[gmx-users] MARTINI crushing

[Kroon, P.C.]

passing -rdd with a larger value forces mdrun to make larger domain cells,
basically reducing the number of ranks you can use and hampering
parallelization. I don't think it affects the physics.
Reducing the CPU count does the same thing.

Peter

On Thu, Apr 14, 2016 at 9:57 AM, James Starlight <jmsstarlight at gmail.com>
wrote:

> an question: might the bigger -rdd like 1.8 or 2.0  produce ssmth bad
> in simulation? generally I found that with rdd 1.8 the siduation is
> better, also I reduced number of CPU for that job from 256 to 128 and
> it works OK by now!
>
> Gleb
>
> 2016-04-14 9:40 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> > Hi James,
> >
> > 1) use a newer version of Gromacs
> > 2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn are so
> > long and flexible they occasionally confuse gromacs' domain
> decomposition.
> >
> > Peter
> >
> > On Thu, Apr 14, 2016 at 8:49 AM, James Starlight <jmsstarlight at gmail.com
> >
> > wrote:
> >
> >> Dear Gromacs Users!
> >>
> >> I faced with the problems while simulating of big MARTINI system of
> >> membrane protein complex within big membrane consisted totally of 55k
> >> martini CG atoms.
> >>
> >> On the early stage of the NPT equilibration I have a error
> >>
> >> Program g_mdrun_openmpi, VERSION 4.5.7
> >> Source code file:
> >> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line: 173
> >>
> >> Software inconsistency error:
> >> Some interactions seem to be assigned multiple times
> >> For more information and tips for troubleshooting, please check the
> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >> -------------------------------------------------------
> >>
> >>
> >> does the problem is related to paralelization or smth wrong with
> >> setup? Amazing that on the same system without Elnedyn applied I have
> >> no such promlems at ell.
> >>
> >> Thanks so much for help!
> >>
> >> J.
> >> --
> >> 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-request at 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-request at 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-request at gromacs.org.
>