[gmx-users] gromacs error

Tue Sep 12 16:18:06 CEST 2017

Hi,

It's hard to say, but you should look at the log file and terminal output,
and install the latest in the series of bug fixes... 5.0.7 rather than
choose a version known to have dozens more bugs...

Mark

On Tue, Sep 12, 2017 at 3:55 PM Vidya R <vidyadevi2811 at gmail.com> wrote:

> 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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