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

[Peter Kroon]

Hi,

Digging through my old submission scripts show that when I ran gromacs
with `srun` MPI communication would not work, and I would end up with a
lot of files. If I ran with `mpirun` everything worked as expected.
Which was why I blamed my cluster and their OpenMPI installation. I'm
not sure this is the thing OP is experiencing.


Peter


On 01-02-18 12:24, Mark Abraham wrote:
> 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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