[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 15:31:09 CEST 2017


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

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) 

>> /home/cloison/Softwares/GROMACS2016/gromacs-2016.3/gromacs-2016.3/build_ilmfixe160/./bin/gmx
>> --version 

:-) GROMACS - gmx, 2016.1 (-:

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                            Meulenhoff    Erik Marklund Teemu
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                            Wolf and the project leaders: Mark Abraham,
                            Berk Hess, Erik Lindahl, and David van der

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Copyright (c) 2001-2015, The GROMACS development team at
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check out http://www.gromacs.org for more information.

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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
-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
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2  -std=c++0x   -O3 -DNDEBUG -funroll-all-loops

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