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

[Mark Abraham]

Hi,

The fact that the binary you ran was named gmx_mpi yet does not seem to be
compiled with MPI is suspicious - either the cmake process that was used
handled suffixes explicitly (which is unnecessary if all you want is the
standard thing) and was wrong, or we implemented the standard suffixing
wrong (but it's been fine for years and we didn't touch it lately), or
something is broken with your wrapper compiler.

It is very likely that you have not succeeded in compiling with MPI
support. Inspect the report in md.log to see what it says about the MPI
library. If so, then you need to consult with the cluster docs/admins to
find out how to direct the MPI wrapper compiler to use the intended base
compiler (here icc) and give that to cmake. Additionally, setting cmake
-DGMX_MPI=on will make sure that you can't accidentally build a non-MPI
version of GROMACS.

Mark

On Thu, Feb 1, 2018 at 11:40 AM Peter Kroon <p.c.kroon at rug.nl> wrote:

> 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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