[gmx-users] Dual Xeon workstation - starting one job/cpu

Jernej Zidar jernej.zidar at gmail.com
Wed Mar 23 06:27:55 CET 2016

  Recently I received a dual Xeon ( 2x E5-2630v3) workstation with two
Tesla K40c cards.

  I'm now trying to figure out how to start one job/cpu.

  For CPU1, this is not a problem:
gmx mdrun -v -deffnm test -gpu_id 0000 -ntomp 4 -pin on -maxh 0.15 -nsteps
#above starts a job on CPU1 with 4 MPI tasks and 4 OpenMP tthreads

  Fro CPU2, this is a bit more problematic because neither "-pinoffset" or
"-pinstride" make no difference. The second job appears to always start on
the CPU2.
  I had some success running a job like this:
gmx mdrun -v -deffnm test2 -gpu_id 1111 -ntomp 4 -maxh 0.15 -nsteps -1
#above starts a job on CPU2 but without CPU pinning performance is poor

  How to overcome this? From the tests I've done so fare it is actually to
run two jobs that occupy one CPU each rather that a job that would occupy
both CPUs at the same time.
  Is this even possible without resorting to OpenMPI?

Jernej Zidar

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