[Beowulf] Parallel software for chemists

Chris Samuel csamuel at vpac.org
Thu Dec 11 18:54:57 EST 2008


----- "Prentice Bisbal" <prentice at ias.edu> wrote:

> NAMD is also parallel, but I don't know much about it. I compiled it,
> installed it, but then I don't think the comp chemists ever used it
> (don't you hate that?).

We've got NAMD here (it's a molecular dynamics
program), it's not what you'd call a trivial
application to build. ;-)

Building it as an MPI application (i.e. getting
Charm++ to use MPI rather than its own custom
framework) makes it a lot easier to use though,
especially if you use PBS and have a TM aware
MPI launcher installed (like OpenMPI, LAM or
Pete Wyckoffs excellent mpiexec replacement).

cheers,
Chris
-- 
Christopher Samuel - (03) 9925 4751 - Systems Manager
 The Victorian Partnership for Advanced Computing
 P.O. Box 201, Carlton South, VIC 3053, Australia
VPAC is a not-for-profit Registered Research Agency
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