rafaelab
commented
3 years ago Hi! Could you paste here the error message of the tests that went wrong?
Closed MarcoChianese closed 7 months ago
rafaelab
commented
3 years ago Hi! Could you paste here the error message of the tests that went wrong?
rafaelab
commented
3 years ago If the error is a segfault when running testMagneticLensPythonInterface.py, this is because from Python >3.2 there was a function whose name changed.
If you replace line 63 self.assertEquals(len(self.maps.getParticleIds()), 1) by assertEqual, the test should run correctly. If this is the only problem, CRPropa should run just fine.
MarcoChianese
commented
3 years ago In which file can i find that line 63?
MarcoChianese
commented
3 years ago I have try to change the line in testMagneticLensPythonInterface.py, but I still get the error: Segmentation fault: 11
MarcoChianese
commented
3 years ago With make test I get:
Running tests... Test project /Users/Obimark/CRPropa3/build Start 1: testCore 1/20 Test #1: testCore .......................... Passed 0.03 sec Start 2: testVector3 2/20 Test #2: testVector3 ....................... Passed 0.01 sec Start 3: testModuleList 3/20 Test #3: testModuleList .................... Passed 0.01 sec Start 4: testMagneticField 4/20 Test #4: testMagneticField ................. Passed 0.01 sec Start 5: testTurbulentField 5/20 Test #5: testTurbulentField ................ Passed 0.18 sec Start 6: testAdvectionField 6/20 Test #6: testAdvectionField ................ Passed 0.01 sec Start 7: testDensity 7/20 Test #7: testDensity ....................... Passed 0.01 sec Start 8: testDINT 8/20 Test #8: testDINT .......................... Passed 0.02 sec Start 9: testPropagation 9/20 Test #9: testPropagation ................... Passed 0.01 sec Start 10: testBreakCondition 10/20 Test #10: testBreakCondition ................ Passed 0.01 sec Start 11: testInteraction 11/20 Test #11: testInteraction ................... Passed 19.47 sec Start 12: testSource 12/20 Test #12: testSource ........................ Passed 0.09 sec Start 13: testOutput 13/20 Test #13: testOutput ........................ Passed 0.03 sec Start 14: testFunctionalGroups 14/20 Test #14: testFunctionalGroups .............. Passed 0.01 sec Start 15: testAdiabaticCooling 15/20 Test #15: testAdiabaticCooling .............. Passed 0.01 sec Start 16: testGalacticMagneticLens 16/20 Test #16: testGalacticMagneticLens .......... Passed 0.05 sec Start 17: testMagneticLensPythonInterface 17/20 Test #17: testMagneticLensPythonInterface ...Exception: SegFault 0.07 sec Start 18: testSimulationExecution 18/20 Test #18: testSimulationExecution ...........Exception: SegFault 0.08 sec Start 19: testDiffusionSDE 19/20 Test #19: testDiffusionSDE ..................Exception: SegFault 0.17 sec Start 20: testPythonExtension 20/20 Test #20: testPythonExtension ...............Exception: SegFault 0.06 sec
80% tests passed, 4 tests failed out of 20
Total Test time (real) = 20.38 sec
The following tests FAILED: 17 - testMagneticLensPythonInterface (SEGFAULT) 18 - testSimulationExecution (SEGFAULT) 19 - testDiffusionSDE (SEGFAULT) 20 - testPythonExtension (SEGFAULT) Errors while running CTest make: *** [test] Error 8
MarcoChianese
commented
3 years ago The main problem is that when I import CRPropa in a jupyter notebook with from crpropa import * the kernel just dies. I think that this is related to the failures of those tests.
rafaelab
commented
3 years ago These errors cannot be fixed with what I told you. These are python-related.
What happens if you type: python -c "from crpropa import *"? What if instead of python you call the exact version you used for the installation (python3.7)?
I am also assuming that you are exporting the PYTHONPATH to the directory where crpropa.py is (normally CRPropa3/build/) when trying to use it from jupyter.
MarcoChianese
commented
3 years ago I get Segmentation fault: 11
rafaelab
commented
3 years ago I have tested a similar combination (but on OS X Catalina) with clang 11.0.3, python 3.7.2, swig 4.0.2. It works just fine. I will check the same clang version as yours later.
To troubleshoot this we'll have to check each individual dependency.
But before doing that, could you please try reinstalling CRPropa with -DENABLE_OPENMP=Off (when calling cmake .. [options]?
MarcoChianese
commented
3 years ago I have tried what you said, using the following flags for cmake:
CMAKE_PREFIX_PATH=$CRPROPA_DIR cmake -DCMAKE_INSTALL_PREFIX=$CRPROPA_DIR \ -DPYTHON_EXECUTABLE=/anaconda3/bin/python \ -DPYTHON_LIBRARY=/anaconda3/pkgs/python-3.7.2-haf84260_0/lib/libpython3.7m.dylib \ -DENABLE_PYTHON=ON \ -DENABLE_OPENMP=OFF \ ..
but it does still not work. All the python-related tests fail for segfault. I attached below the outputs of cmake, make, make install and otool -L _crpropa.so to check the dependencies. It seems that crpropa uses python v3.7.0 while I think am actually using v3.7.2. As you can see in the attached files, I think I've correctly used the flag to point towards the correct python library but it does not fix the issue.
Finally, at the very end there's the output of gdb to testMagneticLensPythonInterface.py with segfault.
cmake
-- The Fortran compiler identification is GNU 8.2.0 -- The C compiler identification is AppleClang 10.0.1.10010046 -- The CXX compiler identification is AppleClang 10.0.1.10010046 -- 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: /Library/Developer/CommandLineTools/usr/bin/cc -- Check for working C compiler: /Library/Developer/CommandLineTools/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: /Library/Developer/CommandLineTools/usr/bin/c++ -- Check for working CXX compiler: /Library/Developer/CommandLineTools/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: 3.1.6-602-g1aad73b4 1aad73b4c2ee6e7005f43dd33695ee6c943b9241 refs/heads/master -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
Using provided EIGEN -- Google perftools: Found! -- Include: /usr/local/include -- FFTW3 with single precision (FFTW3F): Found! -- Include: /usr/local/include -- Library: /usr/local/lib/libfftw3f.a -- Quimby: NOT Found! -- Include: QUIMBY_INCLUDE_DIR-NOTFOUND -- Library: QUIMBY_LIBRARY-NOTFOUND -- SAGA: NOT Found! -- Include: SAGA_INCLUDE_DIR-NOTFOUND -- Library: SAGA_LIBRARY-NOTFOUND -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- muParser: Found! -- Include: /usr/local/Cellar/muparser/2.3.2_2/include -- Library: /usr/local/Cellar/muparser/2.3.2_2/lib/libmuparser.dylib -- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.11") -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /anaconda3/lib/libhdf5.dylib;/usr/lib/libpthread.dylib;/anaconda3/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (found version "1.10.2") found components: C -- Downloading data file from crpropa.desy.de ~ 50 MB -- Extracting data file -- Found PythonInterp: /anaconda3/bin/python (found version "3.7.2") -- Found PythonLibs: /anaconda3/pkgs/python-3.7.2-haf84260_0/lib/libpython3.7m.dylib (found version "3.7.2") -- Found SWIG: /usr/local/bin/swig (found suitable version "4.0.2", minimum required is "3.0") -- Using user provided Python library: /anaconda3/pkgs/python-3.7.2-haf84260_0/lib/libpython3.7m.dylib -- Python: Found! -- Version: 3.7/37 -- Executeable: /anaconda3/bin/python -- Include: /anaconda3/include/python3.7m -- Library: /anaconda3/pkgs/python-3.7.2-haf84260_0/lib/libpython3.7m.dylib -- Site-package directory: lib/python3.7/site-packages -- Found numpy headers in /anaconda3/lib/python3.7/site-packages/numpy/core/include -- Sphinx not found: cannot build documentation -- Configuring done -- Generating done -- Build files have been written to: /Users/Obimark/CRPropa3/build
make
lukasmerten
tdwiser
ke-fang
reichherzerp
adundovi
QuinFin
JulienDoerner
Dear developers,
I have problems installing CRPropa on my system since the tests 17,18,19,20 related to python provides SegFault. I have followed the installing instructions and read few similar threads, though I am still struggling with this issue. I have mac OS Mojave 10.14, python version 3.7.4 through anaconda, swig version 4.0.2, cmake version 3.17.0.
This is the output of cmake:
Could you please help me? Let me know what else you need.