[gmx-users] At what point is the random seed generated?
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 -- 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.
Re: [gmx-users] At what point is the random seed generated?
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.sehttp://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.
Re: [gmx-users] At what point is the random seed generated?
Indeed. grompp does report the seed it uses to stderr. Mark On Tue, Jan 28, 2014 at 8:51 AM, David van der Spoel 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.sehttp://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.
Re: [gmx-users] At what point is the random seed generated?
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. 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 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 > 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.sehttp://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.
Re: [gmx-users] At what point is the random seed generated?
On Jan 29, 2014 4:59 AM, "Trayder Thomas" 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? It has that effect, which is very useful for debugging. I think of the design more like that the tpr should describe the physics, and command line options to mdrun should relate to its implementation (though this divide is not perfectly implemented, either). Setting up the initial velocities is considered part of setting up the model physics. Whether you want to simulate copies of the same or different systems is your business. > 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. This kind of thing is expected - see http://www.gromacs.org/Documentation/Terminology/Reproducibility > 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. True, but http://manual.gromacs.org/online/mdp_opt.html#vel specifies "in grompp" for gen-vel. We can't repeat ourselves everywhere, unfortunately, lest one copy falls out of date! :-( Mark > Oh well, Thanks guys. > > -Trayder > > > > > On Tue, Jan 28, 2014 at 10:55 PM, Mark Abraham 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 > > 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.sehttp://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.
Re: [gmx-users] At what point is the random seed generated?
On Wed, Jan 29, 2014 at 4:46 AM, Trayder Thomas 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 > 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 >> 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.sehttp://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.
