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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