I am not sure I can give an affirmative working answer, but you may check ssh to each node, use "top" to see whether it's really run or just occupy the node but not use.
On Sat, Jul 9, 2011 at 8:56 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote: >> >> Hi >> >> >> I have a problem related to submitting a mdrun job on cluster. I tried to >> ask help or gromacs and rocks users-group. >> >> My machine specs. >> Cluster of Intel Xeon processors:QC with Rocks Cluster. 8 processors (16 >> threads) >> >> When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px >> pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads and >> the job completes in a day. But when I try submitting it to the cluster >> using following qsub script the job takes ~16 days >> >> ----------------------------------------------------------------------- >> #!/bin/bash >> # >> #$ -cwd >> #$ -S /bin/bash >> # >> #$ -N umbrella0 >> #$ -e umbrella0.errout >> #$ -o umbrella0.out >> # >> #$ -pe mpi 16 >> >> echo -n "Running on: " >> >> /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines >> /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf >> pullf-umbrella0.xvg -px pullx-umbrella0.xvg >> >> echo "Done." >> --------------------------------------- > > That's fine as far as GROMACS is concerned, so long as mdrunmpi really has > been compiled with MPI. You can get what diagnostic information it knows > about the MPI setup from the very top of the .log file. Otherwise, you'll > have troubleshoot your use of MPI and your batch queue system. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Best Regards, lina -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
