Re: namd ibverbs

From: Gianluca Interlandi (
Date: Thu Jul 16 2015 - 15:31:34 CDT

Hi Maxime,

I usually use the option "++mpiexec" to run NAMD with ibverbs (the
following is a single line):

$BINDIR/charmrun +p${NPROCS} ++mpiexec ++remote-shell mpiexec_wrapper
$BINDIR/namd2 config.namd

$BINDIR is the path to your NAMD executable.

"mpiexec_wrapper" is a script that I got a while ago from Jim Philipps.
You can copy the following lines to a file called "mpiexec_wrapper" and
make it executable:


exec mpiexec -machinefile $PBS_NODEFILE $*

If you run on GPU as well, you should be able to simply add to the line

+devices 0,1,2 +idlepoll

However, I need to say that if you are running on a single node and you do
not need to use the network, the multicore version might be slightly
faster than ibverbs. This is because you will not have the overhead of the
network libraries. I usually use ibverbs only if running on more than one


On Thu, 16 Jul 2015, Maxime Boissonneault wrote:

> Hi,
> One of our user would like to use namd 2.10 ibverbs with GPU on our GPU
> cluster. I cannot find documentation on how to use it. Is there such
> documentation ? We're used to either use the multicore-cuda version or the
> Cuda+MPI version, but since you now provide an ibverbs+GPU binaries, we
> downloaded them and wanted to try them.
> Thanks,
> --
> ---------------------------------
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Président - Comité de coordination du soutien à la recherche de Calcul Québec
> Ph. D. en physique

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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