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

Claire Loison claire.loison at univ-lyon1.fr
Mon Sep 25 14:52:04 CEST 2017

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

Here some pieces of information :

0)  I have used the following usual options for  cmake:


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

2) The results of "gmx -version"  show there is  a C compiler

But I do not know how and why this  C compiler flag was chosen by

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
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit
 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per
  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik
   Teemu Murtola       Szilard Pall       Sander Pronk      Roland
  Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter
  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
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
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2   -O3 -DNDEBUG -funroll-all-loops
C++ compiler:       /usr/bin/c++ GNU 6.2.0
C++ compiler flags:  -msse2   -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2  -std=c++0x   -O3 -DNDEBUG -funroll-all-loops


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

Writing final coordinates.
/home/cloison/Softwares/GROMACS2016/bin/gmx: symbol lookup
error: /home/cloison/Softwares/GROMACS2016/bin/gmx: undefined symbol:

The usual performance report is absent.

As far as I understand, in the code, the function
is defined in gromacs2016.3, but not in 2016.1,
so I have the impression that  I get a mixture of the two versions !?

Thanks in advance for any help !
Claire Loison

Claire Loison
Light and Matter Institute
Lyon 1 University/CNRS
Chargee de Recherche CNRS
Theoretical Physical Chemistry Group
tel 	 : 0033 4 72 43 12 57
cellular : 0033 6 31 30 11 72

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