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

[Peter Kroon]

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>
> ​