Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. Any help would be appreciated Carmen > > To, > David van der Spoel > > Dear Sir, > > I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a > problem. > I am giving job for 500000 steps step size 0.002ps (total 1ns) but my > job is stopped after 470000 steps. when i run this on 4 processors. > > But the same job is completed on 2 processors.Why this happing i am not > able to understand. > > Another thing is that job for 1500000 steps step size 0.002ps (total > 3ns) is stopped after 375000 steps on 2 processors > and after 587000 steps on 4 processors, without any error message. > > What could be the problem and how to solve it, please help me. > > even i tried the 2 same jobs for 1000000 steps step size 0.002ps (total > 2ns), one on single processor it is completed in 8 days > but the same job is stop after 550000 steps on 4 processors. > > Is there any change is required in MPI coding or in .mdp files. Sir if > you need any other please let me know. > > Please solve my problem, I will be highly obliged. > > > DvdS: > > Please upgrade to a recent version. 3.2.1 is more than five years old. > > > > With warm regards. > Shikhar > > > > -- > ------------------------------------------------------------ > Shikhar Gupta > Senior Research Fellow > Pharmacoinformatics Department > Block- A (Room No.- 208) > National Institute of Pharmaceutical Education & Research( NIPER ) > Sec- 67, S.A.S Nagar > Mohali, Punjab (India) > Web-Site: www.niper.ac.in <http://www.niper.ac.in> > PIN- 160062 > Email:shik_...@rediffmail.com > <mailto:email%3ashik_...@rediffmail.com>,shik...@gmail.com > <mailto:shik...@gmail.com> > > > > > -- > ------------------------------------------------------------ > Shikhar Gupta > Senior Research Fellow > Pharmacoinformatics Department > Block- A (Room No.- 208) > National Institute of Pharmaceutical Education & Research( NIPER ) > Sec- 67, S.A.S Nagar > Mohali, Punjab (India) > Web-Site: www.niper.ac.in <http://www.niper.ac.in> > PIN- 160062 > Email:shik_...@rediffmail.com > <mailto:email%3ashik_...@rediffmail.com>,shik...@gmail.com > <mailto:shik...@gmail.com> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > 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/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/mailing_lists/users.php >
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