Thanks for the help.
On 12/09/2009 05:57 PM, Mark Abraham wrote:
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.
Probably it's working fine with the current MPI standards, but you know,
MPI is evolving and some new features will be introduced in MPI 3 and I
want to test if gromacs can take advantage of it. :)
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.
thanks, I found a couple of mdb files on line and I am learning from it.
Is there any repository with come real world example using gromacs 4? I
found some benchmarks based on gromacs 3 and only half of them seem to
work with the new gromacs.
Mark
thanks again for the support, regards S. Pellegrini
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