[gmx-users] mdrun and simulation time

[Francesco]

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.

Fra

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,
> there 
> should be diagnostic information that your admins can access that would
> suggest 
> why this is happening.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
Francesco Carbone
PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone.12 at ucl.ac.uk