Try this: aprun -n (number of nodes) -N 1 (1 mpi-process per node) mdrun_mpi -gpu_id 0 (now your job stuff here)
=================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Michael Weiner <mdw...@cornell.edu> Sent: Tuesday, January 19, 2016 12:14 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] multiple nodes, GPUs on a Cray system Hello. I am trying to run Gromacs on ORNL’s Titan supercomputer (Cray XK7). Specifically, I wish to run a large system across multiple nodes while employing GPUs with Gromacs 4.6.6. However, I cannot figure out the appropriate way to call mdrun in order for this to work. Within a submission script, I have tried many combinations of flags for aprun and mdrun, none of which work. Most specifically, if I request 50 nodes of 16 cores each and use this command: aprun -n 800 -N 16 mdrun_mpi I get the following error: “Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 16 PP MPI processes per node, but only 1 GPU were detected.” I have also tried with the -n flag equal to the number of nodes, but then it decomposes only to that many domains, rather than one per processor. The “mdrun_mpi” command seems to be the only way of calling mdrun on the machine. I would appreciate any help with figuring out the appropriate flags to use for aprun and mdrun. Thank you. Michael Weiner -- 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. -- 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.
