[gmx-users] multiple nodes, GPUs on a Cray system
Smith, Micholas D.
smithmd at ornl.gov
Tue Jan 19 18:44:54 CET 2016
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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michael Weiner <mdw224 at cornell.edu>
Sent: Tuesday, January 19, 2016 12:14 PM
To: gromacs.org_gmx-users at 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
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