[gmx-users] New to Gromacs -- looking for insights
Mark.Abraham at anu.edu.au
Wed Dec 9 17:57:51 CET 2009
Simone Pellegrini wrote:
> Dear all,
> I am researching optimization for MPI parallel programs.
> As I saw Gromacs seems to use MPI and my idea is to test some of the
> program transformations I am aware of to improve the performance.
It's already fairly good - be sure to read the GROMACS 4 paper. Up to
about 64 processors on good network hardware, GROMACS runs are usually
quite CPU-bound, so it is not a good candidate for improvement through
any MPI optimization.
The MPMD communication pattern with PME at high parallelism is
interesting, though, and might benefit from task layout that is cunning
with respect to the network topology.
> The main problem is how should I get started with Gromacs? :) Which of
> the provided programs rely on MPI calls? and furthermore, where can I
> find some significant input files?
Only mdrun uses MPI. Look on the web or the GROMACS wiki for some
pointers to tutorials to learn how to construct a workflow that will
lead to a meaningful test.
More information about the gromacs.org_gmx-users