>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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
