[gmx-users] Comparing Gromacs versions

Szilárd Páll szilard.pall at cbr.su.se
Fri May 17 14:08:41 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.

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.


On Fri, May 17, 2013 at 11:07 AM, Djurre de Jong-Bruinink
<djurredejong at yahoo.com> wrote:
> Dear all,
> We recently did some comparisons of gmx 4.5.5, 4.6.1+group and 4.6.1+verlet cutoff scheme. The system was a protein (amber99) in water (tip3p) in a triclinic box (23k atoms total). We're using pme with a realspace cutoff=0.9nm, gridspacing=0.12nm, npme=-1, which based on g_tune_pme gives (close to) best performance. Below some performance measure (ns/day) from 100,000 step runs:
> CPUs     G455        G461+group               G461+verlet
> 24            34.9          43.1                       35.3
> 36            47.6          57.8                       49.7
> 48            50.8          65.9                       60.4
> 60            59.9          81.8                       71.1
> 72            57.7          78.7                       78.2
> The scaling to more CPUs in 4.6.1 is much better (thank you developers for putting up all the hard work!), however I would have expected more improvements from the verlet scheme. Note that both 455 and 461 have been compiled with MPI only (no OMP, GPU), and 461 was compiled with gcc (4.7.2). I did change the nstlist from 5 to 10 for the verlet scheme only.
> Are these results expected given the setup? Is there anything I'm doing wrong?
> Thanks in advance,
> Djurre de Jong
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