[gmx-users] mpi/openmp setup to avoid #1578 on 5.0

[Johnny Lu]

Thanks for the quick mail.

If I use 20 openmp threads and 1 MPI rank, will that bug happen in gromacs
5.0 (not 5.0.1)?




On Fri, Sep 12, 2014 at 12:10 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> On Fri, Sep 12, 2014 at 5:36 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> > Hi.
> > I wonder if I run with following, will I get bug 1578 of gromacs 5.0?
> >
> > The number of OpenMP threads was set by environment variable
> > OMP_NUM_THREADS to 1
> > Using 12 MPI processes
> > Using 1 OpenMP thread per MPI process
>
> No, as the redmine message states "Note that without OpenMP threads
> there are no issues." (i.e. single thread per rank). Unfortunately the
> redmine auto-update mechanism is not working correctly and the actual
> change that fixed it (6ba80a from Aug 15) did not show up on the
> redmine page. This change is included in the 5.0.1 release.
>
> > And, is it ok to use tpr of version 5.0.1 double precision on gromacs 5.0
> > double precision?
>
> Yes, that should work.
>
> > I have 5.0.1 on one machine, but 5.0 on another machine.
> >
> > By the way, would gromacs 5.0.1 single precision with GPU have nearly as
> > little truncation error (like cutting 3.212 to 3.2) as the double
> precision
> > version, in NVE simulation?
>
> No, but truncation is, typically not a big issue - unless you have a
> very large system (where differences in coordinates can be coordinates
> can be 2-3 orders of magnitude).
>
> --
> Szilárd
>
> > --
> > 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.
>