[gmx-users] Too many LINCS warning
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 26 13:24:39 CEST 2008
vivek sharma wrote:
> Hi There,
> I am trying to scale my system(system with 45000 atoms which is one
> protein molecule in water box) to run on more number of processor
> I have asked a number of related queries, but now I am getting warning
> pasted below...
> Fatal error:
> Too many LINCS warnings (11587) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently
> equilibrated,or if you are changing lambda too fast in free energy
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file, but normally it is better to fix the problem.
> and the same run is running well with 20 processor, but I got the error
> pasted above in aan attempt to run the same problem for 40
> processor...and it followed by writing the intermediate step.pdb
> Can anybody suggest how should I tackle the problem, and what other
> option I can try in this scenario ?
I have seen this too, when I try to use too many processors. I don't know the
reason. Did you adhere to my previous advice (regarding Gromacs 3.3.x, you
still haven't told us which version of Gromacs you're using):
Max # of CPU = (total atoms)/(protein atoms)?
The goal is to keep the load evenly distributed over nodes. The above is not
necessarily necessary under 4.0rc1 with the advent of P-LINCS.
> With Thanks,
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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