[gmx-users] gromacs error

Vidya R vidyadevi2811 at gmail.com
Tue Sep 12 15:55:22 CEST 2017


Hi,

I fixed that error.

However,I now encounter a new one...

GROMACS:    gmx grompp, VERSION 5.0.2

GROMACS is written by:
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
Peter Tieleman     Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx grompp -f mdp/min.mdp -o min -pp min -po min

Setting the LD random seed to 1842076191
Generated 349030 of the 349030 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 349030 of the 349030 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'LIG'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 11837.00
Estimate for the relative computational load of the PME mesh part: 0.17

gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello)

GROMACS:    gmx mdrun, VERSION 5.0.2

GROMACS is written by:
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
Peter Tieleman     Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min

Reading file min.tpr, VERSION 5.0.2 (single precision)
Using 1 MPI thread
Using 8 OpenMP threads
mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local
exited on signal 11 (Segmentation fault).


What is segmentation fault?

What am I supposed to do?

Please tell me.

Thanks,
Vidya.R


On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Yeah I've never seen that, so I assume it's something weird related to how
> GROMACS was originally compiled vs how the system has been updated since.
> Since a rebuild is the way to investigate that, definitely update to at
> least the latest 5.0.x while you do it.
>
> Mark
>
> On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett <w.barnett at columbia.edu>
> wrote:
>
> > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R <vidyadevi2811 at gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > >
> > > When I give these two commands
> > >
> > > gmx grompp -f mdp/min.mdp -o min -pp min -po min
> > > gmx mdrun -deffnm min
> > >
> > > I get this error.
> > >
> > > What to do?
> > >
> > >
> > >
> > > Reading file min.tpr, VERSION 5.0.2 (single precision)
> > > tMPI error: tMPI Initialization error (in valid comm)
> > >
> > > Thanks,
> > > Vidya.R
> > >
> >
> > I can't speak to that exact error, but there have been several bug fix
> > releases to the 5.0.x series since 5.0.2, so an upgrade may be in order.
> I
> > would even suggest upgrading to the latest release (2016.x series).
> >
> >
> > --
> > James "Wes" Barnett
> > Postdoctoral Research Scientist
> > Department of Chemical Engineering
> > Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
> > Columbia University
> > w.barnett at columbia.edu
> > http://wbarnett.us
> > --
> > Gromacs Users mailing list
> >
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