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

Wes Barnett w.barnett at columbia.edu
Mon Sep 25 15:06:15 CEST 2017 

On Mon, Sep 25, 2017 at 7:44 AM, Claire Loison <claire.loison at univ-lyon1.fr>
wrote:

>
> Dear gmx users,
>
> I am trying to compile gromacs 2016.3 (or 2016.4) on a linux
> workstation (Linux ilmfixe160 4.7.0-1-amd64 #1 SMP Debian 4.7.5-1
> (2016-09-26) x86_64 GNU/Linux).
>
> The compilation seems to work smoothly  and in fact tests simulations
> (EM, MD, ... ) are even performed almost as expected, but I see several
> problems.
>
>
> Here some pieces of information :
>
> 0)  I have used the following usual options for  cmake:
>
>  cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DCMAKE_INSTALL_PREFIX=/home/cloison/Softwares/GROMACS2016/gromacs-2016.3
>
>
> 1) when I use the executable, gmx writes that is it the version
>   2016.1, despite the fact that I am using an executable obtained using
>   the gromacs2016.3 files. (I gave the explicit path to the right
>   directory)
>
>
>
> 2) The results of "gmx -version"  show there is  a C compiler
> flag
> -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.
>
> But I do not know how and why this  C compiler flag was chosen by
> cmake....
>
>
> Here is the full output
> ------------------------------------------------------------
> ---------------
>
> > ./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:  /usr
> Working
> dir:  /home/cloison/Softwares/GROMACS2016/gromacs-2016.3/
> gromacs-2016.3/build_ilmfixe160
> 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
>
> ------------------------------------------
>
>
>
>
> 3) Several tests of the regressions tests (2016.3) are not passed :
> here an extract of the output
> ------------------------------------------
> 89% tests passed, 3 tests failed out of 27
>
> Label Time Summary:
> GTest                 =   2.77 sec (18 tests)
> IntegrationTest       =   0.32 sec (2 tests)
> MpiIntegrationTest    =   0.13 sec (1 test)
> UnitTest              =   2.77 sec (18 tests)
>
> Total Test time (real) = 198.07 sec
>
> The following tests FAILED:
>          15 - GmxPreprocessTests (Failed)
>          20 - MdrunTests (Failed)
>          21 - MdrunMpiTests (Failed)
> ------------------------------------
>
>
>
> 3) when using mdrun, at the end of an md, for example, in a basic
> test, I see an undefined symbol  error :
>
> The end of the output :
> ------------------------------------
> starting mdrun 'DSPC BILAYER'
> 4000 steps,    100.0 ps.
>
> step 40 Turning on dynamic load balancing, because the performance loss
> due to load imbalance is 4.1 %.
>
>
> step 3600 Turning off dynamic load balancing, because it is degrading
> performance.
>
>
> Writing final coordinates.
> /home/cloison/Softwares/GROMACS2016/bin/gmx: symbol lookup
> error: /home/cloison/Softwares/GROMACS2016/bin/gmx: undefined symbol:
> walltime_accounting_set_valid_finish
> ------------------------------------
>
> The usual performance report is absent.
>
> As far as I understand, in the code, the function
> walltime_accounting_set_valid_finish
> is defined in gromacs2016.3, but not in 2016.1,
> so I have the impression that  I get a mixture of the two versions !?
>
>
>
It looks like to me you also have 2016.1 installed and are calling that one.

You specified "/home/cloison/Softwares/GROMACS2016/gromacs-2016.3" as the
installation path for 2016.3, but gmx shows to be located at '
/home/cloison/Softwares/GROMACS2016/gromacs-2016.3/gromacs-2016.3/build_ilmfixe160/./bin/gmx',
which is not what you specified. Additionally the error is saying gmx is
located "/home/cloison/Softwares/GROMACS2016/bin/gmx", which again is not
what you specified. Ensure that you build in a clean, empty directory, and
also install to an empty directory. Then make sure PATH is correctly set.


-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us

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