What does --loadbalance do? What do the .log files say about OMP_NUM_THREADS, thread affinities, pinning, etc?
Mark On Fri, Jul 12, 2013 at 3:46 AM, gigo <g...@poczta.ibb.waw.pl> wrote: > Dear GMXers, > With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were > separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 cores > with OpenMP. There is Torque installed on the cluster build of 12-cores > nodes, so I used the following script: > > #!/bin/tcsh -f > #PBS -S /bin/tcsh > #PBS -N test > #PBS -l nodes=48:ppn=12 > #PBS -l walltime=300:00:00 > #PBS -l mem=288Gb > #PBS -r n > cd $PBS_O_WORKDIR > mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4 > -replex 2000 > > It was working just great with 4.6.2. It does not work with 4.6.3. The new > version was compiled with the same options in the same environment. Mpiexec > spreads the replicas evenly over the cluster. Each replica forks 4 threads, > but only one of them uses any cpu. Logs end at the citations. Some empty > energy and trajectory files are created, nothing is written to them. > Please let me know if you have any immediate suggestion on how to make it > work (maybe based on some differences between versions), or if I should fill > the bug report with all the technical details. > Best Regards, > > Grzegorz Wieczorek > > -- > 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 -- 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