[gmx-users] segmantation fault

[Alessandra Villa]

Hi,

Maybe the nvt.log file provides you more information on the problem

Best regards
Alessandra


On Fri, Dec 20, 2019 at 9:40 AM Bratin Kumar Das <
177cy500.bratin at nitk.edu.in> wrote:

> Dear all,
>              During running nvt equilibration I got the following error.
> gmx mdrun -v -s nvt.tpr -deffnm nvt -cpi nvt.cpt -append
>                       :-) GROMACS - gmx mdrun, 2016.5 (-:
>
>                             GROMACS is written by:
>      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
> Bjelkmar
>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof
>  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios
> Karkoulis
>     Peter Kasson        Jiri Kraus      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
>   Teemu Virolainen  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) 2001-2017, 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 2016.5
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:
>
>  /home/workstation/Desktop/Desktop/users/bratin/GROMACS/GROMACS-DHPS/GROMACS-DHPS-57
> Command line:
>   gmx mdrun -v -s nvt.tpr -deffnm nvt -cpi nvt.cpt -append
>
> No previous checkpoint file present with -cpi option, assuming this is a
> new run.
>
> Back Off! I just backed up nvt.log to ./#nvt.log.1#
>
> Running on 1 node with total 4 cores, 4 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: Intel
>     Brand:  Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz
>     SIMD instructions most likely to fit this hardware: AVX2_256
>     SIMD instructions selected at GROMACS compile time: AVX2_256
>
>   Hardware topology: Basic
>
> Reading file nvt.tpr, VERSION 2016.5 (single precision)
> Changing nstlist from 20 to 25, rlist from 1.222 to 1.239
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
>
> Back Off! I just backed up nvt.xtc to ./#nvt.xtc.1#
>
> Back Off! I just backed up nvt.edr to ./#nvt.edr.1#
> starting mdrun 'TRANSFERASE in water'
> 500000 steps,   1000.0 ps.
> step 2100, will finish Fri Dec 20 14:48:35 2019
> Segmentation fault (core dumped)
>
> Why this is coming....please suggest me
> --
> 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.
>