On Wed, Jan 29, 2014 at 4:46 AM, Trayder Thomas <trayder.tho...@monash.edu> wrote: > Curses! Kinda seemed intuitive that way. I assume the philosophy being > worked towards is that every unique run should have a unique .tpr file that > it is reproducible from? > > Curiously, I ran and checked a first batch on a different cluster and the > simulations rapidly diverged (even between simulations run one after the > other on the same node), while the second cluster managed to create 50 > identical simulations across 50 different nodes. The most obvious > difference being that the diverging simulations used GPUs.
GPU runs will naturally diverge as we use atomic operations for the final step in force reduction/accumulation, hence the implementation is inherently non-deterministic. Your runs on the "second cluster" must have used no-domain decomposition, though, otherwise those runs would also be non-deterministic. > > I suspect I never would have noticed if I had of stuck to the one cluster. > Might be worth stating explicitly in the manual for gen-seed, with > reproducibility being what it is. > > Oh well, Thanks guys. > > -Trayder > > > > > On Tue, Jan 28, 2014 at 10:55 PM, Mark Abraham > <mark.j.abra...@gmail.com>wrote: > >> Indeed. grompp does report the seed it uses to stderr. >> >> Mark >> >> >> On Tue, Jan 28, 2014 at 8:51 AM, David van der Spoel >> <sp...@xray.bmc.uu.se>wrote: >> >> > On 2014-01-28 08:37, Trayder Thomas wrote: >> > >> >> Hi, >> >> When using 'gen-seed = -1' at what point is the random seed assigned? >> >> >> >> e.g. Does it use the process ID of grompp and embed the seed number in >> the >> >> tpr file, or does it use the process ID of mdrun? >> >> >> >> I ask because I have 50 identical simulations started from the same tpr >> >> file :( >> >> >> >> Thanks, >> >> -Trayder >> >> >> >> I guess you found out. Sorry about that. It is done in grompp and same >> > tpr should give reproducible results. So you want to generate 50 >> different >> > tpr files. >> > >> > -- >> > David van der Spoel, Ph.D., Professor of Biology >> > Dept. of Cell & Molec. Biol., Uppsala University. >> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> > sp...@xray.bmc.uu.se http://folding.bmc.uu.se >> > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at http://www.gromacs.org/ >> > Support/Mailing_Lists/GMX-Users_List before posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.