[gmx-users] mdrun and simulation time
fracarb at myopera.com
Mon May 13 14:11:04 CEST 2013
thank you for the reply, I'm in contact with my admin and I hope that he
will tell me something soon.
One thing that I really don't understand is why only the last
nanoseconds are "affected".
I run the same simulation (with the same paramenters) and I've never had
problems in the first 4 ns , only in the last 4.
On Mon, 13 May 2013, at 11:53 AM, Justin Lemkul wrote:
> On 5/13/13 6:41 AM, Francesco wrote:
> > Good morning all,
> > This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
> > noticed a strange behaviour:
> > The fist two simulations (each 2ns) ended up correctly and they both
> > took 2h 06min to finish.
> > The second two were still running when the cluster time was over (I
> > asked for 2.30) and
> > were truncated.
> > My system contains around 160k atoms and all the previous 2ns simulation
> > took between 2h and 2h:10min (77 cores, no gpu).
> > I had a look at the log and it seems that in the last two simulations
> > mdrun
> > did only 120.000 steps instead of 1.000.000.
> > Is it strange or it is possible/normal that with the increase of the ns
> > (always splitted in 2ns and extended) the running time is bigger?
> Random performance loss often happens when one or more nodes being used
> for the
> job get stuck or have errors. If you're submitting to a queuing system,
> should be diagnostic information that your admins can access that would
> why this is happening.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Institute of Structural and Molecular Biology
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