geromueller
commented
9 years ago Hi,
- you need to set the executable, not the include file for the -DPYTHON_EXECUTABLE flag:
-> WRONG! -DPYTHON_EXECUTABLE=/Applications/Canopy.app/appdata/canopy-1.5.5.3123.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h
-> Correct: -DPYTHON_EXECUTABLE=/Users/avanvliet/Library/Enthought/Canopy_64bit/User/bin/python
Try to set only the PYTHONEXECUTABLE, and not the other PYTHON flags.
Gero
Am 09.08.2015 um 20:13 schrieb avvliet:
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. 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[ 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 — Reply to this email directly or view it on GitHub <https://github.com/CRPropa/CRPropa3/issues/36>.
avvliet
rafaelab
adundovi
TobiasWinchen
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/mathutil.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);