[gmx-users] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5

[Mark Abraham]

OK, thanks.

Please open a new issue at redmine.gromacs.org, describe your observations
as above, and upload a tarball of your input files.

Mark


On Fri, Nov 8, 2013 at 2:14 PM, Qin Qiao <qiaoqin47 at gmail.com> wrote:

> On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > Hi,
> >
> > That shouldn't happen if your MPI library is working (have you tested it
> > with other programs?) and configured properly. It's possible this is a
> > known bug, so please let us know if you can reproduce it in the latest
> > releases.
> >
> > Mark
> >
> >
> > Hi,
>
> I installed different versions of gromacs with the same MPI library.
> Surprisingly, the problem doesn't occur in gromacs-4.5.1.. but still in the
> gromacs-4.6.3... The MPI version is MVAPICH2-1.9a for infinite band.
>
> Best,
>
> Qin
>
> On Fri, Nov 8, 2013 at 6:55 AM, Qin Qiao <qiaoqin47 at gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT
> > > ensemble, and I got the following errors when I tried to use 2 cores
> per
> > > replica:
> > >
> > > "[node-ib-4.local:mpi_rank_25][error_sighandler] Caught error:
> > Segmentation
> > > fault (signal 11)
> > > [node-ib-13.local:mpi_rank_63][error_sighandler] Caught error:
> > Segmentation
> > > fault (signal 11)
> > > ...
> > > "
> > >
> > > Surprisingly, it worked fine when I tried to use only 1 core per
> > replica..
> > > I have no idea what caused the problem.. Could you give me some advice?
> > >
> > > ps. the command I used is
> > > "srun .../gromacs-4.5.5-mpi-slurm/bin/mdrun_infiniband -s remd_.tpr
> > -multi
> > > 48 -replex 1000 -deffnm remd_ -cpi remd_.cpt -append"
> > >
> > > Best
> > > Qin
> > > --
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