[gmx-users] New to Gromacs -- looking for insights
spellegrini at dps.uibk.ac.at
Thu Dec 10 14:06:45 CET 2009
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.
thanks again for the support, regards S. Pellegrini
More information about the gromacs.org_gmx-users