[gmx-users] Initial cell size is smaller than the cell size
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 12 20:15:35 CEST 2016
On 12/09/16 17:34, Faust SHI wrote:
> Hi David,
>
> I have tried using -dd 4 3 2 but get the same error. The entire error message in the queue output file is:
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> /share/apps/gromacs_5.1.2/bin/gmx_mpi: /lib64/libz.so.1: no version information available (required by /share/apps/gromacs_5.1.2/bin/gmx_mpi)
> [compute-0-19][[16320,1],8][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],7][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],11][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],1][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],6][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],5][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],9][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],3][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],0][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],10][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],2][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> [compute-0-19][[16320,1],4][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[16320,1],12]
> :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>
> 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 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) 2001-2015, 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 5.1.2
> Executable: /share/apps/gromacs_5.1.2/bin/gmx_mpi
> Data prefix: /share/apps/gromacs_5.1.2
> Command line:
> gmx_mpi mdrun -dd 4 3 2
>
> Number of logical cores detected (24) does not match the number reported by OpenMP (12).
> Consider setting the launch configuration manually!
>
> Running on 2 nodes with total 24 cores, 48 logical cores
> Cores per node: 12
> Logical cores per node: 24
> Hardware detected on host compute-0-19.local (the node of MPI rank 0):
> CPU info:
> Vendor: GenuineIntel
> Brand: Intel(R) Xeon(R) CPU E5-2620 0 @ 2.00GHz
> SIMD instructions most likely to fit this hardware: AVX_256
> SIMD instructions selected at GROMACS compile time: AVX_256
>
> Reading file topol.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 20 to 40, rlist from 1.5 to 1.508
>
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.2
> Source code file: /share/apps/home_2/yshi/GROMACS2016/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6964
>
> Fatal error:
> The initial cell size (3.135000) is smaller than the cell size limit (11.011738), change options -dd, -rdd or -rcon, see the log file for details
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> [compute-0-19][[16320,1],9][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],7][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],6][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],1][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],8][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],5][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],4][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],2][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],3][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],11][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19][[16320,1],10][btl_openib_xrc.c:57:mca_btl_openib_xrc_check_api] XRC error: bad XRC API (require XRC from OFED pre 3.12).
> [compute-0-19.local:13963] 11 more processes have sent help message help-mpi-btl-openib.txt / no active ports found
> [compute-0-19.local:13963] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
>
> I can simulate water successfully with the same mdp.file and top.file but failed after I added surfactants into the system, which is quite strange.
>
> Yours sincerely,
> Faust
>
I suspect your surfactants are cut in two by periodic boundary
conditions. There must be more information in the log file about the
distance of bonded interactions which are strange. Normally a bond is
0.15 nm but in your case it seems like yo have bonds that are 11 nm.
If your molecules are periodic you need to set the appropriate option in
the mdp file.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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