[gmx-users] paralllelized gromacs run creating same file in many times -reg

[venkat]

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>
​