From: Maxime Boissonneault (maxime.boissonneault_at_calculquebec.ca)
Date: Fri Nov 20 2015 - 08:13:58 CST
The IB cards are Mellanox, and the cluster is Sun (back in 2009).
Here is how our namd was compiled :
Do you see anything wrong (beside versions being old) ?
That was back in August 2013.
Le 2015-11-20 09:02, Jim Phillips a écrit :
> The MPI version you have been building should work, and with replicas
> you probably won't see much of a performance difference.
> Who made your IB cards? They may now be supported directly, either in
> the released binaries or with a recompilation.
> The requirement for replicas is mpi, verbs, netlrts, or gni, so in
> your case you would want (copying from the release notes):
> Build and test the Charm++/Converse library (InfiniBand version):
> cd charm-6.7.0-pre
> ./build charm++ verbs-linux-x86_64 --with-production
> cd verbs-linux-x86_64/tests/charm++/megatest
> make pgm
> ./charmrun ++mpiexec +p4 ./pgm (uses mpiexec to launch processes)
> cd ../../../../..
> ./config Linux-x86_64-g++ --charm-arch verbs-linux-x86_64
> cd Linux-x86_64-g++
> make (or gmake -j4, which should run faster)
> If you have Intel compilers use those (verbs-linux-x86_64-iccstatic
> and Linux-x86_64-icc).
> On Fri, 20 Nov 2015, Maxime Boissonneault wrote:
>> A user of our cluster asked for us to install
>> His need is to be able to perform replica exchanges, and he says that
>> only this version allowed him to do so. We have an older 2.9 version
>> of NAMD that we compiled, and apparently it does not support replica
>> The thing is, we have a cluster with non-blocking QDR Infiniband. We
>> usually compile Namd from source, with MPI.
>> What version would you recommend me to install, and if it's a
>> compilation from source, what should be the compilation options to
>> enable replica exchanges ?
>> 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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