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Viveca Lindahl, 03/13/2018 04:32 PM

 
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            :-) GROMACS - gmx mdrun, 2018.1-dev-20180313-3500c87 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
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    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
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  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
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 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
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  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
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  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
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    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
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   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
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 Christian Wennberg    Maarten Wolf   
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                           and the project leaders:
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        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS:      gmx mdrun, version 2018.1-dev-20180313-3500c87
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Executable:   /data/viveca/gromacs/build-release-2018-debug-mpi/bin/gmx_mpi_debug
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Data prefix:  /home/viveca/gromacs (source tree)
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Working dir:  /home/viveca/tmp/test-maxh/dna/replica-0
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Command line:
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  gmx_mpi_debug mdrun -v -stepout 1 -nstlist 1 -npme 0 -ntomp 1 -maxh 0.0001 -multidir sim-0/
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Reading file topol.tpr, VERSION 2018.1-dev-20180313-3500c87 (single precision)
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Changing nstlist from 10 to 1, rlist from 1 to 1
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This is simulation 0 out of 1 running as a composite GROMACS
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multi-simulation job. Setup for this simulation:
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Using 1 MPI process
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Using 1 OpenMP thread 
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[tcbl07:2852] *** An error occurred in MPI_comm_size
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[tcbl07:2852] *** on communicator MPI_COMM_WORLD
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[tcbl07:2852] *** MPI_ERR_COMM: invalid communicator
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[tcbl07:2852] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
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--------------------------------------------------------------------------
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mpirun has exited due to process rank 0 with PID 2852 on
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node tcbl07 exiting improperly. There are two reasons this could occur:
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1. this process did not call "init" before exiting, but others in
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the job did. This can cause a job to hang indefinitely while it waits
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for all processes to call "init". By rule, if one process calls "init",
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then ALL processes must call "init" prior to termination.
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2. this process called "init", but exited without calling "finalize".
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By rule, all processes that call "init" MUST call "finalize" prior to
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exiting or it will be considered an "abnormal termination"
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This may have caused other processes in the application to be
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terminated by signals sent by mpirun (as reported here).
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