[gmx-users] speed issue, gmx runtime estimate = f(t)
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 6 15:38:00 CEST 2011
Michael Brunsteiner wrote:
> Dear all,
> I am trying to optimize runtimes/speed for a series of
> calculations i plan to do with a rather complex system.
> When looking at runtimes I observed one peculiar issue:
> the estimated runtime written to stderr by mdrun with the "-v"
> option keepsgrowing ... in my experience this estimate normally
> converges to a fairly accurate value within a few hundred
> steps. not so here ..
> for example, starting a job at 12:14 gromacs writes to stderr:
> step 100, will finish Wed Apr 6 12:40:35 2011vol 0.97 imb F 1%
> step 200, will finish Wed Apr 6 12:39:42 2011vol 0.95 imb F 2%
> step 300, will finish Wed Apr 6 12:39:47 2011vol 0.95 imb F 1%
> step 400, will finish Wed Apr 6 12:39:52 2011vol 0.96 imb F 1%
> step 38400, will finish Wed Apr 6 14:09:11 2011vol 0.91 imb F 29%
The decrease in DD cell volume coupled with the large increase in force
imbalance suggests that your system is undergoing changes that cause the DD
algorithm to slow down.
> so the estimated run time grows steadily from 25 to 110 minutes
> within about one hour...
This is likely due to the force imbalance.
> energygrps = SOL CC CF
> energygrp_table = CF CF CF SOL CF CC
Tabulated potentials also run quite a bit slower than normal functions. In
conjunction with double precision (which is slower by itself) and the DD
changes/force imbalances, I'd say this explains the runtime issues.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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