Re: [ppl] Help Regarding NAMD Application Testing

From: Phil Miller (
Date: Mon Mar 21 2011 - 09:00:13 CDT

On Mon, Mar 21, 2011 at 07:17, Kannan Govindarajan
<> wrote:
> I am G.Kannan, working as research associate in MIT, Anna University. I am
> trying to test  our Care Resource Broker performance using NAMD application.
> I have successfully tested the NAMD application using charm++.
> I am using NAMD-2.6 and mpich-1.2.6 version. Is it possible to run the namd
> application using mpich?  and PBS as local scheduler ?

Before going any further, I'll note two things:
1. NAMD 2.6 is rather old, and was superseded by NAMD 2.7 several months ago
2. This (ppl@) is not the mailing list for NAMD. That list is (CCed). The NAMD developers also have an excellent
list of problem-solving resources [0]

Now, to the core of your questions:
NAMD is implemented in Charm++. Charm++ has an MPI backend, but we
don't recommend its use, since the machine-specific backends tend to
perform better. Even when using a non-MPI version of Charm++, it is
straightforward to run Charm++ applications in an MPI-centric
environment, by telling Charm++ to take advantage of the available MPI
job launcher. This is described in the manual [1], conveniently linked
from [0].

If you have suggestions for how we can improve our documentation so
that it would have answered your question, please let us know.


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