Hi, Sounds like an issue with some infrastructure being mismatched (e.g. different MPI at compile and run time). Does it work when you run a different MPI-used program, compiled and run using the same approach?
Mark On Fri, Aug 25, 2017 at 3:25 PM Souparno Adhikary <[email protected]> wrote: > Hi, > > This is related to running GROMACS through mpirun and Torque. After I > installed Torque in our lab cluster, I went on to test GROMACS using a > simple run. I wrote a Torque script as follows: > > #!/bin/sh > #PBS -N asyn > #PBS -q batch > #PBS -l nodes=4:ppn=4 > #PBS -l walltime=120:00:00 > cd $PBS_O_WORKDIR > cat $PBS_NODEFILE>nodes > mpirun -np 16 gmx_mpi mdrun -deffnm asyn_10ns > > After I submit this file using qsub command, the job is properly > showing using pbsnodes command in other mom units. > > But, the job stays as R in 00:00:00 in the list. I presume, this might > be an error from my part in setting up GROMACS with Torque. I compiled > GROMACS with -DGMX_MPI=ON > > The nodes file is not written and the job stays stuck. > > Can anyone familiar with job scheduling help me in this regard??? > > > Souparno Adhikary, > CHPC Lab, > Department of Microbiology, > University of Calcutta. > -- > 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 [email protected]. > -- 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 [email protected].
