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 | 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.
