Re: Which namd to use

From: Jim Phillips (
Date: Fri Nov 20 2015 - 08:02:36 CST

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:

> Hi,
> A user of our cluster asked for us to install
> Linux-x86_64-netlrts
> 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 ?
> 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

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