[Beowulf] Re: Physics Problems for Beowulf

David Mathog mathog at caltech.edu
Tue Feb 21 12:01:26 PST 2006

Stuart Midgley wrote:

> Molecular dynamics is a good area to look at.

I've spent the last month using Gromacs, which is a free
MD program, and it is definitely NOT an appropriate tool for
learning about MPI and Beowulf's in general.  In short, the
scaling in the current version is not very good.  Also MD programs
are pretty arcane and prone to bizarre problems that a naive
user would never expect.  Example:  couple protein and solvent
together to the same temperature bath in Gromacs and the two
sets of atoms will be driven to very different temperatures.

For just learning to use MPI etc. it would probably be best
to start with a problem that is known to scale well.  Heat flow
might be good, since at least there you could run problems that can
be solved completely, so that there is a known solution to check 
the results against.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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