Hi again the MPI coding is OPEN MPI 1.2.7 that is found in the ROCKS CLUSTER 5.1 distribution thanks Carmen > > ceste...@unsl.edu.ar wrote: >> 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 > > Which MPI implementation are you using? Some are known to be buggy. > Also, to > rule out any other potentially buggy behavior, upgrade to version 4.0.5; > 4.0.2 > is several months old. > > -Justin > >> 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 >>> >> >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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 >
_______________________________________________ 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
