Re: Replica Exchange Simulations on Blue Gene/P

From: Axel Kohlmeyer (
Date: Tue Apr 12 2011 - 10:03:16 CDT


it may be hard for some to come to terms with this, but
blue gene class machines are not very popular, since it
takes so much effort to use them well and with the same
or less effort, one get much more work done elsewhere.
thus one has to live with the fact, that there is not much
incentive to add workarounds for problems that are
endemic to the blue gene architecture.

the easiest solution would be to not use NAMD, but
some other code that supports replica exchange over MPI.

the next best solution would be to implement the same
communication patterns via MPI commands and then
write a tcl-mpi wrapper and link NAMD with it.


On Tue, Apr 12, 2011 at 10:54 AM, Dong Luo <> wrote:
> I looked at replica exchange on Blue Gene/L before and did not find a way.
> So I'd like to know any one get a solution as well.
> Dong
> ________________________________
> From: Jan H. Meinke <>
> To:
> Sent: Tuesday, April 12, 2011 8:09 AM
> Subject: Re: namd-l: Replica Exchange Simulations on Blue Gene/P
> Dear all,
> Replica exchange for NAMD is implemented using sockets within a TCL script.
> As
> far as I can tell, this doesn't work on a Blue Gene/P. Does anybody have a
> working solution to run a replica exchange simulation with NAMD on a Blue
> Gene?
> Jan
> --
> Jan Meinke
> Juelich Supercomputing Centre
> Institute for Advanced Simulation
> JSC is the coordinator of the
> John von Neumann Institute for Computing
> and member of the
> Gauss Centre for Supercomputing
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Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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