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

From: Éric Germaneau <>
Date: Thu, 09 Jul 2015 08:02:08 +0800

Thank you Gerarld for the info,

That really surprises me, multri-threading on CPU in never useless when
using GPU since CPU is always highly solicited.
Anyway I note that Amber doesn't support OpenMP.
Thanks again.


On 07/08/2015 04:10 PM, Gerald Monard wrote:
> Hi,
> 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.
> Gerald.
>> Thank you,
>> Éric.

Éric Germaneau (艾海克), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China Mobi:+86-136-4161-6480
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Received on Wed Jul 08 2015 - 17:30:03 PDT
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