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 gmx-users-requ...@gromacs.org.
