Re: [AMBER] using two GPUs

From: Jason Swails <>
Date: Wed, 25 Apr 2012 12:05:13 -0400


On Wed, Apr 25, 2012 at 1:34 AM, Vijay Manickam Achari <
> wrote:

> Thank you for the kind reply.
> I have tried to figure out based on your info and other sources as well to
> get the two GPUs work.
> For the machinefile:
> I checked /dev folder and I saw list of NVIDIA card names as :- nvidia0,
> nvidia1, nvidia2, nvidia3, nvidia4. I understand these names should be
> listed in the mahcinefile. I comment out nvidia0, nvidia1, nvidia2 since I
> only wanted to use two GPUs.

The names in the hostfile (or machinefile) are the host name (you can get
this via "hostname"). However, machinefiles are really only necessary if
you plan on going off-node. What it tells the MPI is *where* on the
network each thread should be launched.

If you want to run everything locally on the same machine, every MPI
implementation that I've ever used allows you to just say:

mpirun -np 2 pmemd.cuda.MPI -O -i mdin ...etc.

If you need to use the hostfile or machinefile, look at the mpirun manpage
to see how your particular MPI reads them.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Apr 25 2012 - 09:30:10 PDT
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