Fortunately, the GPUs are all mine.
Thanks for the wrapper, I'll give it a try.
On Tue, Apr 8, 2014 at 9:59 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2014-04-08 at 09:36 -0500, Milo Westler wrote:
> > So from the tutorial:
> >
> > mpirun -np 8 $AMBERHOME/exe/sander.MPI -ng 8 -groupfile
> > equilibrate.groupfile
> >
> > For multiple GPUs using pmemd.cuda.MPI, do I need to use the "setenv
> > CUDA_VISIBLE_DEVICES #" environmental variable?
>
> My suggestion is to just make sure that you are using every GPU on every
> node you are assigned to avoid the CUDA_VISIBLE_DEVICES problem
> altogether. It's not entirely straightforward to make sure that
> CUDA_VISIBLE_DEVICES is propagated to all of the threads correctly.
>
> The UF HPC staff has written a nifty little wrapper that will handle
> this 'correctly' using the GPU-aware torque scheduler:
>
> http://wiki.hpc.ufl.edu/doc/CUDA_PBS
>
> Of course this really only works if _everyone_ uses the cluster
> 'correctly' (i.e., only uses GPUs they're assigned to by the scheduler).
> If you are given exclusive access to each node's GPU resources,
> CUDA_VISIBLE_DEVICES becomes unnecessary.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
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Received on Tue Apr 08 2014 - 10:00:03 PDT
