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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists