[gmx-users] compilation of gromacs 2016.3 or 4 with C compiler flag -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.

[Mark Abraham]

Hi,

Clearly you have multiple versions installed and your dynamic linking setup
is confused. Please follow the instructions for doing this reliably, found
in the installation instructions at
http://manual.gromacs.org/documentation/2016.4/install-guide/index.html#getting-access-to-gromacs-after-installation.
You may wish to simplify your setup and not have multiple versions
installed until you work out how things are going wrong. For example,
inspect the output of ldd /path/to/gmx

Mark

On Mon, 25 Sep 2017 15:31 Claire Loison <claire.loison at univ-lyon1.fr> wrote:

>
>
> Thank you James for your quick reply !
>
> I indeed call the executable obtained by compiling the gromacs2016.3
> files.  Calling with the explicit path give me the same results (see
> below)
>
> Since, as you,  I first suspected that I had some mixing between path
> definitions, I reinstalled gromacs2016.3 separatedly once more, but
> the problem remains.
>
> Moreover, the error at the end of mdrun execution indicates me that
> I do not use the version2016,1.
>
> In fact, when I compile and use the version 2016.1 with the very same
> inputs, I have no errors, and the regression tests are all ok.
> (This is why at the moment I use version 2016.1)
>
>  Claire
>
> --------------------------------------------------------------------------------------
> >>
> /home/cloison/Softwares/GROMACS2016/gromacs-2016.3/gromacs-2016.3/build_ilmfixe160/./bin/gmx
> >> --version
>
> :-) GROMACS - gmx, 2016.1 (-:
>
>                             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) 2001-2015, 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, version 2016.1
> Executable:
>  /home/cloison/Softwares/GROMACS2016/gromacs-2016.3/gromacs-2016.3/build_ilmfixe160/./bin/gmx
> Data prefix:  /home/cloison/Softwares/GROMACS2016
> Working dir:  /home/cloison
> Command line:
>   gmx --version
>
> GROMACS version:    2016.1
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:        disabled
> SIMD instructions:  SSE2
> FFT library:        fftw-3.3.5-sse2-avx
> RDTSCP usage:       disabled
> TNG support:        enabled
> Hwloc support:      hwloc-1.11.0
> Tracing support:    disabled
> Built on:
> Built by:           buildd at debian [CMAKE]
> Build OS/arch:      Linux x86_64
> Build CPU vendor:   AMD
> Build CPU brand:    AMD Opteron 23xx (Gen 3 Class Opteron)
> Build CPU family:   15   Model: 6   Stepping: 1
> Build CPU features: apic clfsh cmov cx8 cx16 lahf misalignsse mmx msr
> popcnt pse sse2 sse3 sse4a x2apic C compiler:         /usr/bin/cc GNU
> 6.2.0 C compiler flags:    -msse2   -g -O2
> -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2   -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast C++ compiler:       /usr/bin/c++ GNU 6.2.0 C++
> compiler flags:  -msse2   -g -O2
> -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2  -std=c++0x   -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
>
> --
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