS -e errorfile.err #PBS -o logfile.log tpdir=`echo $PBS_JOBID | cut -f 1 -d .` tempdir=$HOME/work/job$tpdir mkdir -p $tempdir cd $tempdir cp -R $PBS_O_WORKDIR/* . mpiexec.hydra -np 4 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi mdrun -v -dlb yes -ntomp 16 -s equilibration3.tpr Interestingly, I am using the same script to run CPU only jobs, which are not creating any problems. Please check the generated log file here: https://www.dropbox.com/s/dtfsuh6dv635n6q/md.log?dl=0 On Thu, Apr 7, 2016 at 6:18 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > On Thu, Apr 7, 2016 at 2:35 PM, Venkat Reddy <venkat...@gmail.com> wrote: > > Thank you Mark for the quick response. > > I tried to change -np option to 4. But it seems that mdrun is using only > > one GPU in single node with four ranks. The nvidia-smi command shows > > > > | 0 7977 C /Apps/gromacs512/bin/gmx_mpi > > 130MiB | > > | 0 7978 C /Apps/gromacs512/bin/gmx_mpi > > 130MiB | > > | 0 7979 C /Apps/gromacs512/bin/gmx_mpi > > 130MiB | > > | 0 7980 C /Apps/gromacs512/bin/gmx_mpi > > 130MiB | > > No command line, no log file shown nothing to comment on. > > Additionally, if all four ranks you requested are on the same node > rather than split over two nodes, that likely means you're using an > incorrect job script -- definitely not a GROMACS issue. Please make > sure you can launch an MPI "Hello world" program over multiple nodes > first. > > > > Also the job folder has four backed up copies of same run. > > > > On Thu, Apr 7, 2016 at 5:07 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> Hi, > >> > >> mpiexec.hydra -np 1 asks for a single MPI rank, which is what you got. > But > >> you need at least two, ie. at least one on each rank, and at least four > if > >> you want to make use of the two GPUs on each of two nodes. > >> > >> Mark > >> > >> > >> On Thu, Apr 7, 2016 at 1:14 PM Venkat Reddy <venkat...@gmail.com> > wrote: > >> > >> > Dear all, > >> > > >> > Please neglect my previous mail which was incomplete. > >> > > >> > I am trying to execute mdrun our GPU cluster with 7 nodes where each > node > >> > is populated by 16 processors and two K40 GPU cards. I have no problem > >> with > >> > mdrun on single node. However, when I try to execute parallel run on > two > >> > nodes with gmx_mpi executable (gromacs-5.1.2), the performance is > very > >> > slow. When I logged into individual nodes, I found that mdrun is not > >> > utilizing both GPUs. The generated log file shows the following > message. > >> > > >> > Using 1 MPI process > >> > Using 16 OpenMP threads > >> > > >> > 2 compatible GPUs are present, with IDs 0,1 > >> > 1 GPU auto-selected for this run. > >> > Mapping of GPU ID to the 1 PP rank in this node: 0 > >> > > >> > > >> > NOTE: potentially sub-optimal launch configuration, gmx_mpi started > with > >> > less > >> > PP MPI process per node than GPUs available. > >> > Each PP MPI process can use only one GPU, 1 GPU per node will be > >> > used. > >> > > >> > I read the manual and instructions in > >> > > >> > > >> > http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html > >> > to > >> > execute the parallel run. But I couldn't find the right flags to > initiate > >> > it. Please help me in this aspect. The script I used to execute the > >> > parallel run is given below. > >> > > >> > #! /bin/bash > >> > #PBS -l cput=5000:00:00 > >> > #PBS -l select=2:ncpus=16:ngpus=2 > >> > #PBS -e errorfile.err > >> > #PBS -o logfile.log > >> > tpdir=`echo $PBS_JOBID | cut -f 1 -d .` > >> > tempdir=$HOME/work/job$tpdir > >> > mkdir -p $tempdir > >> > cd $tempdir > >> > cp -R $PBS_O_WORKDIR/* . > >> > mpiexec.hydra -np 1 -hostfile $PBS_NODEFILE > /Apps/gromacs512/bin/gmx_mpi > >> > mdrun -v -dlb yes -ntomp 16 -s equilibration3.tpr > >> > > >> > > >> > > >> > -- > >> > With Best Wishes > >> > Venkat Reddy Chirasani > >> > PhD student > >> > Laboratory of Computational Biophysics > >> > Department of Biotechnology > >> > IIT Madras > >> > Chennai > >> > INDIA-600036 > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.