Hi gmx-users We have an HPC setup running HP_MPI and LSF/SLURM. Gromacs 4.5.3 has been compiled with mpi support The compute nodes on the system contain 2 x dual core Xeons which the system sees as 4 processors
An LSF script called gromacs_run.lsf is as shown below #BSUB -N #BSUB -J "gromacsTest5" #BSUB -u l.larco...@cranfield.ac.uk #BSUB -n 4 #BSUB -q short #BSUB -o %J.log mpirun -srun mdrun_mpi -v -s xxx.tpr -o xxx.trr Queued with: Bsub < gromacs_run.lsf This is intended to run 1 mdrun on a single node using all four cores of the two xeons. The result is that although the job is only submitted to one compute node, 4 mdruns are launched on each of the 4 cores = 16 jobs. These are all the same as if mdrun has not been compiled with mpi support. If I tell srun to start just one task with "mpirun -srun -n1 mdrun_mpi -v -s xxx.tpr –o xxx.trr" it starts one job on each core instead of 4: NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 Logs show 4 mdrun_mpi starts, 4 file read ins and I get 4 of all run files in CWD. I am sure that mdrun_mpi is indeed compiled with mpi support - although our sysadmin did that, not me. For example, if I try and execute "mdrun_mpi –h" I get a message from HP–MPI and have to execute "mpirun mdrun_mpi –h" to see the help text. Does anyone have any experience of running with this setup - any ideas? Thanks Lee -- 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
