Re: any experiences with executing parallel NAMD in a NAMD simulation

From: Peter Freddolino (
Date: Mon Feb 09 2009 - 16:26:39 CST

Hi Yinglong,
how long is your embedded run, relative to your overall simulation? Is
it on the same system? Do you end up running on the same nodes? Have you
verified that you're running on as many processors as you think you are?

What you're doing is quite unusual, and depending on the exact
relationship between your two systems there is probably a better way to
handle it. Especially if the embedded runs are small relative to the
full run, please keep in mind that namd has a high startup cost. If your
embedded run is on a system whose topology doesn't change (and only
needs coordinates once in awhile) you will probably be better off
starting two separate namd jobs on disjoint sets of nodes and having
them communicate with sockets (as is done in the replica exchange
scripts distributed with namd). This gets around both the startup costs
and other potential problems with having two copies of namd running (if
your system is large, for example, you're putting a lot of stress on the
head node in terms of memory).


Yinglong Miao wrote:
> Dear NAMD developers/users,
> I have been trying to embed a parallel NAMD run in a bigger NAMD
> simulation; that is by calling "exec mpirun -np $nprocessors
> -machinefile $machinelist namd2 ${str}.conf" in a NAMD configuration
> script to run a different structure and generate proper output for the
> big simulation. The program runs fine except that the embedded part is
> executed much more slowly than expected (~1/5 of the speed) and
> sometimes such error messages pop up: "Max retransmit retries reached
> (829) for message". I thought it's because the message passing is
> slowed down and the MPI environment is messed up upon NAMD exit for
> the embedded run. Is there anybody have experiences with this? How to
> run the embedded part with normal speed? Any suggestions will be
> greatly appreciated.
> Thanks!
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981

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