Problem with installing

Ricardo · April 30, 2021, 2:22am

I have installed ROOT and Geant4 as requested.
However, after cmake, the output is:
– Source tarball build - no repository present.
– Building Allpix^2 version v1.6.0.
– Building “RelWithDebInfo”
– Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
– Could NOT find LATEX (missing: LATEX_COMPILER)
CMake Warning at doc/CMakeLists.txt:177 (MESSAGE):
No LaTeX found, cannot compile user manual.

– The CXX compiler identification is GNU 10.3.0
– Detecting CXX compiler ABI info
– Detecting CXX compiler ABI info - done
– Check for working CXX compiler: /usr/local/bin/c++ - skipped
– Detecting CXX compile features
– Detecting CXX compile features - done
– Performing Test CXX_FLAG_WORKS__pedantic
– Performing Test CXX_FLAG_WORKS__pedantic - Success
– Performing Test CXX_FLAG_WORKS__Wall
– Performing Test CXX_FLAG_WORKS__Wall - Success
– Performing Test CXX_FLAG_WORKS__Wextra
– Performing Test CXX_FLAG_WORKS__Wextra - Success
– Performing Test CXX_FLAG_WORKS__Wcast_align
– Performing Test CXX_FLAG_WORKS__Wcast_align - Success
– Performing Test CXX_FLAG_WORKS__Wcast_qual
– Performing Test CXX_FLAG_WORKS__Wcast_qual - Success
– Performing Test CXX_FLAG_WORKS__Wconversion
– Performing Test CXX_FLAG_WORKS__Wconversion - Success
– Performing Test CXX_FLAG_WORKS__Wuseless_cast
– Performing Test CXX_FLAG_WORKS__Wuseless_cast - Success
– Performing Test CXX_FLAG_WORKS__Wctor_dtor_privacy
– Performing Test CXX_FLAG_WORKS__Wctor_dtor_privacy - Success
– Performing Test CXX_FLAG_WORKS__Wzero_as_null_pointer_constant
– Performing Test CXX_FLAG_WORKS__Wzero_as_null_pointer_constant - Success
– Performing Test CXX_FLAG_WORKS__Wdisabled_optimization
– Performing Test CXX_FLAG_WORKS__Wdisabled_optimization - Success
– Performing Test CXX_FLAG_WORKS__WformatE2
– Performing Test CXX_FLAG_WORKS__WformatE2 - Success
– Performing Test CXX_FLAG_WORKS__Winit_self
– Performing Test CXX_FLAG_WORKS__Winit_self - Success
– Performing Test CXX_FLAG_WORKS__Wlogical_op
– Performing Test CXX_FLAG_WORKS__Wlogical_op - Success
– Performing Test CXX_FLAG_WORKS__Wmissing_declarations
– Performing Test CXX_FLAG_WORKS__Wmissing_declarations - Success
– Performing Test CXX_FLAG_WORKS__Wmissing_include_dirs
– Performing Test CXX_FLAG_WORKS__Wmissing_include_dirs - Success
– Performing Test CXX_FLAG_WORKS__Wnoexcept
– Performing Test CXX_FLAG_WORKS__Wnoexcept - Success
– Performing Test CXX_FLAG_WORKS__Wold_style_cast
– Performing Test CXX_FLAG_WORKS__Wold_style_cast - Success
– Performing Test CXX_FLAG_WORKS__Wredundant_decls
– Performing Test CXX_FLAG_WORKS__Wredundant_decls - Success
– Performing Test CXX_FLAG_WORKS__Wsign_conversion
– Performing Test CXX_FLAG_WORKS__Wsign_conversion - Success
– Performing Test CXX_FLAG_WORKS__Wsign_promo
– Performing Test CXX_FLAG_WORKS__Wsign_promo - Success
– Performing Test CXX_FLAG_WORKS__Wstrict_null_sentinel
– Performing Test CXX_FLAG_WORKS__Wstrict_null_sentinel - Success
– Performing Test CXX_FLAG_WORKS__Wstrict_overflowE5
– Performing Test CXX_FLAG_WORKS__Wstrict_overflowE5 - Success
– Performing Test CXX_FLAG_WORKS__Wswitch_default
– Performing Test CXX_FLAG_WORKS__Wswitch_default - Success
– Performing Test CXX_FLAG_WORKS__Wundef
– Performing Test CXX_FLAG_WORKS__Wundef - Success
– Performing Test CXX_FLAG_WORKS__Wshadow
– Performing Test CXX_FLAG_WORKS__Wshadow - Success
– Performing Test CXX_FLAG_WORKS__Wformat_security
– Performing Test CXX_FLAG_WORKS__Wformat_security - Success
– Performing Test CXX_FLAG_WORKS__Wdeprecated
– Performing Test CXX_FLAG_WORKS__Wdeprecated - Success
– Performing Test CXX_FLAG_WORKS__fdiagnostics_colorEauto
– Performing Test CXX_FLAG_WORKS__fdiagnostics_colorEauto - Success
– Performing Test CXX_FLAG_WORKS__Wheader_hygiene
– Performing Test CXX_FLAG_WORKS__Wheader_hygiene - Failed
– NOT adding -Wheader-hygiene to CXX_FLAGS - unsupported flag
– Performing Test CXX_FLAG_WORKS__Wno_overloaded_virtual
– Performing Test CXX_FLAG_WORKS__Wno_overloaded_virtual - Success
– Performing Test SUPPORT_STD_CXX17
– Performing Test SUPPORT_STD_CXX17 - Success
– Looking for C++ include pthread.h
– Looking for C++ include pthread.h - found
– Performing Test CMAKE_HAVE_LIBC_PTHREAD
– Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
– Looking for pthread_create in pthreads
– Looking for pthread_create in pthreads - not found
– Looking for pthread_create in pthread
– Looking for pthread_create in pthread - found
– Found Threads: TRUE
– Could NOT find clang-format
– Could NOT check for clang-tidy, wrong compiler: GNU
– Building module ON - CSADigitizer
– Building module ON - CapacitiveTransfer
– Building module ON - CorryvreckanWriter
– Building module OFF - DatabaseWriter
– Building module ON - DefaultDigitizer
– Building module ON - DepositionGeant4
– Found EXPAT: /usr/lib/x86_64-linux-gnu/libexpat.so (found suitable version “2.2.5”, minimum required is “2.2.5”)
– Check if compiler accepts -pthread
– Check if compiler accepts -pthread - yes
– Found XercesC: /usr/lib/x86_64-linux-gnu/libxerces-c.so (found suitable version “3.2.0”, minimum required is “3.2.0”)
– Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so
– Found X11: /usr/include
– Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
– Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
– Looking for gethostbyname
– Looking for gethostbyname - found
– Looking for connect
– Looking for connect - found
– Looking for remove
– Looking for remove - found
– Looking for shmat
– Looking for shmat - found
– Looking for IceConnectionNumber in ICE
– Looking for IceConnectionNumber in ICE - found
– Found Motif: /usr/lib/x86_64-linux-gnu/libXm.so
– Building module ON - DepositionPointCharge
– Building module ON - DepositionReader
– Building module ON - DetectorHistogrammer
– Building module ON - Dummy
– Building module ON - ElectricFieldReader
– Building module ON - GDMLOutputWriter
– Building module ON - GenericPropagation
– Building module ON - GeometryBuilderGeant4
– Building module ON - InducedTransfer
– Building module OFF - LCIOWriter
– Building module ON - MagneticFieldReader
– Building module ON - ProjectionPropagation
– Building module ON - PulseTransfer
– Building module ON - RCEWriter
– Building module ON - ROOTObjectReader
– Building module ON - ROOTObjectWriter
– Building module ON - SimpleTransfer
– Building module ON - TextWriter
– Building module ON - TransientPropagation
– Building module ON - VisualizationGeant4
– Building module ON - WeightingPotentialReader
– Unit tests: 15 examples
– Unit tests: 52 module functionality tests
– Unit tests: 4 performance tests
– Unit tests: 29 framework core functionality tests
– Configuring done
– Generating done
– Build files have been written to: /home/chtian/allpix-squared-v1.6.0/build

After make, there is a fatal error:
[ 6%] Building CXX object tools/apf_tools/CMakeFiles/field_converter.dir/FieldConverter.cpp.o
In file included from /home/chtian/allpix-squared-v1.6.0/tools/weightingpotential_generator/WeightingPotentialGenerator.cpp:7:
/home/chtian/allpix-squared-v1.6.0/src/core/geometry/DetectorModel.hpp:23:10: fatal error: Math/Point2D.h: No such file or directory
23 | #include <Math/Point2D.h>
| ^~~~~~~~~~~~~~~~
compilation terminated.
tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/build.make:75: recipe for target ‘tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/WeightingPotentialGenerator.cpp.o’ failed
make[2]: *** [tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/WeightingPotentialGenerator.cpp.o] Error 1
CMakeFiles/Makefile2:1764: recipe for target ‘tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/all’ failed
make[1]: *** [tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs…

Is there something wrong with my ROOT lib? It seems that it cannot find my ROOT lib

Ricardo · April 30, 2021, 3:00am

Then, I tried to install version 1.4.3
It is interesting that i can compile it successfully.
But, when i “make test”: there several example cannot pass:
The following tests FAILED:
20 - test_modules/test_03-13_deposition_fano.conf (Failed)
22 - test_modules/test_03-1_deposition.conf (Failed)
23 - test_modules/test_03-2_deposition_mc.conf (Failed)
24 - test_modules/test_03-3_deposition_track.conf (Failed)
25 - test_modules/test_03-4_deposition_source_point.conf (Failed)
26 - test_modules/test_03-5_deposition_source_square.conf (Failed)
27 - test_modules/test_03-6_deposition_source_sphere.conf (Failed)
28 - test_modules/test_03-7_deposition_source_macro.conf (Failed)
31 - test_modules/test_04-1_propagation_project.conf (Failed)
32 - test_modules/test_04-2_propagation_generic.conf (Failed)
33 - test_modules/test_04-3_propagation_generic-magnetic.conf (Failed)
34 - test_modules/test_04-4_propagation_project_integration.conf (Failed)
35 - test_modules/test_05-1_transfer_simple.conf (Failed)
36 - test_modules/test_05-2_transfer_simple_implant.conf (Failed)
37 - test_modules/test_06-1_digitization_charge.conf (Failed)
39 - test_modules/test_06-3_digitization_gain.conf (Failed)
41 - test_modules/test_08-1_writer_root.conf (Failed)
43 - test_modules/test_08-3_writer_lcio.conf (Failed)
45 - test_modules/test_08-5_writer_corryvreckan_mc.conf (Failed)
46 - test_modules/test_08-6_writer_text.conf (Failed)
47 - test_modules/test_08-7_writer_lcio_detector_assignment.conf (Failed)
48 - test_modules/test_08-8_writer_lcio_no_mc_truth.conf (Failed)
49 - test_modules/test_09-1_reader_root.conf (Failed)

simonspa · April 30, 2021, 3:02pm

Dear @Ricardo

thanks for reporting this issue - may I ask how you compile and how you source ROOT? And which version you are using? The issue you are describing in your first post looks to me like you were running make but did not actually install ROOT using make install but sourced the environment from its build folder. This is known to be problematic because some of the CMake targets are only generated in the install step. But maybe I’m wrong and it’s something else…?

The tests (at least in all version up to v1.6.2) are expected to fail on local machines because they depend on specific versions of the C++ STL implementation - if you want to have a longer read on this, I can recommend this merge request description and the linked blog post therein. This has been changes with the upcoming version 2.0, but for now the tests are only meant to run in the controlled environment if the CI - so nothing to worry about here!

All the best,
Simon

Ricardo · May 1, 2021, 2:52am

Dear Simon:
Thank you so much for your help. Actually, I have installed ROOT in the build directory before. The issue has been solved after using make install. Everything seems to be good.

Cheers