I'm trying to install CRPropa 3 on my Mac (Mac OS X Yosemite 10.10.4) at the moment. When running "cmake ..", "make" and "sudo make install" I get a bunch of warnings but no errors. However, when running "make test" test 11 (testMagneticLensPythonInterface) fails. And when I try to import crpropa in python it gives a segmentation violation. I've pasted the output of "cmake ..", "make" and "python; from crpropa import *" below.
I thought this might be due to a problem with linking to python, so I tried "cmake .. -DPYTHON_EXECUTABLE=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h -DPYTHON_LIBRARIES=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib" but then I get these error messages:
Arjens-MacBook-Pro:build avanvliet$ cmake .. -DPYTHON_EXECUTABLE=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h -DPYTHON_LIBRARIES=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Build Type: Release
-- CRPropa version: -128-NOTFOUND
Using provided EIGEN
-- ROOT: Found!
-- CFlags: -pthread -stdlib=libc++ -std=c++11 -m64 -I/Users/avanvliet/Documents/Werk/software/root-6.04.02/include
-- Libs: -L/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -Wl,-rpath,/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -stdlib=libc++ -lm -ldl
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
-- Google perftools: NOT Found!
-- Include: GOOGLE_PERFTOOLS_INCLUDE_DIR-NOTFOUND
-- FFTW3 with single precision (FFTW3F): Found!
-- Include: /usr/local/include
-- Library: /usr/local/lib/libfftw3f.a
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- CFITSIO: NOT Found!
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- Library: CFITSIO_LIBRARY-NOTFOUND
-- Quimby: NOT Found!
-- Include: QUIMBY_INCLUDE_DIR-NOTFOUND
-- Library: QUIMBY_LIBRARY-NOTFOUND
-- SAGA: NOT Found!
-- Include: SAGA_INCLUDE_DIR-NOTFOUND
-- Library: SAGA_LIBRARY-NOTFOUND
-- SQLite3: NOT Found!
-- Include: /usr/include
-- Library: SQLITE3_LIBRARY-NOTFOUND
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
-- muParser: NOT Found!
-- Include: MUPARSER_INCLUDE_DIR-NOTFOUND
-- Library: MUPARSER_LIBRARY-NOTFOUND
Searching for data archive
File found: /Users/avanvliet/Documents/Werk/software/CRPropa3/build/data.tar.gz
MD5sum matching
-- Using user provided Python library: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib
-- Python: Found!
-- Version: ./
-- Executeable: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h
-- Include:
-- Library: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/lib/python2.7/config/libpython2.7.dylib
-- Site-package directory:
-- Numpy not found.
CMake Error at CMakeLists.txt:379 (install):
install DIRECTORY given no DESTINATION!
-- Configuring incomplete, errors occurred!
See also "/Users/avanvliet/Documents/Werk/software/CRPropa3/build/CMakeFiles/CMakeOutput.log".
See also "/Users/avanvliet/Documents/Werk/software/CRPropa3/build/CMakeFiles/CMakeError.log".
Arjens-MacBook-Pro:build avanvliet$ cmake ..
-- The Fortran compiler identification is GNU 5.1.0
-- The C compiler identification is AppleClang 6.1.0.6020053
-- The CXX compiler identification is AppleClang 6.1.0.6020053
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Check for working Fortran compiler: /usr/local/bin/gfortran
-- Check for working Fortran compiler: /usr/local/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/bin/gfortran supports Fortran 90
-- Checking whether /usr/local/bin/gfortran supports Fortran 90 -- yes
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Build Type: Release
-- CRPropa version: -128-NOTFOUND
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
Using provided EIGEN
-- ROOT: Found!
-- CFlags: -pthread -stdlib=libc++ -std=c++11 -m64 -I/Users/avanvliet/Documents/Werk/software/root-6.04.02/include
-- Libs: -L/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -Wl,-rpath,/Users/avanvliet/Documents/Werk/software/root-6.04.02/lib -stdlib=libc++ -lm -ldl
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP Fortran flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
-- Google perftools: NOT Found!
-- Include: GOOGLE_PERFTOOLS_INCLUDE_DIR-NOTFOUND
-- FFTW3 with single precision (FFTW3F): Found!
-- Include: /usr/local/include
-- Library: /usr/local/lib/libfftw3f.a
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- CFITSIO: NOT Found!
-- Include: CFITSIO_INCLUDE_DIR-NOTFOUND
-- Library: CFITSIO_LIBRARY-NOTFOUND
-- Quimby: NOT Found!
-- Include: QUIMBY_INCLUDE_DIR-NOTFOUND
-- Library: QUIMBY_LIBRARY-NOTFOUND
-- SAGA: NOT Found!
-- Include: SAGA_INCLUDE_DIR-NOTFOUND
-- Library: SAGA_LIBRARY-NOTFOUND
-- SQLite3: NOT Found!
-- Include: /usr/include
-- Library: SQLITE3_LIBRARY-NOTFOUND
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
-- muParser: NOT Found!
-- Include: MUPARSER_INCLUDE_DIR-NOTFOUND
-- Library: MUPARSER_LIBRARY-NOTFOUND
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5")
Searching for data archive
File not found: data.tar.gz
Downloading from crpropa.desy.de ~ 60 MB
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 30.8M 100 30.8M 0 0 4150k 0 0:00:07 0:00:07 --:--:-- 4908k
Unpacking to CRPropa3/data
-- Found SWIG: /usr/local/bin/swig (found version "3.0.6")
-- Running on Mac OS X < 10.9: Linking to Python as framework
INFOLooking for python framework as on apple system
-- Python: Found!
-- Version: 2.7/27
-- Executeable: /Users/avanvliet/Library/Enthought/Canopy_64bit/User/bin/python
-- Include: /Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7
-- Library: -framework Python
-- Site-package directory: /usr/local/lib/python2.7/site-packages
-- Found numpy headers in /Users/avanvliet/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/core/include
-- Configuring done
CMake Warning (dev):
Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake
--help-policy CMP0042" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
MACOSX_RPATH is not specified for the following targets:
crpropa
This warning is for project developers. Use -Wno-dev to suppress it.
-- Generating done
-- Build files have been written to: /Users/avanvliet/Documents/Werk/software/CRPropa3/build
Arjens-MacBook-Pro:build avanvliet$ make
Scanning dependencies of target healpix_base
[ 0%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/error_handling.cc.o
[ 1%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/geom_utils.cc.o
[ 2%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/healpix_base.cc.o
[ 3%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/healpix_tables.cc.o
[ 3%] Building CXX object libs/healpix_base/CMakeFiles/healpix_base.dir/pointing.cc.o
[ 4%] Linking CXX static library libhealpix_base.a
[ 4%] Built target healpix_base
Scanning dependencies of target sophia
[ 5%] Building Fortran object libs/sophia/CMakeFiles/sophia.dir/sophia_interface.f.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/sophia/sophia_interface.f:1827:72: Warning: Deleted feature: PAUSE statement at (1)
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/sophia/sophia_interface.f:16396:72: Warning: Deleted feature: PAUSE statement at (1)
[ 6%] Linking Fortran static library libsophia.a
[ 6%] Built target sophia
Scanning dependencies of target HepPID
[ 6%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/ParticleIDMethods.cc.o
[ 7%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/ParticleName.cc.o
[ 8%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/Version.cc.o
[ 9%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateEvtGen.cc.o
[ 9%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateGeanttoPDT.cc.o
[ 10%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateHerwig.cc.o
[ 11%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateIsajet.cc.o
[ 12%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePDG.cc.o
[ 12%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePDTtoGeant.cc.o
[ 13%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translatePythia.cc.o
[ 14%] Building CXX object libs/HepPID/CMakeFiles/HepPID.dir/src/translateQQ.cc.o
[ 15%] Linking CXX static library libHepPID.a
[ 15%] Built target HepPID
Scanning dependencies of target eleca
[ 16%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Common.cpp.o
In file included from /Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/Common.cpp:1:
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/include/EleCa/Common.h:20:31: warning: use of right-shift operator ('>>') in template argument will require parentheses
in C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
1 warning generated.
[ 17%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/EnergyLoss.cpp.o
In file included from /Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/EnergyLoss.cpp:6:
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/include/EleCa/Common.h:20:31: warning: use of right-shift operator ('>>') in template argument will require parentheses
in C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/EnergyLoss.cpp:464:3: warning: control may reach end of non-void function [-Wreturn-type]
}
^
2 warnings generated.
[ 17%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Particle.cpp.o
[ 18%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Process.cpp.o
[ 19%] Building CXX object libs/EleCa/CMakeFiles/eleca.dir/src/Propagation.cpp.o
In file included from /Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/src/Propagation.cpp:4:
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/EleCa/include/EleCa/Common.h:20:31: warning: use of right-shift operator ('>>') in template argument will require parentheses
in C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
1 warning generated.
[ 20%] Linking CXX static library libeleca.a
[ 20%] Built target eleca
Scanning dependencies of target kiss
[ 21%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/logger.cpp.o
[ 22%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/path.cpp.o
[ 22%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/string.cpp.o
[ 23%] Building CXX object libs/kiss/CMakeFiles/kiss.dir/src/uuid.cpp.o
[ 24%] Linking CXX static library libkiss.a
[ 24%] Built target kiss
Scanning dependencies of target pugixml
[ 25%] Building CXX object libs/pugixml/CMakeFiles/pugixml.dir/pugixml.cpp.o
[ 25%] Linking CXX static library libpugixml.a
[ 25%] Built target pugixml
Scanning dependencies of target dint
[ 26%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/advance.cpp.o
[ 27%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/background.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/dint/src/background.cpp:9:31: warning: use of right-shift operator ('>>') in template argument will require parentheses in
C++11 [-Wc++11-compat]
return pow_integer> 1>(base_base) * (((exponent & 1) > 0) ? base : 1);
^
( )
1 warning generated.
[ 27%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/binfread.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/dint/src/binfread.cpp:58:73: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long')
[-Wformat]
fprintf(stderr,"DINT / binfread : Strange member size = %d. Exit",size);
~~ ^~~~
%lu
1 warning generated.
[ 28%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/check.cpp.o
[ 29%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/cvector.cpp.o
[ 30%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/decay.cpp.o
[ 30%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/deriv.cpp.o
[ 31%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/error.cpp.o
[ 32%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/final.cpp.o
[ 33%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/fold.cpp.o
[ 33%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/frag.cpp.o
[ 34%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/gauleg.cpp.o
[ 35%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/inject.cpp.o
[ 36%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/io_util.cpp.o
[ 36%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/load.cpp.o
[ 37%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/math_util.cpp.o
[ 38%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/prepare.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/libs/dint/src/prepare.cpp:235:15: warning: format specifies type 'double ' but the argument has type 'int *' [-Wformat]
scanf("%lf", pTauNeutrinoMassSwitch);
~~~ ^~~~~~~~~~~~~~~~~~~~~~
%d
1 warning generated.
[ 39%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/prop_second.cpp.o
[ 39%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/rate.cpp.o
[ 40%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/spectrum.cpp.o
[ 41%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/sync.cpp.o
[ 42%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/vector.cpp.o
[ 42%] Building CXX object libs/dint/CMakeFiles/dint.dir/src/DintEMCascade.cpp.o
[ 43%] Linking CXX static library libdint.a
[ 43%] Built target dint
Scanning dependencies of target crpropa
[ 43%] Building CXX object CMakeFiles/crpropa.dir/src/Random.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:228:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 s1;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:288:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = 1;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:289:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 j = 0;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:290:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int k = (N > seedLength ? N : seedLength);
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:325:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *s = bigSeed;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:326:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:327:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register bool success = true;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:342:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *s = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:343:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *r = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:344:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = 1;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:353:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *p = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:354:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:383:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *sa = saveArray;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:384:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register const uint32 *s = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:385:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:392:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *s = state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:393:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register uint32 *la = loadArray;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:394:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:402:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register const Random::uint32 *s = mtrand.state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:403:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = mtrand.N;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:410:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register Random::uint32 *s = mtrand.state;
^~~~~~~~~
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/Random.cpp:411:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int i = mtrand.N;
^~~~~~~~~
22 warnings generated.
[ 44%] Building CXX object CMakeFiles/crpropa.dir/src/Clock.cpp.o
[ 45%] Building CXX object CMakeFiles/crpropa.dir/src/ModuleList.cpp.o
[ 46%] Building CXX object CMakeFiles/crpropa.dir/src/Module.cpp.o
[ 46%] Building CXX object CMakeFiles/crpropa.dir/src/Candidate.cpp.o
[ 47%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleState.cpp.o
[ 48%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleID.cpp.o
[ 49%] Building CXX object CMakeFiles/crpropa.dir/src/ParticleMass.cpp.o
[ 49%] Building CXX object CMakeFiles/crpropa.dir/src/ProgressBar.cpp.o
[ 50%] Building CXX object CMakeFiles/crpropa.dir/src/Cosmology.cpp.o
[ 51%] Building CXX object CMakeFiles/crpropa.dir/src/Source.cpp.o
[ 52%] Building CXX object CMakeFiles/crpropa.dir/src/Common.cpp.o
[ 52%] Building CXX object CMakeFiles/crpropa.dir/src/PhotonBackground.cpp.o
[ 53%] Building CXX object CMakeFiles/crpropa.dir/src/PhotonPropagation.cpp.o
[ 54%] Building CXX object CMakeFiles/crpropa.dir/src/GridTools.cpp.o
[ 55%] Building CXX object CMakeFiles/crpropa.dir/src/XmlExecute.cpp.o
[ 55%] Building CXX object CMakeFiles/crpropa.dir/src/module/BreakCondition.cpp.o
[ 56%] Building CXX object CMakeFiles/crpropa.dir/src/module/Boundary.cpp.o
[ 57%] Building CXX object CMakeFiles/crpropa.dir/src/module/Observer.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/module/Observer.cpp:215:11: warning: using floating point absolute value function 'fabs' when argument is of integer type
[-Wabsolute-value]
int id = fabs(c->current.getId());
^
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/module/Observer.cpp:215:11: note: use function 'std::abs' instead
int id = fabs(c->current.getId());
^~~~
std::abs
1 warning generated.
[ 58%] Building CXX object CMakeFiles/crpropa.dir/src/module/SimplePropagation.cpp.o
[ 58%] Building CXX object CMakeFiles/crpropa.dir/src/module/PropagationCK.cpp.o
[ 59%] Building CXX object CMakeFiles/crpropa.dir/src/module/ElectronPairProduction.cpp.o
[ 60%] Building CXX object CMakeFiles/crpropa.dir/src/module/NuclearDecay.cpp.o
[ 61%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotoPionProduction.cpp.o
[ 61%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotoDisintegration.cpp.o
[ 62%] Building CXX object CMakeFiles/crpropa.dir/src/module/Redshift.cpp.o
[ 63%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputTXT.cpp.o
[ 64%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputShell.cpp.o
/Users/avanvliet/Documents/Werk/software/CRPropa3/src/module/OutputShell.cpp:48:8: warning: expression result unused [-Wunused-value]
for (i; i != c->properties.end(); i++) {
^
1 warning generated.
[ 64%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputROOT.cpp.o
[ 65%] Building CXX object CMakeFiles/crpropa.dir/src/module/OutputCRPropa2.cpp.o
[ 66%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonOutput1D.cpp.o
[ 67%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonDINT.cpp.o
[ 67%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonDINT1D.cpp.o
[ 68%] Building CXX object CMakeFiles/crpropa.dir/src/module/PhotonEleCa.cpp.o
[ 69%] Building CXX object CMakeFiles/crpropa.dir/src/module/Tools.cpp.o
[ 70%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/MagneticField.cpp.o
[ 70%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/MagneticFieldGrid.cpp.o
[ 71%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/TurbulentMagneticField.cpp.o
[ 72%] Building CXX object CMakeFiles/crpropa.dir/src/magneticField/JF12Field.cpp.o
[ 73%] Building CXX object CMakeFiles/crpropa.dir/src/Version.cpp.o
[ 73%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/MagneticLens.cpp.o
[ 74%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/ModelMatrix.cpp.o
[ 75%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/Pixelization.cpp.o
[ 76%] Building CXX object CMakeFiles/crpropa.dir/src/magneticLens/ParticleMapsContainer.cpp.o
[ 76%] Linking CXX shared library libcrpropa.dylib
clang: warning: argument unused during compilation: '-pthread'
ld: warning: could not create compact unwind for lushow: stack subq instruction is too different from dwarf stack size
[ 76%] Built target crpropa
[ 77%] Generating crpropa_wrap.cxx
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:172: Warning 361: operator! ignored
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/module/PropagationCK.h:46: Warning 325: Nested class not currently supported (Y ignored)
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:124: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:129: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:124: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:168: Warning 508: Declaration of 'get' shadows declaration accessible via operator->(),
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Grid.h:129: Warning 508: previous declaration of 'get'.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:158: Warning 503: Can't wrap 'operator crpropa::Grid< crpropa::Vector3< float > >' unless renamed to a valid identifier.
/Users/avanvliet/Documents/Werk/software/CRPropa3/include/crpropa/Referenced.h:158: Warning 503: Can't wrap 'operator crpropa::Grid< float >*' unless renamed to a valid identifier.
Scanning dependencies of target crpropa-swig
[ 78%] Building CXX object CMakeFiles/crpropa-swig.dir/crpropa_wrap.cxx.o
[ 79%] Linking CXX shared module _crpropa.so
clang: warning: argument unused during compilation: '-pthread'
[ 79%] Built target crpropa-swig
Scanning dependencies of target crpropa-xmlrun
[ 79%] Building CXX object CMakeFiles/crpropa-xmlrun.dir/src/main.cpp.o
[ 80%] Linking CXX executable crpropa-xmlrun
clang: warning: argument unused during compilation: '-pthread'
[ 80%] Built target crpropa-xmlrun
Scanning dependencies of target gtest
[ 80%] Building CXX object libs/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 81%] Linking CXX static library libgtest.a
[ 81%] Built target gtest
Scanning dependencies of target gtest_main
[ 82%] Building CXX object libs/gtest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 83%] Linking CXX static library libgtest_main.a
[ 83%] Built target gtest_main
Scanning dependencies of target testBreakCondition
[ 84%] Building CXX object CMakeFiles/testBreakCondition.dir/test/testBreakCondition.cpp.o
[ 84%] Linking CXX executable testBreakCondition
clang: warning: argument unused during compilation: '-pthread'
[ 84%] Built target testBreakCondition
Scanning dependencies of target testCore
[ 85%] Building CXX object CMakeFiles/testCore.dir/test/testCore.cpp.o
[ 86%] Linking CXX executable testCore
clang: warning: argument unused during compilation: '-pthread'
[ 86%] Built target testCore
Scanning dependencies of target testDINT
[ 87%] Building CXX object CMakeFiles/testDINT.dir/test/testDINT.cpp.o
[ 87%] Linking CXX executable testDINT
clang: warning: argument unused during compilation: '-pthread'
[ 87%] Built target testDINT
Scanning dependencies of target testGalacticMagneticLens
[ 88%] Building CXX object CMakeFiles/testGalacticMagneticLens.dir/test/testMagneticLens.cpp.o
[ 89%] Linking CXX executable testGalacticMagneticLens
clang: warning: argument unused during compilation: '-pthread'
[ 89%] Built target testGalacticMagneticLens
Scanning dependencies of target testInteraction
[ 90%] Building CXX object CMakeFiles/testInteraction.dir/test/testInteraction.cpp.o
[ 90%] Linking CXX executable testInteraction
clang: warning: argument unused during compilation: '-pthread'
[ 90%] Built target testInteraction
Scanning dependencies of target testMagneticField
[ 91%] Building CXX object CMakeFiles/testMagneticField.dir/test/testMagneticField.cpp.o
[ 92%] Linking CXX executable testMagneticField
clang: warning: argument unused during compilation: '-pthread'
[ 92%] Built target testMagneticField
Scanning dependencies of target testModuleList
[ 93%] Building CXX object CMakeFiles/testModuleList.dir/test/testModuleList.cpp.o
[ 93%] Linking CXX executable testModuleList
clang: warning: argument unused during compilation: '-pthread'
[ 93%] Built target testModuleList
Scanning dependencies of target testPropagation
[ 94%] Building CXX object CMakeFiles/testPropagation.dir/test/testPropagation.cpp.o
[ 95%] Linking CXX executable testPropagation
clang: warning: argument unused during compilation: '-pthread'
[ 95%] Built target testPropagation
Scanning dependencies of target testSource
[ 96%] Building CXX object CMakeFiles/testSource.dir/test/testSource.cpp.o
[ 96%] Linking CXX executable testSource
clang: warning: argument unused during compilation: '-pthread'
[ 96%] Built target testSource
Scanning dependencies of target testVector3
[ 97%] Building CXX object CMakeFiles/testVector3.dir/test/testVector3.cpp.o
[ 98%] Linking CXX executable testVector3
clang: warning: argument unused during compilation: '-pthread'
[ 98%] Built target testVector3
Scanning dependencies of target test_uuid
[ 99%] Building CXX object libs/kiss/CMakeFiles/test_uuid.dir/test/test_uuid.cpp.o
[100%] Linking CXX executable test_uuid
[100%] Built target test_uuid
Arjens-MacBook-Pro:build avanvliet$ python
Enthought Canopy Python 2.7.9 | 64-bit | (default, Jun 30 2015, 19:41:21)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.6)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
from crpropa import *
*** Break *** segmentation violation
Generating stack trace...
0x00000001039f3c77 in 0x00000001039f3c77 (in Python) + 50
0x0000000101908a72 in init_crpropa (in crpropa.so) + 66
0x00000001000c29ca in PyImport_LoadDynamicModule (in Python) + 170
0x00000001000bf4a5 in imp_load_module (in Python) + 341
0x00000001000a8fab in PyEval_EvalFrameEx (in Python) + 17995
0x00000001000ac3b3 in fast_function (in Python) + 179
0x00000001000a905d in PyEval_EvalFrameEx (in Python) + 18173
0x00000001000ac273 in PyEval_EvalCodeEx (in Python) + 2083
0x00000001000ac2f6 in PyEval_EvalCode (in Python) + 54
0x00000001000bfc53 in PyImport_ExecCodeModuleEx (in Python) + 243
0x00000001000c0257 in load_source_module (in Python) + 1351
0x00000001000c1147 in import_submodule (in Python) + 327
0x00000001000c134b in load_next (in Python) + 251
0x00000001000c2192 in PyImport_ImportModuleLevel (in Python) + 1170
0x000000010009f364 in builtin___import (in Python) + 132
0x000000010000f2b1 in PyObject_Call (in Python) + 97
0x00000001000a3d64 in PyEval_CallObjectWithKeywords (in Python) + 180
0x00000001000aad3b in PyEval_EvalFrameEx (in Python) + 25563
0x00000001000ac273 in PyEval_EvalCodeEx (in Python) + 2083
0x00000001000ac2f6 in PyEval_EvalCode (in Python) + 54
0x00000001000cc292 in PyRun_InteractiveOneFlags (in Python) + 578
0x00000001000cc3ee in PyRun_InteractiveLoopFlags (in Python) + 222
0x00000001000cc497 in PyRun_AnyFileExFlags (in Python) + 119
0x00000001000dfc7b in Py_Main (in Python) + 3435
0x000000010000281f in from /Users/avanvliet/Library/Enthought/Canopy_64bit/User/Resources/Python.app/Contents/MacOS/Python
0x0000000100001f94 in from /Users/avanvliet/Library/Enthought/Canopy_64bit/User/Resources/Python.app/Contents/MacOS/Python
0x0000000000000001 in