[gmx-developers] Performance checklist
Mark.Abraham at anu.edu.au
Sat Oct 13 03:33:00 CEST 2012
On 13/10/2012 12:21 AM, Berk Hess wrote:
> I added a performance check-list on the Gromacs site:
> 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).
More information about the gromacs.org_gmx-developers