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

Qin Qiao qiaoqin47 at gmail.com
Fri Nov 8 14:14:16 CET 2013


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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