[gmx-users] Re: Restarting a simulation after replacing an empty md.trr file
Hello Sir, Thanks for the reply. now is it fine if i use 100 threads in my restart. is there any impact on the over all simulation? -- View this message in context: http://gromacs.5086.x6.nabble.com/Restarting-a-simulation-after-replacing-an-empty-md-trr-file-tp5012443p5012459.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Restarting a simulation after replacing an empty md.trr file
On 11/12/13 11:10 AM, arunjones wrote: Hello Sir, Thanks for the reply. now is it fine if i use 100 threads in my restart. is there any impact on the over all simulation? Only if that is the number of threads originally used in the run. If not, there will be a mismatch between the DD grid setup, the .cpt file will complain, and the run will fail. Rule of thumb: don't change settings or alter files mid-run ;) -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] Re: Restarting a simulation after replacing an empty md.trr file
Thank you Sir, initially i was running on 60 threads, now i changed it to 100. simulation is running with out any error, but i found a note in the log file as fallows #nodes mismatch, current program: 100 checkpoint file: 60 #PME-nodes mismatch, current program: -1 checkpoint file: 12 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. Initializing Domain Decomposition on 100 nodes is it a good idea to continue or shall i stick with 60 threads. -- View this message in context: http://gromacs.5086.x6.nabble.com/Restarting-a-simulation-after-replacing-an-empty-md-trr-file-tp5012443p5012463.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: Restarting a simulation after replacing an empty md.trr file
On 11/12/13 12:07 PM, arunjones wrote: Thank you Sir, initially i was running on 60 threads, now i changed it to 100. simulation is running with out any error, but i found a note in the log file as fallows #nodes mismatch, current program: 100 checkpoint file: 60 #PME-nodes mismatch, current program: -1 checkpoint file: 12 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. Initializing Domain Decomposition on 100 nodes is it a good idea to continue or shall i stick with 60 threads. Like I said, I think it is a bad idea to switch settings haphazardly during the run. As the note indicates, the continuation is exact, but not binary identical. Check the website for what all that means if you're not sure. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
