So to summarize -- the problem appears to be with particle decomposition.
On Thu, May 2, 2013 at 4:15 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > I'll look at the 4.6.1 version next week, I could install it but I got a > conflict between the environmental variable defining openMP variable but I > turned it off during compilation … > > You could try to run on particle decomposition to see if you get a problem … > it should one quite quick. > > On May 2, 2013, at 2:36 PM, Michael Shirts <mrshi...@gmail.com> wrote: > >> Both. So if 4.6.1 doesn't work, I want to know so we can patch it >> before 4.6.2 comes out. If it does work, then there is probably stuff >> that can be backported. >> >> On Thu, May 2, 2013 at 8:32 AM, XAvier Periole <x.peri...@rug.nl> wrote: >>> >>> You mean working with or working on the code? >>> >>> I'll try gmx-4.6.1 >>> >>> On May 2, 2013, at 2:26 PM, Michael Shirts <mrshi...@gmail.com> wrote: >>> >>>> Quick check here -- is 4.6 behaving correctly? I actually spent some >>>> time working on REMD in 4.6, and it seems to be behaving correctly in >>>> my hands with temperature and pressure control. >>>> >>>> Thanks for any additional info on this! >>>> >>>> On Thu, May 2, 2013 at 8:18 AM, Mark Abraham <mark.j.abra...@gmail.com> >>>> wrote: >>>>> On Thu, May 2, 2013 at 12:58 PM, XAvier Periole <x.peri...@rug.nl> wrote: >>>>> >>>>>> >>>>>> I saw that redmine report, which could be related but it seems to happen >>>>>> only for runs done outside the domain and particle decompositions. >>>>>> >>>>>> I'll fill up a red mine. >>>>>> >>>>>> Anything I could do to help speeding the fix? >>>>>> >>>>> >>>>> What'd be really nice is some thought on how one can demonstrate that the >>>>> implementation of the exchange matches what would be expected from the >>>>> theory. For T-exchange under NVT, it is sufficient to rescale velocities >>>>> and quantities derived from them by the correct factor. That includes >>>>> various things like T-coupling history and integrator half-step quantities >>>>> (and does REMD with leap-frog make sense anyway?). For NPT, there's >>>>> probably also some P-coupling quantities to scale, and the box to >>>>> exchange. >>>>> Anything I've missed? Hopefully virial contributions don't matter either >>>>> way? >>>>> >>>>> Perhaps a decent first step is to hack the code to do a "self exchange," >>>>> by >>>>> clearing the entire state and rebuilding with what would/should be >>>>> received >>>>> from an exchange with a hypothethetical replica in an identical >>>>> pre-exchange state. Only if the code can do that (i.e. mdrun -reprod >>>>> produces a trajectory indistinguishable from a run that does not attempt >>>>> this self exchange) is it worth considering proper state exchanges, and >>>>> the >>>>> process of making the code do the former should illustrate what is >>>>> required >>>>> for the latter. >>>>> >>>>> Mark >>>>> -- >>>>> 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/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 mailing list gmx-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 mailing list gmx-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 mailing list gmx-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 mailing list gmx-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 mailing list gmx-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
