[gmx-users] mdrun and simulation time

Justin Lemkul jalemkul at vt.edu
Mon May 13 13:53:22 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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