[gmx-developers] Blue Gene/P compilation issue with git version

Whitford, Paul p.whitford at neu.edu
Fri Sep 21 05:53:44 CEST 2012

GMX Developers,

I am trying to compile the git version on a Blue Gene/P machine. I made it past ccmake with the following command

ccmake .. \
  -DFFTW_INCLUDE_DIR=/opt/apps/fftw/3.3.2-single/include \
  -DFFTW_LIBRARY=/opt/apps/fftw/3.3.2-single/lib/libfftw3f.a \
  -DCMAKE_TOOLCHAIN_FILE=../cmake/Toolchain-BlueGeneP.cmake \
  -DCMAKE_C_FLAGS="-O3 -qarch=450d -qtune=450" \

It appears that a few flags have changed since the instruction page was made, so I am using the flags that ccmake asked for.  Other than that, I believe I am following the instructions on the page.

The only warnings I received were the following

"No compatible git version found, won't be able to generate proper development version information.

 Boost >= 1.44 not found. Using minimal internal version. Not recommended if GROMACS is used as library!"

These both seems like harmless warnings, but perhaps I am underestimating their importance.

When I issue "make mdrun" it stops with the following output.

 Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 327.13: 1540-0300 (S) The "private" member "gmx::AnalysisDataStorageFrame::AnalysisDataStorageFrame(AnalysisDataStorage *, int, int)" cannot be accessed.
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 352.20: 1540-0300 (S) The "private" member "gmx::AnalysisDataStorageFrame::header_" cannot be accessed.
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 353.20: 1540-0300 (S) The "private" member "gmx::AnalysisDataStorageFrame::clearValues()" cannot be accessed.
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 361.10: 1540-0301 (S) The "protected" member "gmx::AbstractAnalysisData::notifyPointsAdd(const AnalysisDataPointSetRef &) const" cannot be accessed.
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 390.18: 1540-0301 (S) The "protected" member "gmx::AbstractAnalysisData::notifyFrameStart(const AnalysisDataFrameHeader &) const" cannot be accessed.
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 391.18: 1540-0301 (S) The "protected" member "gmx::AbstractAnalysisData::notifyPointsAdd(const AnalysisDataPointSetRef &) const" cannot be accessed.
"/home/paul/gromacs.git.092012/src/gromacs/analysisdata/datastorage.cpp", line 392.18: 1540-0301 (S) The "protected" member "gmx::AbstractAnalysisData::notifyFrameFinish(const AnalysisDataFrameHeader &)" cannot be accessed.
make[3]: *** [src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o] Error 1
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2

I'm not sure if this is a bug, or if I am still missing a flag. Advice would be greatly appreciated.

If there is any additional information that I can provide, please let me know.

Paul Whitford, Assistant Professor
Department of Physics
Dana Research Center, Room 123
Northeastern University
Boston, MA 02115
Office: 617-373-2952
Email: p.whitford at neu.edu<mailto:p.whitford at neu.edu>

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