Re: [AMBER] issue using CUDA+MPI+OpenMP

From: Gerald Monard <>
Date: Wed, 08 Jul 2015 10:10:42 +0200


On 07/08/2015 08:12 AM, Éric Germaneau wrote:
> Dear all,
> I'm helping a user running Amber on our machine.
> I basically compiled it doing
> ./configure -intelmpi -mkl -cuda -openmp intel

As far as I known, the -openmp configuration option does not have any
effect on the compilation of pmemd (except for MIC?).

> We have two 8-cores CPU and two GPU per node, we use LSF as job scheduler.
> I submit a 2 MPI process per node job.
> Each of the process takes care of one GPU as expected, however only one
> threads per MPI process is used (even if I set OMP_NUM_THREADS).
> Is there a way to perform a multi-threading job using MPI and CUDA?

The way pmemd.cuda works is that it uses 1 thread per GPU. Most of the
computations are done in the GPU (unlike NAMD for example), thus
multi-threading on the CPU is useless here.


> Thank you,
> Éric.

  Prof. Gerald MONARD
  SRSMC, Université de Lorraine, CNRS
  Boulevard des Aiguillettes B.P. 70239
  F-54506 Vandoeuvre-les-Nancy, FRANCE
  e-mail :
  tel.   : +33 (0)383.684.381
  fax    : +33 (0)383.684.371
  web    :
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Received on Wed Jul 08 2015 - 01:30:03 PDT
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