impossible to disable automated nstlist tuning with verlet scheme
In v4.6 the
GMX_NSTLIST environment variable can be used to set/override
nslist at runtime. This functionality provided the additional benefit of allowing to bypass the automated
nstlist tuning. This can be necessary in cases where the tuning can lead to performance drop, e.g. with GPU accelerated runs when using a not sufficiently fast GPU, in this case a larger
nstlist will often cause greater slowdown in the non-bonded kernel (translating to "GPU wait time and idling on CPU threads) than the benefit of less frequent pair search (and DD).
In 5.0 the
GMX_NSTLIST environment variable has been removed which makes it impossible to prevent mdrun from switching tot a larger
nstlist additionally to making it harder to switch
nstlist without regenerating the tpr.
I suggest that we add back the
GMX_NSTLIST environment variable and as the pair search frequency has a clear role in performance tuning, we should consider adding an
mdrun command-line option "-nstlist".
#4 Updated by Mark Abraham over 6 years ago
Szilárd Páll wrote:
PS: for my own purposes keeping the environment variable would be great, otherwise I'll need to go through all my scripts that use it. Do you think there would be any use to it? I'm not sure...
It's useful, but two-edged. Easy for someone to have it set and not remember/know it is set, particularly if there's a script within a script ever (Copernicus?).
I like the semantic divide between "public" command-line options, and things that are more hidden (environment variables even when they are documented, hidden command-line options, etc.)