Dear IMP users,
I am having problems in compiling IMP on my mac (OS X version 10.9.5).
These are the steps I followed in some details and I hope you can help
me to fix my problem.
1 - I downloaded IMP from github with this command in a directory in my
home folder ~/IMP
git clone git@github.com:salilab/imp.git
2 - I renamed the downloaded imp directory as src
mv imp/ src
3 - In the src folder I executed the python script
./setup_git.py
4 - In ~/IMP I created the directory build-fast and from the latter
directory I launched
. ../prep_env_fast.sh
where prep_env_fast.sh contains the following:
cmake ../src/ -G Ninja
-DIMP_DISABLED_MODULES=domino:multifit:system:example:misc:em3d:modeller:membrane
-DCMAKE_POLICY_DEFAULT_CMP0054=OLD -DCMAKE_POLICY_DEFAULT_CMP0042=OLD
-DCM\
AKE_BUILD_TYPE=Release -DIMP_MAX_LOG=SILENT -DIMP_MAX_CHECKS=NONE
-DCMAKE_INSTALL_PREFIX=$HOME -DIMP_PER_CPP_COMPILATION="core:isd"
It is meant to run the cmake command excluding some of the modules and
tuning some other flags. The output of the script is:
-- The C compiler identification is AppleClang 6.0.0.6000056
-- The CXX compiler identification is AppleClang 6.0.0.6000056
-- Check for working C compiler using: Ninja
-- Check for working C compiler using: Ninja -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler using: Ninja
-- Check for working CXX compiler using: Ninja -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Running check_common_problems
-- Running clean_build_dir
-- Running setup_cmake
-- Enabling clang C++11 support
-- Wrong doxygen version at /usr/local/bin/doxygen. Found 1.8.9.1, but
needed 1.8.6
-- core is percpp
-- isd is percpp
-- Python binary is /usr/bin/python (version 2.7.5)
-- Found PythonLibs: /usr/lib/libpython2.7.dylib (found suitable exact
version "2.7.5")
-- Running setup
-- Running setup_all
-- Running making containers
-- Running setup_module_alias for kernel
-- Setting up alias for module kernel as
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- system
-- filesystem
-- thread
-- program_options
-- Performing Test IMP_COMPILER_HAS_AUTO
-- Performing Test IMP_COMPILER_HAS_AUTO - Success
-- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR
-- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Failed
-- Found GPERFTOOLS
-- Performing Test GPerfTools_found
-- Performing Test GPerfTools_found - Success
-- Found GPerfTools
-- Found LOG4CXX
-- Performing Test Log4CXX_found
-- Performing Test Log4CXX_found - Success
-- Found Log4CXX
-- Performing Test TCMalloc_HeapChecker_found
-- Performing Test TCMalloc_HeapChecker_found - Failed
TCMalloc_HeapChecker not found
-- Performing Test TCMalloc_HeapProfiler_found
-- Performing Test TCMalloc_HeapProfiler_found - Failed
TCMalloc_HeapProfiler not found
-- Running generate paths.cpp
Configuring module base ... yes
-- Running setup_swig_wrappers base
-- Running IMP.base making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/base.h
Configuring module benchmark ... yes
-- Running setup_swig_wrappers benchmark
-- Running IMP.benchmark making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/benchmark.h
-- Build type: Release
-- USING CXXFLAGS = ' -w -O3 -DNDEBUG'
-- USING EXEFLAGS = ' -framework CoreFoundation '
-- Targetting Ninja
-- Using /usr/bin/c++ compiler.
-- DARWIN_VERSION=13
-- Mac Leopard detected
-- Requested component: MPFR
-- Requested component: GMP
Configuring module cgal ... yes
-- Running setup_swig_wrappers cgal
-- Running IMP.cgal making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/cgal.h
Configuring module kmeans ... yes
-- Running setup_swig_wrappers kmeans
-- Running IMP.kmeans making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/kmeans.h
Configuring module module_template ... yes
-- Running setup_swig_wrappers module_template
-- Running IMP.module_template making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/module_template.h
-- Found MPI_C: /usr/local/Cellar/open-mpi/1.8.4/lib/libmpi.dylib
-- Found MPI_CXX:
/usr/local/Cellar/open-mpi/1.8.4/lib/libmpi_cxx.dylib;/usr/local/Cellar/open-mpi/1.8.4/lib/libmpi.dylib
-- MPI found
Configuring module mpi ... yes
-- Running setup_swig_wrappers mpi
-- Running IMP.mpi making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/mpi.h
Configuring module test ... yes
-- Running setup_swig_wrappers test
-- Running IMP.test making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/test.h
-- Found ANN
-- Performing Test ANN_found
-- Performing Test ANN_found - Success
-- Found ANN
Configuring module algebra ... yes
-- Running setup_swig_wrappers algebra
-- Running IMP.algebra making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/algebra.h
Configuring module kernel ... yes
-- Running setup_swig_wrappers kernel
-- Running IMP.kernel making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/kernel.h
Configuring module display ... yes
-- Running setup_swig_wrappers display
-- Running IMP.display making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/display.h
-- Found GSL
-- Performing Test GSL_found
-- Performing Test GSL_found - Success
-- Found GSL
Configuring module gsl ... yes
-- Running setup_swig_wrappers gsl
-- Running IMP.gsl making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/gsl.h
Configuring module parallel ... yes
-- Running setup_swig_wrappers parallel
-- Running IMP.parallel making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/parallel.h
-- Found HDF5
-- Performing Test HDF5_found
-- Performing Test HDF5_found - Success
-- Found HDF5
Configuring module score_functor ... yes
-- Running setup_swig_wrappers score_functor
-- Running IMP.score_functor making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/score_functor.h
Configuring module statistics ... yes
-- Running setup_swig_wrappers statistics
-- Running IMP.statistics making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/statistics.h
Configuring module core ... yes
-- Running setup_swig_wrappers core
-- Running IMP.core making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/core.h
Configuring module container ... yes
-- Running setup_swig_wrappers container
-- Running IMP.container making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/container.h
modeller is disabled
Different data/build_info/sorted_modules
-modeller
Module IMP.modeller disabled
Configuring module symmetry ... yes
-- Running setup_swig_wrappers symmetry
-- Running IMP.symmetry making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/symmetry.h
Configuring module atom ... yes
-- Running setup_swig_wrappers atom
-- Running IMP.atom making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/atom.h
Configuring module pmi ... yes
-- Running setup_swig_wrappers pmi
-- Running IMP.pmi making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/pmi.h
Configuring module scratch ... yes
-- Running setup_swig_wrappers scratch
-- Running IMP.scratch making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/scratch.h
Configuring module em ... yes
-- Running setup_swig_wrappers em
-- Running IMP.em making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/em.h
Configuring module kinematics ... yes
-- Running setup_swig_wrappers kinematics
-- Running IMP.kinematics making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/kinematics.h
misc is disabled
Different data/build_info/sorted_modules
-misc
Module IMP.misc disabled
-- Building internal RMF
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- system
-- filesystem
-- thread
-- program_options
-- iostreams
-- Found HDF5:
/usr/local/lib/libhdf5.dylib;/usr/local/lib/libhdf5.dylib;/usr/local/Cellar/hdf5/1.8.14/lib/libhdf5.dylib;/usr/local/opt/szip/lib/libsz.dylib;/usr/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib
-- Found HDF5:
/usr/local/lib/libhdf5.dylib;/usr/local/lib/libhdf5.dylib;/usr/local/Cellar/hdf5/1.8.14/lib/libhdf5.dylib;/usr/local/opt/szip/lib/libsz.dylib;/usr/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib
(Required is at least version "1.8")
-- Deprecated backends (and hdf5) are enabled
-- Found Log4CXX
-- Enabling clang C++11 support
-- Running Making RMF/HDF5.h
-- Updating
/Users/marco/IMP/build-fast/src/dependency/RMF/include/RMF/HDF5.h
-- Running Making RMF.h
-- Updating /Users/marco/IMP/build-fast/src/dependency/RMF/include/RMF.h
-- Running setup_cmake.py
-- Running Running setup_cmake.py
-- Logging enabled
-- Using VMD headers found in
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/plugins/vmd/include
-- Found SWIG: swig (found suitable version "3.0.2", minimum required is
"1.3.40")
-- Wrong doxygen version at /usr/local/bin/doxygen. Found 1.8.9.1, but
needed 1.8.6
-- RMF doc disabled
Configuring module rmf ... yes
-- Running setup_swig_wrappers rmf
-- Running IMP.rmf making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/rmf.h
Configuring module rotamer ... yes
-- Running setup_swig_wrappers rotamer
-- Running IMP.rotamer making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/rotamer.h
Configuring module saxs ... yes
-- Running setup_swig_wrappers saxs
-- Running IMP.saxs making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/saxs.h
-- Found HDF5
-- Found HDF5
domino is disabled
Different data/build_info/sorted_modules
-domino
Module IMP.domino disabled
Configuring module isd ... yes
-- Running setup_swig_wrappers isd
-- Running IMP.isd making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/isd.h
-- Found FFTW3
-- Performing Test FFTW3_found
-- Performing Test FFTW3_found - Success
-- Found FFTW3
OpenCV21 not found
-- Found OPENCV22
-- Performing Test OpenCV22_found
-- Performing Test OpenCV22_found - Success
-- Found OpenCV22
Configuring module em2d ... IMP.domino not found
Different data/build_info/sorted_modules
-em2d
Module IMP.em2d disabled
ExampleDependency not found
example is disabled
Different data/build_info/sorted_modules
-example
Module IMP.example disabled
-- Found FFTW3
-- Found FFTW3
multifit is disabled
Different data/build_info/sorted_modules
-multifit
Module IMP.multifit disabled
Configuring module pepdock ... IMP.domino not found
Different data/build_info/sorted_modules
-pepdock
Module IMP.pepdock disabled
Configuring module probC ... yes
-- Running setup_swig_wrappers probC
-- Running IMP.probC making all header
-- Updating /Users/marco/IMP/build-fast/include/IMP/probC.h
-- Found LIBTAU
-- Performing Test libTau_found
-- Performing Test libTau_found - Success
-- Found libTau
Configuring module cnmultifit ... IMP.multifit not found
Different data/build_info/sorted_modules
-cnmultifit
Module IMP.cnmultifit disabled
-- Running setup_swig_dependencies
-- Creating thread pool with 8
Configuring application EMageFit ... no
Different data/build_info/applications
-EMageFit
Application EMageFit disabled
Configuring application cnmultifit_tools ... no
Different data/build_info/applications
-cnmultifit_tools
Application cnmultifit_tools disabled
Configuring application em_tools ... yes
Configuring application example_app ... yes
Configuring application foxs ... yes
Configuring application integrative_docking ... no
Different data/build_info/applications
-integrative_docking
Application integrative_docking disabled
Configuring application ligand_score ... yes
Configuring application multifit_tools ... no
Different data/build_info/applications
-multifit_tools
Application multifit_tools disabled
Configuring application pdb_tools ... yes
Configuring application rmf_tools ... yes
Configuring application saxs_merge ... yes
Configuring application saxs_tools ... yes
-- Running setup_imppy
-- Documentation disabled as doxygen not found
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/marco/IMP/build-fast
5 - Then I launch from build-fast the command
ninja -j1 RMF
and I obtained the following error.
[98/118] Swig source
FAILED: cd /Users/marco/IMP/build-fast/src/dependency/RMF/swig &&
/usr/local/Cellar/cmake/3.1.0/bin/cmake -E make_directory
/Users/marco/IMP/build-fast/lib && swig -python -castmode -naturalvar
-Wextra -fvirtual -DPySwigIterator=RMF_PySwigIterator -c++
-DSwigPyIterator=RMF_SwigPyIterator -DRMFEXPORT -outdir
/Users/marco/IMP/build-fast/lib -c++
-I/Users/marco/IMP/build-fast/include -I/usr/local/include
-I/Users/marco/IMP/build-fast/src/dependency/RMF/src
-I/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/src
-I/usr/local/Cellar/hdf5/1.8.14/include
-I/Users/marco/IMP/build-fast/src/dependency/RMF/include
-I/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include
-I/System/Library/Frameworks/Python.framework/Headers
-I/Users/marco/IMP/src/swig
-I/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/swig -o
/Users/marco/IMP/build-fast/lib/RMFPYTHON_wrap.cxx
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/swig/RMF.i
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41:
Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments
ninja: build stopped: subcommand failed.
In the mac I have the following versions of swig , clang , python and
hdf5
SWIG Version 3.0.2
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Python 2.7.5
hdf5-1.8.14
I hope this message is enough to understand my problem.
Best regards and thanks in advance for your help,
Marco Di Stefano
