From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Nov 20 2015 - 11:11:30 CST
Mellanox cards should work with verbs as they are the most common and what
we have. The script looks fine as well.
On Fri, 20 Nov 2015, Maxime Boissonneault wrote:
> 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
>> 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 exchanges.
>>> 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
>>> 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
> Team lead - Research Support National Team, Compute Canada
> Instructeur Software Carpentry
> Ph. D. en physique
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