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

Simone Pellegrini 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.
> Mark

thanks again for the support, regards S. Pellegrini

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