Re: Running NAMD on Intel OmniPath

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Thu Jul 27 2017 - 14:18:47 CDT

Dear Maxime,

As Mauro indicated, NAMD on Omnipath works best using Charm++ MPI with SMP support. To also enable CUDA support, add --with-cuda and possibly --cuda-prefix to your NAMD config command line.

All of these matters are discussed in the NAMD 2.12 Release Notes: http://www.ks.uiuc.edu/Research/namd/2.12/notes.html <http://www.ks.uiuc.edu/Research/namd/2.12/notes.html>

Best regards,
Dave

--
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/
> On Jul 27, 2017, at 1:47 PM, Maxime Boissonneault <maxime.boissonneault_at_calculquebec.ca> wrote:
> 
> Hi Mauro,
> We are already building from source. MPI will work, but that will not support GPUs. We need GPUs + OPA, and the verbs version does not seem to want to work.
> 
> Maxime
> 
> On 17-07-27 14:06, Mauro Lapelosa wrote:
>> Hi Maxime,
>> You may want to compile the source.
>> 
>> ./build charm++ mpi-linux-x86_64 smp --with-production -j8
>> 
>> and for NAMD is something like:
>> 
>> ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
>> 
>> It should work.
>> 
>> Best Regards,
>> 
>> Mauro Lapelosa
>> 
>> On Thu, Jul 27, 2017 at 8:00 PM, Maxime Boissonneault <maxime.boissonneault_at_calculquebec.ca <mailto:maxime.boissonneault_at_calculquebec.ca>> wrote:
>> Hi,
>> 
>> We just deployed a cluster with Intel OmniPath instead of InfiniBand as a network fabric. We are having problems running NAMD on that hardware. It works within a node, but not between nodes.
>> 
>> Is there anything special we should do for compiling it to work on this ?
>> 
>> 
>> Thanks,
>> 
>> -- 
>> ---------------------------------
>> Maxime Boissonneault
>> Analyste de calcul - Calcul Québec, Université Laval
>> Président - Comité de coordination du soutien à la recherche de Calcul Québec
>> Team lead - Research Support National Team, Compute Canada
>> Instructeur Software Carpentry
>> Ph. D. en physique
>> 
>> 
> 
> 
> -- 
> ---------------------------------
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Président - Comité de coordination du soutien à la recherche de Calcul Québec
> Team lead - Research Support National Team, Compute Canada
> Instructeur Software Carpentry
> Ph. D. en physique

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