Re: NAMD on Stampede 2

From: Giacomo Fiorin (
Date: Fri Oct 06 2017 - 07:50:50 CDT

Please find out how NAMD was compiled there and what part of Stampede
you're using. Without this information, it's impossible to figure out your

If the executable and the related environment module were provided by the
TACC staff, you should contact them for clarifications.

Understand that the command line you pasted will launch two MPI tasks, each
of which will spawn 64 threads. So you need 128 available cores on the
node(s) that you requested.

For more information, look at the files notes.txt that comes with the NAMD


On Thu, Oct 5, 2017 at 7:23 PM, Chitrak Gupta <> wrote:

> Hello,
> I am trying to run NAMD on Stampede 2 but it is not scaling the way it
> should. Here is what I have in my submission script
> *module load intel/16.0.3module load impimodule load namd/2.12mpiexec -np
> 2 namd2 +ppn 64 filename.conf > logfile.log*
> I have also tried "ibrun" instead of mpiexec but the problem persists.
> Best,
> Chitrak.

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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