Hi Venkat,
I've seen similar behaviour with OpenMPI and a home-patched version of Gromacs. I blamed OpenMPI/the cluster and contacted the admins (but I don't remember what the result was). In the end I solved/worked around the issue by compiling Gromacs with IntelMPI. HTH Peter On 01-02-18 06:11, venkat wrote: > Hello, > I installed Gromacs-2016.4 using (compiled using: > intel-parallel-studio-2016, gcc4.8.5), > I tried gromacs run parallelized on 32 cores, i seen multiple instances of > mdrun, each one using one MPI process, > also many gromacs header in the log file, in directory log, ene, traj_comp > files are creating multiple times > > so, I expecting your suggestions to rectify this issue. > > thank you > > *################FOR JOB SUBMISSION FOLLOWED SCRIPT USED * > #! /bin/bash > ##PBS -l walltime=48:00:00 > #PBS -N gromacs > #PBS -q workq > #PBS -l select=2:ncpus=16:mpiprocs=16 > #PBS -S /bin/csh > #PBS -V > # Go to the directory from which you submitted the job > > cd $PBS_O_WORKDIR > > module purge > module load gcc4.8.5 > module load gsl-2.0 > module load intel-parallel-studio-2016 > module load gromacs-2016.4_Plumbedpatch > module load openmpi-3.0 > module load plumed-2.4 > > export MPI_DEBUG=all > export MPI_IB_RAILS=2 > export MPI_DSM_DISTRIBUTE=1 > export MPI_VERBOSE=1 > export MPI_BUFS_THRESHOLD=1 > export MPI_BUFS_PER_PROC=1024 > export OMP_NUM_THREADS=1 > > mpirun -np 32 /app/gromacs-2016.4_plumbSWpatch/bin/gmx_mpi mdrun -v -s > topol -nsteps 5000000 &> 6ter.log > > > *##########DIRECTORY * > *ls -lrt * > > Feb 1 10:52 #ener.edr.51# > Feb 1 10:52 #ener.edr.50# > Feb 1 10:52 #ener.edr.49# > Feb 1 10:52 #ener.edr.48# > Feb 1 10:52 #ener.edr.47# > Feb 1 10:52 #ener.edr.46# > Feb 1 10:52 #ener.edr.45# > Feb 1 10:52 #ener.edr.44# > Feb 1 10:52 #ener.edr.43# > Feb 1 10:52 #ener.edr.42# > Feb 1 10:52 #ener.edr.41# > Feb 1 10:52 #ener.edr.40# > Feb 1 10:52 #ener.edr.39# > Feb 1 10:52 #ener.edr.38# > Feb 1 10:52 #ener.edr.37# > Feb 1 10:52 #ener.edr.36# > Feb 1 10:52 #ener.edr.35# > Feb 1 10:52 #ener.edr.34# > Feb 1 10:52 #ener.edr.33# > Feb 1 10:52 #ener.edr.32# > Feb 1 10:52 ener.edr > Feb 1 10:52 #traj_comp.xtc.57# > Feb 1 10:52 #traj_comp.xtc.56# > Feb 1 10:52 #traj_comp.xtc.55# > Feb 1 10:52 #traj_comp.xtc.54# > Feb 1 10:52 #traj_comp.xtc.53# > Feb 1 10:52 #traj_comp.xtc.52# > Feb 1 10:52 #traj_comp.xtc.51# > Feb 1 10:52 #traj_comp.xtc.50# > Feb 1 10:52 #traj_comp.xtc.49# > Feb 1 10:52 #traj_comp.xtc.48# > Feb 1 10:52 #traj_comp.xtc.47# > Feb 1 10:52 #traj_comp.xtc.46# > Feb 1 10:52 #traj_comp.xtc.45# > Feb 1 10:52 #traj_comp.xtc.44# > Feb 1 10:52 #traj_comp.xtc.43# > Feb 1 10:52 #traj_comp.xtc.42# > Feb 1 10:52 #traj_comp.xtc.41# > Feb 1 10:52 #traj_comp.xtc.40# > Feb 1 10:52 #traj_comp.xtc.39# > Feb 1 10:52 traj_comp.xtc > Feb 1 10:52 #md.log.70# > Feb 1 10:52 #md.log.69# > Feb 1 10:52 #md.log.68# > Feb 1 10:52 #md.log.67# > Feb 1 10:52 #md.log.66# > Feb 1 10:52 #md.log.65# > Feb 1 10:52 #md.log.64# > Feb 1 10:52 #md.log.63# > Feb 1 10:52 #md.log.62# > Feb 1 10:52 #md.log.61# > Feb 1 10:52 #md.log.60# > Feb 1 10:52 #md.log.59# > Feb 1 10:52 #md.log.58# > Feb 1 10:52 #md.log.57# > Feb 1 10:52 #md.log.56# > Feb 1 10:52 #md.log.55# > Feb 1 10:52 #md.log.54# > Feb 1 10:52 md.log > Feb 1 10:52 6ter.log > > *################KINDLY GET LOG FROM ATTACHMENT* > > 6ter.log > <https://drive.google.com/file/d/1p68O_azo1lV7ucS6zoXZtFNLWehv17p6/view?usp=drive_web> >
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