[gmx-users] Initial cell size is smaller than the cell size

[Faust SHI]

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 (-:

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 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner
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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