[gmx-developers] Performance checklist

Mark Abraham Mark.Abraham at anu.edu.au
Sat Oct 13 03:33:00 CEST 2012

On 13/10/2012 12:21 AM, Berk Hess wrote:
> Hi,
> I added a performance check-list on the Gromacs site:
> http://www.gromacs.org/Documentation/Performance_checklist
> If something is unclear or you have something to add, pease tell me.
> Note that about half of the points on the list only apply to version 4.6.

The correct compiler on BlueGene is XLC. Even if the BlueGene gcc 
happens to be present and work, I expect GROMACS will not compile, and 
the performance will be bad.

"absolutely" in the first dot point

How does pdb2gmx -vsite aromatic affect the choice of time step?

When running a multi-simulation (e.g. REMD), adjust mdrun -gcom (and 
perhaps increase nstcalcenergy) on massively parallel systems, 
particularly if there is external network contention or variable load 
imbalance between simulations. (The implementation of inter-simulation 
signal checks is currently awkward and uses the same mechanism and 
period as intra-simulation energy communication, which can scale badly. 
I've not had time to get https://gerrit.gromacs.org/#/c/416/ fully 
checked and done for 4.6.)

Suggest checking the first line of .log files to know how many compute 
cores are being used (though I must admit I don't know whether this is 
true with all the new toys).


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