[gmx-users] Comparing Gromacs versions

[Djurre de Jong-Bruinink]

>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:
http://md.chem.rug.nl/~djurre/logs/N6_gmx455.log
http://md.chem.rug.nl/~djurre/logs/N6_gmx461_group.log
http://md.chem.rug.nl/~djurre/logs/N6_gmx461_verlet.log

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.


Groetnis,
Djurre