[Beowulf] Parallel software for chemists

Prentice Bisbal prentice at ias.edu
Thu Dec 11 09:35:15 EST 2008


Dr Cool Santa wrote:
> Currently in the lab we use Schrodinger and we are looking into NWchem.
> We'd be interested in knowing about software that a chemist could use
> that makes use of a parallel supercomputer. And better if it is linux.
> 

Clarification: I supported Schodinger up until a year ago. Unless things
have changed, Jaguar is the only Schrodinger application that can truly
make use of a "parallel" supercomputer. The other Schrodinger programs
perform calculations that are embarassingly parallel and require no
inter-process communications during calculations. In these cases, the
data to be analyzed is broken up into smaller pieces that are analyzed
individually by the computers with no communication between them. When
they are done, the main program reassembles their output to a final
result. This is parallel computing, but doesn't require a "parallel
supercomputer". It works great, BTW.

OpenEye provides some commercial computational chemistry software
(conformer generation, docking, etc.), that uses parallel code. Their
code uses PVM instead of MPI, which makes OpenEye kind of an odd duck.
Last I spoke to OpenEye, they were planning on porting their code to
MPI, but don't know if that's been done yet, since I no longer support
their software.

If you're doing molecular simulations, there's LAMMPS (
Large-scale Atomic/Molecular Massively Parallel Simulator), which is
open-source. I actually submitted a *very* small patch to when I ported
it to IRIX 6.5 a few years ago.

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?).


-- 
Prentice
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