[gmx-users] Comparing Gromacs versions

Djurre de Jong-Bruinink djurredejong at yahoo.com
Fri May 17 14:48:58 CEST 2013

>The answer is in the log files, in particular the performance summary
>should indicate where is the performance difference. If you post your
>log files somewhere we can probably give further tips on optimizing
>your run configurations.

I put the log files for 72 CPUs, using GMX455, GMX461+group and GMX461+verlet here:

It would be great if you could point out some  possible optimizations.

>Note that with such a small system the scaling with the group scheme
>surely becomes limited by imbalance and probably it won't scale much
>further than 72 cores. At the same time, simulations with the verlet
>scheme have shown scaling to below 100 atoms/core.

I tried running on 84 cpus (56PP cores=400 atoms/PP core), but I did get an domain decomposition error. Maybe I could optimize -rcon and -dds further, however although the scaling to more CPUs is better with the verlet scheme, I think you will never win:  with 72 CPUs Verlet is almost as fast as with group at 60 CPUs, however compared to 24 cpus the scaling per CPU is already down to 60%.

But as Mark Abraham mentioned, it might be that my system is just to small to get the advantage of scaling that will be there in larger systems.


More information about the gromacs.org_gmx-users mailing list