Hi, Yes, that's another point of failure - the command to launch the MPI executable needs to provide the correct context, including linking the right libraries.
Mark On Thu, Feb 1, 2018 at 2:40 PM Peter Kroon <p.c.kr...@rug.nl> wrote: > 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.kr...@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 > >>> > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
