[MMTK] build problem - barrier

Toon Verstraelen Toon.Verstraelen at UGent.be
Wed Dec 8 14:57:19 CET 2004


Hi,

I've tried to install MMTK, but get a strange error during the build 
proccess.

# python setup.py build
running build
running build_py
creating build
creating build/lib.linux-i686-2.3
creating build/lib.linux-i686-2.3/MMTK
copying MMTK/Database.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Features.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/PyMOL.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/FourierBasis.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/NucleicAcids.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/surfm.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Skeleton.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Proteins.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Random.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Geometry.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/PDB.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ChemicalObjects.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ChargeFit.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Installation.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Trajectory.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/NormalModes.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ProteinEnvironment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ParticleProperties.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Dynamics.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ConfigIO.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Visualization_win32.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/NewModuleNames.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/tess.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Visualization.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Minimization.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Environment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/AtomEnvironment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Subspace.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ComplexEnvironment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Bonds.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Universe.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Solvation.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Utility.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/ThreadManager.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Deformation.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Collection.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Units.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/MoleculeEnvironment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/CrystalEnvironment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/__init__.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/GroupEnvironment.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Biopolymers.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/MolecularSurface.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/Field.py -> build/lib.linux-i686-2.3/MMTK
copying MMTK/DCD.py -> build/lib.linux-i686-2.3/MMTK
creating build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/MMForceField.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/BondedInteractions.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/Restraints.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/BondFF.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/ForceField.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/CalphaFF.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/ForceFieldTest.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/NonBondedInteractions.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/SPCEFF.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/DeformationFF.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/LennardJonesFF.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
copying MMTK/ForceFields/__init__.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields
creating build/lib.linux-i686-2.3/MMTK/ForceFields/Amber
copying MMTK/ForceFields/Amber/AmberForceField.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields/Amber
copying MMTK/ForceFields/Amber/AmberData.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields/Amber
copying MMTK/ForceFields/Amber/__init__.py -> 
build/lib.linux-i686-2.3/MMTK/ForceFields/Amber
creating build/lib.linux-i686-2.3/MMTK/Tk
copying MMTK/Tk/ProteinVisualization.py -> build/lib.linux-i686-2.3/MMTK/Tk
copying MMTK/Tk/__init__.py -> build/lib.linux-i686-2.3/MMTK/Tk
creating build/lib.linux-i686-2.3/MMTK/Tools
copying MMTK/Tools/__init__.py -> build/lib.linux-i686-2.3/MMTK/Tools
creating build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/TrajectoryServer.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/manager.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/TrajectoryViewer.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/TrajectoryInspector.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/test.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/Tkwindow.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/TrajectoryManager.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
copying MMTK/Tools/TrajectoryViewer/__init__.py -> 
build/lib.linux-i686-2.3/MMTK/Tools/TrajectoryViewer
running build_ext
building 'lapack_mmtk' extension
creating build/temp.linux-i686-2.3
creating build/temp.linux-i686-2.3/Src
gcc -fno-strict-aliasing -DNDEBUG -fPIC -DLIBM_HAS_ERFC -DEXTENDED_TYPES 
-IInclude -I/usr/include/python2.3 -c Src/lapack_subset.c -o 
build/temp.linux-i686-2.3/Src/lapack_subset.o -O3 -ffast-math 
-fomit-frame-pointer -fkeep-inline-functions
gcc -fno-strict-aliasing -DNDEBUG -fPIC -DLIBM_HAS_ERFC -DEXTENDED_TYPES 
-IInclude -I/usr/include/python2.3 -c Src/lapack_mmtk.c -o 
build/temp.linux-i686-2.3/Src/lapack_mmtk.o -O3 -ffast-math 
-fomit-frame-pointer -fkeep-inline-functions
creating build/lib.linux-i686-2.3/MMTK/linux2
gcc -pthread -shared build/temp.linux-i686-2.3/Src/lapack_subset.o 
build/temp.linux-i686-2.3/Src/lapack_mmtk.o -lm -o 
build/lib.linux-i686-2.3/MMTK/linux2/lapack_mmtk.so
building 'MMTK_DCD' extension
gcc -fno-strict-aliasing -DNDEBUG -fPIC -DLIBM_HAS_ERFC -DEXTENDED_TYPES 
-IInclude -I/usr/include/python2.3 -c Src/ReadDCD.c -o 
build/temp.linux-i686-2.3/Src/ReadDCD.o
gcc -fno-strict-aliasing -DNDEBUG -fPIC -DLIBM_HAS_ERFC -DEXTENDED_TYPES 
-IInclude -I/usr/include/python2.3 -c Src/MMTK_DCD.c -o 
build/temp.linux-i686-2.3/Src/MMTK_DCD.o
gcc -pthread -shared build/temp.linux-i686-2.3/Src/MMTK_DCD.o 
build/temp.linux-i686-2.3/Src/ReadDCD.o -lm -o 
build/lib.linux-i686-2.3/MMTK/linux2/MMTK_DCD.sobuilding 
'MMTK_deformation' extension
gcc -fno-strict-aliasing -DNDEBUG -fPIC -DLIBM_HAS_ERFC -DEXTENDED_TYPES 
-IInclude -I/usr/include/python2.3 -c Src/MMTK_deformation.c -o 
build/temp.linux-i686-2.3/Src/MMTK_deformation.o -O3 -ffast-math 
-fomit-frame-pointer -fkeep-inline-functions
In file included from Src/MMTK_deformation.c:9:
Include/MMTK/forcefield_private.h:26:56: macro "barrier" passed 3 
arguments, but takes just 0
Include/MMTK/forcefield_private.h:26: error: storage size of `barrier' 
isn't known
error: command 'gcc' failed with exit status 1

I'm working with gcc 3.3.4, Python 2.3, ScientificPython 2.4.3 and 
Numeric 23.1. Does someone have clue what the problem might be?

thanks,

Toon



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