[gmx-users] New to Gromacs -- looking for insights

Mark Abraham 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.


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