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bad_run.txt

Szilárd Páll, 07/16/2015 12:19 AM

 
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# gmx mdrun -nb gpu -resethway -noconfout -v -nsteps 1000 -ntmpi 2 -ntomp 6
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                  :-) GROMACS - gmx mdrun, VERSION 5.1-rc1 (-:
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                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch
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  Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
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 Dimitrios Karkoulis    Peter Kasson     Carsten Kutzner      Per Larsson
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  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund
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   Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz
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  Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman
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  Teemu Virolainen  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) 2001-2015, 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 5.1-rc1
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Executable:   /var/data0/sandbox/gromacs/bmdir/data/gromacs-runnable/bin//gmx
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Data prefix:  /var/data0/sandbox/gromacs/bmdir/data/gromacs-runnable
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Command line:
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  gmx mdrun -nb gpu -resethway -noconfout -v -nsteps 1000 -ntmpi 2 -ntomp 6
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Back Off! I just backed up md.log to ./#md.log.7#
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Running on 1 node with total 24 cores, 24 logical cores, 2 compatible GPUs
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Hardware detected:
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  CPU info:
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    Vendor: GenuineIntel
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    Brand:  Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz
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    SIMD instructions most likely to fit this hardware: AVX_256
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    SIMD instructions selected at GROMACS compile time: AVX_256
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  GPU info:
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    Number of GPUs detected: 2
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    #0: NVIDIA Tesla K40c, compute cap.: 3.5, ECC:  no, stat: compatible
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    #1: NVIDIA Tesla K40c, compute cap.: 3.5, ECC:  no, stat: compatible
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Reading file topol.tpr, VERSION 5.1-rc1 (single precision)
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Changing nstlist from 10 to 40, rlist from 1 to 1.101
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Overriding nsteps with value passed on the command line: 1000 steps, 2 ps
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Using 2 MPI threads
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Using 6 OpenMP threads per tMPI thread
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2 compatible GPUs are present, with IDs 0,1
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2 GPUs auto-selected for this run.
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Mapping of GPU IDs to the 2 PP ranks in this node: 0,1
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Note: NVML support was not found (CUDA runtime 6.50, driver 7.50), so your
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      Tesla K40c GPU cannot use application clock support to improve performance.
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NOTE: The number of threads is not equal to the number of (logical) cores
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      and the -pin option is set to auto: will not pin thread to cores.
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      This can lead to significant performance degradation.
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      Consider using -pin on (and -pinoffset in case you run multiple jobs).
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Back Off! I just backed up ener.edr to ./#ener.edr.6#
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NOTE: DLB will not turn on during the first phase of PME tuning
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starting mdrun 'Water'
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1000 steps,      2.0 ps.
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step   80: timed with pme grid 200 100 100, coulomb cutoff 1.000: 1989.6 M-cycles
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step  160: timed with pme grid 168 84 84, coulomb cutoff 1.187: 2006.8 M-cycles
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step  240: timed with pme grid 144 72 72, coulomb cutoff 1.384: 2664.3 M-cycles
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step  320: timed with pme grid 160 80 80, coulomb cutoff 1.246: 2205.9 M-cycles
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step  400: timed with pme grid 168 84 84, coulomb cutoff 1.187: 2016.8 M-cycles
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step  480: timed with pme grid 192 96 96, coulomb cutoff 1.038: 2097.2 M-cycles
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              optimal pme grid 200 100 100, coulomb cutoff 1.000
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step 500: resetting all time and cycle counters
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-------------------------------------------------------
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Program gmx mdrun, VERSION 5.1-rc1
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Source code file: /var/data0/sandbox/gromacs/bmdir/data/source/src/gromacs/ewald/pme-load-balancing.cpp, line: 927
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Software inconsistency error:
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pme_loadbal_do called at an interval != nstlist
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For more information and tips for troubleshooting, please check the GROMACS
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website at http://www.gromacs.org/Documentation/Errors
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-------------------------------------------------------
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-------------------------------------------------------
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Program gmx mdrun, VERSION 5.1-rc1
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Source code file: /var/data0/sandbox/gromacs/bmdir/data/source/src/gromacs/ewald/pme-load-balancing.cpp, line: 927
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Software inconsistency error:
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pme_loadbal_do called at an interval != nstlist
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For more information and tips for troubleshooting, please check the GROMACS
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website at http://www.gromacs.org/Documentation/Errors
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-------------------------------------------------------
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: Unknown error 255
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Segmentation fault (core dumped)