Installation error - Mac OS Sonoma

hchu · May 4, 2024, 12:05am

While trying to install on Mac OS Sonoma, I met the error while building (‘make’ command)

clang-13: error: **linker command failed with exit code 1 (use -v to see invocation)

I am installing it inside anaconda environment that I created, and below are the basic information for installation.
Clang version 13.0.1
Target x86_64-apple-darwin23.4.0
Thread model: posix
cmake version 3.29.2

For better explanation, I attach the full output I get when I compile and build.
Is there any other solutions suggested regarding this issue?

(allpixsq) hyeyeunchu@anps-MBP allpix-sq-build % cmake /Users/hyeyeunchu/allpix-squared
CMake Warning (dev) at cmake/tools.cmake:18 (EXEC_PROGRAM):
  Policy CMP0153 is not set: The exec_program command should not be called.
  Run "cmake --help-policy CMP0153" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Use execute_process() instead.
Call Stack (most recent call first):
  CMakeLists.txt:30 (GET_VERSION)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at cmake/tools.cmake:29 (EXEC_PROGRAM):
  Policy CMP0153 is not set: The exec_program command should not be called.
  Run "cmake --help-policy CMP0153" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Use execute_process() instead.
Call Stack (most recent call first):
  CMakeLists.txt:30 (GET_VERSION)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Git project directory is dirty:
 fatal: not a git repository (or any of the parent directories): .git.
-- Building Allpix^2 version v3.0.0-350-g4fa539bea-dirty.
-- Building "RelWithDebInfo"
-- Installing to "/Users/hyeyeunchu/allpix-squared"
-- Unit tests: 20 examples
-- Found Python: /opt/anaconda3/envs/allpixsq/bin/python3.10 (found version "3.10.8") found components: Interpreter
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
-- Could NOT find Doxybook2 (missing: DOXYBOOK2_EXECUTABLE) 
-- Could NOT find Pandoc (missing: PANDOC_EXECUTABLE) 
-- Could NOT find Latexmk (missing: LATEXMK_EXECUTABLE) 
-- Could NOT find Lualatex (missing: LUALATEX_EXECUTABLE) 
-- Could NOT find Biber (missing: BIBER_EXECUTABLE) 
-- Found Pygmentize: /opt/anaconda3/envs/allpixsq/bin/pygmentize (found version "2.17.2")
-- The CXX compiler identification is Clang 13.0.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/anaconda3/envs/allpixsq/bin/x86_64-apple-darwin13.4.0-clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The C compiler identification is Clang 13.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/anaconda3/envs/allpixsq/bin/x86_64-apple-darwin13.4.0-clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Found nlohmann_json: /opt/anaconda3/envs/allpixsq/lib/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found suitable version "3.10.5", minimum required is "3.10.5")
-- 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 - Failed
-- NOT adding -Wuseless-cast to CXX_FLAGS - unsupported flag
-- 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 - Failed
-- NOT adding -Wlogical-op to CXX_FLAGS - unsupported flag
-- 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 - Failed
-- NOT adding -Wnoexcept to CXX_FLAGS - unsupported flag
-- 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 - Failed
-- NOT adding -Wstrict-null-sentinel to CXX_FLAGS - unsupported flag
-- 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 - Success
-- 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
-- Performing Test SUPPORT_STD_CXX20
-- Performing Test SUPPORT_STD_CXX20 - Success
-- Building against C++ version 17
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found Boost: /opt/anaconda3/envs/allpixsq/lib/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.64.0") found components: random
CMake Warning at cmake/clang-cpp-checks.cmake:23 (MESSAGE):
  Git hooks are not installed - consider installing them via
  /Users/hyeyeunchu/allpix-squared/etc/git-hooks/install-hooks.sh
Call Stack (most recent call first):
  CMakeLists.txt:374 (INCLUDE)


-- Could NOT find clang-format
-- Could NOT find clang-tidy version 12
-- Building module ON	- CSADigitizer
-- Building module ON	- CapacitiveTransfer
-- Checking for module 'eigen3'
--   Found eigen3, version 3.4.0
-- Building module ON	- CorryvreckanWriter
-- Building module OFF	- DatabaseWriter
-- Building module ON	- DefaultDigitizer
-- Building module ON	- DepositionCosmics
-- Found EXPAT: /opt/anaconda3/envs/allpixsq/lib/libexpat.dylib (found suitable version "2.6.2", minimum required is "2.2.5")
-- Found ZLIB: /opt/anaconda3/envs/allpixsq/lib/libz.dylib (found suitable version "1.2.13", minimum required is "1.2.13")
-- Found XercesC: /opt/anaconda3/envs/allpixsq/lib/libxerces-c.dylib (found suitable version "3.2.4", minimum required is "3.2.4")
-- Found Freetype: /opt/anaconda3/envs/allpixsq/lib/libfreetype.dylib (found suitable version "2.12.1", minimum required is "2.12.1")
-- Found OpenGL: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks/OpenGL.framework
-- Found Geant4: /opt/anaconda3/envs/allpixsq/lib/Geant4-11.0.3/Geant4Config.cmake (found version "11.0.3")
-- Building module ON	- DepositionGeant4
CMake Warning (dev) at src/modules/DepositionGeant4/CMakeLists.txt:30 (EXEC_PROGRAM):
  Policy CMP0153 is not set: The exec_program command should not be called.
  Run "cmake --help-policy CMP0153" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Use execute_process() instead.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at src/modules/DepositionGeant4/CMakeLists.txt:31 (EXEC_PROGRAM):
  Policy CMP0153 is not set: The exec_program command should not be called.
  Run "cmake --help-policy CMP0153" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Use execute_process() instead.
This warning is for project developers.  Use -Wno-dev to suppress it.

--   Found Geant4 Examples, building add. physics lists
--   Found MicroElectronics physics lists
-- Building module ON	- DepositionGenerator
--   HepMC3 not found, not building HepMC3 interface
-- Building module ON	- DepositionLaser
-- Building module ON	- DepositionPointCharge
-- Building module ON	- DepositionReader
-- Building module ON	- DetectorHistogrammer
-- Building module ON	- DopingProfileReader
-- 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
-- Building Geant4 Interface
-- Unit tests: 74 framework core functionality tests
-- Unit tests: 170 module functionality tests
-- Modules without functionality tests:
--    Dummy
--    GDMLOutputWriter
--    InducedTransfer
--    VisualizationGeant4
-- Unit tests: 5 performance tests
-- Configuring done (19.3s)
-- Generating done (0.9s)
-- Build files have been written to: /Users/hyeyeunchu/allpix-sq-build

(allpixsq) hyeyeunchu@anps-MBP allpix-sq-build % make -j16
[  2%] Generating AllpixObjectsDictionary.cxx, libAllpixObjects_rdict.pcm, libAllpixObjects.rootmap
[  2%] Generating CorryvreckanWriterObjectsDictionary.cxx, libCorryvreckanWriterObjects_rdict.pcm, libCorryvreckanWriterObjects.rootmap
[  2%] Generating /Users/hyeyeunchu/allpix-sq-build/src/modules/DepositionCosmics/data/cosmics_2100.data
[  2%] Generating /Users/hyeyeunchu/allpix-sq-build/src/modules/DepositionCosmics/data/cosmics_0.data
[  3%] Generating /Users/hyeyeunchu/allpix-sq-build/src/modules/DepositionCosmics/data/cosmics_11300.data
[  3%] Building CXX object tools/apf_tools/CMakeFiles/field_converter.dir/__/__/src/core/utils/log.cpp.o
[  4%] Building CXX object tools/apf_tools/CMakeFiles/field_converter.dir/FieldConverter.cpp.o
[  4%] Building CXX object tools/apf_tools/CMakeFiles/field_converter.dir/__/__/src/core/utils/text.cpp.o
[  5%] Building CXX object tools/apf_tools/CMakeFiles/field_converter.dir/__/__/src/core/utils/unit.cpp.o
[  6%] Building CXX object tools/apf_tools/CMakeFiles/apf_dump.dir/DumpHeader.cpp.o
[  6%] Building CXX object tools/apf_tools/CMakeFiles/apf_dump.dir/__/__/src/core/utils/log.cpp.o
[  7%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/WeightingPotentialGenerator.cpp.o
[  8%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/MeshElement.cpp.o
[  9%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_plotter.dir/MeshPlotter.cpp.o
[  9%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/MeshConverter.cpp.o
[ 10%] Building CXX object tools/apf_tools/CMakeFiles/apf_dump.dir/__/__/src/core/utils/text.cpp.o
-- Fetching "file:///eos/project-a/allpix-squared/www/data/MD5/87a94f46c8d982980ed942fe9d370a87"
-- Fetching "file:///eos/project-a/allpix-squared/www/data/MD5/43350bc1295828e1740a27fbac7faf65"
-- Fetching "file:///eos/project-a/allpix-squared/www/data/MD5/0dd6bb7024725d4cb8448aea49caddc9"
-- Fetching "https://project-allpix-squared.web.cern.ch/data/MD5/87a94f46c8d982980ed942fe9d370a87"
-- Fetching "https://project-allpix-squared.web.cern.ch/data/MD5/43350bc1295828e1740a27fbac7faf65"
-- Fetching "https://project-allpix-squared.web.cern.ch/data/MD5/0dd6bb7024725d4cb8448aea49caddc9"
-- [download 0% complete]
-- [download 0% complete]
-- [download 0% complete]
-- [download 1% complete]
-- [download 1% complete]
-- [download 1% complete]
-- [download 2% complete]
-- [download 2% complete]
-- [download 3% complete]
-- [download 2% complete]
-- [download 3% complete]
-- [download 3% complete]
-- [download 4% complete]
-- [download 5% complete]
-- [download 6% complete]
-- [download 4% complete]
-- [download 5% complete]
-- [download 6% complete]
-- [download 4% complete]
-- [download 5% complete]
-- [download 6% complete]
-- [download 7% complete]
-- [download 7% complete]
-- [download 7% complete]
-- [download 8% complete]
-- [download 10% complete]
-- [download 11% complete]
-- [download 12% complete]
-- [download 13% complete]
-- [download 8% complete]
-- [download 9% complete]
-- [download 10% complete]
-- [download 11% complete]
-- [download 12% complete]
-- [download 13% complete]
-- [download 14% complete]
-- [download 15% complete]
-- [download 8% complete]
-- [download 9% complete]
-- [download 10% complete]
-- [download 11% complete]
-- [download 12% complete]
-- [download 14% complete]
-- [download 13% complete]
-- [download 14% complete]
-- [download 15% complete]
-- [download 16% complete]
-- [download 17% complete]
-- [download 18% complete]
-- [download 19% complete]
-- [download 20% complete]
-- [download 21% complete]
-- [download 22% complete]
-- [download 23% complete]
-- [download 24% complete]
-- [download 25% complete]
-- [download 26% complete]
-- [download 16% complete]
-- [download 18% complete]
-- [download 19% complete]
-- [download 20% complete]
-- [download 21% complete]
-- [download 22% complete]
-- [download 23% complete]
-- [download 24% complete]
-- [download 25% complete]
-- [download 26% complete]
-- [download 27% complete]
-- [download 28% complete]
-- [download 29% complete]
-- [download 30% complete]
-- [download 31% complete]
-- [download 16% complete]
-- [download 32% complete]
-- [download 17% complete]
-- [download 18% complete]
-- [download 27% complete]
-- [download 19% complete]
-- [download 28% complete]
-- [download 20% complete]
-- [download 21% complete]
-- [download 22% complete]
-- [download 23% complete]
-- [download 24% complete]
-- [download 25% complete]
-- [download 26% complete]
-- [download 27% complete]
[ 10%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/utils/log.cpp.o
-- [download 28% complete]
-- [download 29% complete]
-- [download 29% complete]
-- [download 30% complete]
[ 10%] Building CXX object tools/apf_tools/CMakeFiles/apf_dump.dir/__/__/src/core/utils/unit.cpp.o
-- [download 31% complete]
-- [download 32% complete]
-- [download 33% complete]
-- [download 34% complete]
-- [download 35% complete]
-- [download 36% complete]
-- [download 37% complete]
-- [download 38% complete]
-- [download 39% complete]
-- [download 40% complete]
-- [download 41% complete]
-- [download 42% complete]
-- [download 43% complete]
-- [download 44% complete]
-- [download 46% complete]
-- [download 47% complete]
-- [download 48% complete]
-- [download 49% complete]
-- [download 50% complete]
-- [download 51% complete]
-- [download 33% complete]
-- [download 34% complete]
-- [download 35% complete]
-- [download 36% complete]
-- [download 38% complete]
-- [download 39% complete]
-- [download 40% complete]
-- [download 41% complete]
-- [download 42% complete]
-- [download 43% complete]
-- [download 44% complete]
-- [download 45% complete]
-- [download 46% complete]
-- [download 47% complete]
-- [download 48% complete]
-- [download 49% complete]
-- [download 50% complete]
-- [download 51% complete]
-- [download 52% complete]
-- [download 53% complete]
-- [download 30% complete]
-- [download 31% complete]
-- [download 33% complete]
-- [download 52% complete]
-- [download 34% complete]
-- [download 35% complete]
-- [download 36% complete]
-- [download 53% complete]
-- [download 54% complete]
-- [download 55% complete]
-- [download 37% complete]
-- [download 38% complete]
-- [download 39% complete]
-- [download 40% complete]
-- [download 41% complete]
-- [download 42% complete]
-- [download 43% complete]
-- [download 44% complete]
-- [download 45% complete]
-- [download 46% complete]
-- [download 47% complete]
-- [download 48% complete]
-- [download 49% complete]
-- [download 50% complete]
-- [download 56% complete]
-- [download 57% complete]
-- [download 58% complete]
-- [download 59% complete]
-- [download 60% complete]
-- [download 61% complete]
-- [download 62% complete]
-- [download 63% complete]
-- [download 64% complete]
-- [download 65% complete]
-- [download 66% complete]
-- [download 67% complete]
-- [download 68% complete]
-- [download 51% complete]
-- [download 52% complete]
-- [download 53% complete]
-- [download 54% complete]
-- [download 69% complete]
-- [download 70% complete]
-- [download 71% complete]
-- [download 72% complete]
-- [download 73% complete]
-- [download 74% complete]
-- [download 75% complete]
-- [download 76% complete]
-- [download 77% complete]
-- [download 78% complete]
-- [download 80% complete]
-- [download 81% complete]
-- [download 82% complete]
-- [download 83% complete]
-- [download 84% complete]
-- [download 54% complete]
-- [download 55% complete]
-- [download 56% complete]
-- [download 57% complete]
-- [download 58% complete]
-- [download 59% complete]
-- [download 60% complete]
-- [download 61% complete]
-- [download 62% complete]
-- [download 63% complete]
-- [download 64% complete]
-- [download 65% complete]
-- [download 66% complete]
-- [download 67% complete]
-- [download 68% complete]
-- [download 69% complete]
-- [download 70% complete]
-- [download 71% complete]
-- [download 72% complete]
-- [download 73% complete]
-- [download 74% complete]
-- [download 75% complete]
-- [download 76% complete]
-- [download 77% complete]
-- [download 78% complete]
-- [download 79% complete]
-- [download 80% complete]
-- [download 81% complete]
-- [download 82% complete]
-- [download 84% complete]
-- [download 85% complete]
-- [download 86% complete]
-- [download 87% complete]
-- [download 88% complete]
-- [download 89% complete]
-- [download 90% complete]
-- [download 91% complete]
-- [download 92% complete]
-- [download 93% complete]
-- [download 94% complete]
-- [download 95% complete]
-- [download 96% complete]
-- [download 55% complete]
-- [download 56% complete]
-- [download 57% complete]
-- [download 87% complete]
-- [download 88% complete]
-- [download 89% complete]
-- [download 90% complete]
-- [download 91% complete]
-- [download 92% complete]
-- [download 93% complete]
-- [download 94% complete]
-- [download 96% complete]
[ 11%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/MeshParser.cpp.o
-- [download 97% complete]
-- [download 100% complete]
-- [download 98% complete]
-- [download 99% complete]
-- [download 100% complete]
-- Downloaded object: "/Users/hyeyeunchu/allpix-sq-build/ExternalData/Objects/MD5/43350bc1295828e1740a27fbac7faf65"
[ 12%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/utils/text.cpp.o
-- Downloaded object: "/Users/hyeyeunchu/allpix-sq-build/ExternalData/Objects/MD5/0dd6bb7024725d4cb8448aea49caddc9"
-- [download 97% complete]
-- [download 98% complete]
-- [download 99% complete]
-- [download 100% complete]
[ 12%] Building CXX object src/objects/CMakeFiles/AllpixObjectsDictionary.dir/AllpixObjectsDictionary.cxx.o
-- Downloaded object: "/Users/hyeyeunchu/allpix-sq-build/ExternalData/Objects/MD5/87a94f46c8d982980ed942fe9d370a87"
[ 12%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/parsers/DFISEParser.cpp.o
[ 12%] Building CXX object src/modules/CorryvreckanWriter/CMakeFiles/CorryvreckanWriterObjects.dir/corryvreckan/Object.cpp.o
[ 12%] Built target fetch_cry_data
[ 12%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_plotter.dir/__/__/src/core/utils/log.cpp.o
[ 12%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/utils/unit.cpp.o
[ 13%] Building CXX object src/modules/CorryvreckanWriter/CMakeFiles/CorryvreckanWriterObjects.dir/corryvreckan/Pixel.cpp.o
[ 14%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_plotter.dir/__/__/src/core/utils/text.cpp.o
[ 15%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/parsers/SilvacoParser.cpp.o
[ 15%] Building CXX object src/modules/CorryvreckanWriter/CMakeFiles/CorryvreckanWriterObjects.dir/corryvreckan/Event.cpp.o
[ 15%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/utils/log.cpp.o
[ 16%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/config/ConfigReader.cpp.o
[ 17%] Linking CXX executable apf_dump
[ 17%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_plotter.dir/__/__/src/core/utils/unit.cpp.o
[ 17%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/utils/text.cpp.o
[ 17%] Built target apf_dump
[ 18%] Building CXX object src/modules/CorryvreckanWriter/CMakeFiles/CorryvreckanWriterObjects.dir/CorryvreckanWriterObjectsDictionary.cxx.o
[ 18%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/config/Configuration.cpp.o
[ 18%] Linking CXX executable field_converter
[ 19%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/config/exceptions.cpp.o
[ 19%] Built target field_converter
[ 20%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/utils/unit.cpp.o
[ 20%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/geometry/DetectorModel.cpp.o
[ 20%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/config/ConfigReader.cpp.o
[ 20%] Built target AllpixObjectsDictionary
[ 20%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/geometry/PixelDetectorModel.cpp.o
[ 20%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/Object.cpp.o
[ 21%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/geometry/HexagonalPixelDetectorModel.cpp.o
[ 22%] Linking CXX executable mesh_plotter
[ 22%] Built target mesh_plotter
[ 23%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/config/Configuration.cpp.o
[ 23%] Linking CXX shared library libCorryvreckanWriterObjects.dylib
ld: unknown option: --no-undefined
clang-13: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/modules/CorryvreckanWriter/libCorryvreckanWriterObjects.dylib] Error 1
make[1]: *** [src/modules/CorryvreckanWriter/CMakeFiles/CorryvreckanWriterObjects.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 24%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/Pixel.cpp.o
[ 24%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/config/exceptions.cpp.o
[ 25%] Building CXX object tools/mesh_converter/CMakeFiles/mesh_converter.dir/__/__/src/core/module/ThreadPool.cpp.o
[ 25%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/SensorCharge.cpp.o
[ 25%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/geometry/RadialStripDetectorModel.cpp.o
[ 26%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/Pulse.cpp.o
[ 26%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/PixelCharge.cpp.o
[ 27%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/DepositedCharge.cpp.o
[ 28%] Building CXX object tools/weightingpotential_generator/CMakeFiles/generate_potential.dir/__/__/src/core/module/ThreadPool.cpp.o
[ 28%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/PropagatedCharge.cpp.o
[ 29%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/PixelHit.cpp.o
[ 29%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/PixelPulse.cpp.o
[ 30%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/MCParticle.cpp.o
[ 30%] Building CXX object src/objects/CMakeFiles/AllpixObjects.dir/MCTrack.cpp.o
[ 30%] Linking CXX executable mesh_converter
[ 30%] Linking CXX shared library libAllpixObjects.dylib
ld: unknown option: --no-undefined
clang-13: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/objects/libAllpixObjects.dylib] Error 1
make[1]: *** [src/objects/CMakeFiles/AllpixObjects.dir/all] Error 2
[ 30%] Built target mesh_converter
[ 30%] Linking CXX executable generate_potential
[ 30%] Built target generate_potential
make: *** [all] Error 2

simonspa · May 6, 2024, 3:51pm

Hi @hchu

could you try to see if it works when deleting --no-undefined from the file cmake/compiler-flag-checks.cmake (Line 32 inside the check for AppleClang)?

/Simon

rheller · May 7, 2024, 6:31pm

Thanks Simon.
Swapping --no-undefined for the AppleClang equivalent was enough to get it all to compile. We have been using OSX systems, but with Clang from conda / miniforge. Oddly enough, though that Clang accepts/rejects flags as if it were AppleClang, it self-identifies as regular Clang based on CMAKE_CXX_COMPILER_ID, so it ends up with incompatible flags after the checks in cmake/compiler-flag-checks.cmake.
Anyway Hyeyeun and I are able to run Allpix now without problems after the adjusting that file.

Best,
Ryan Heller (met you at BTTB Lecce )

simonspa · May 8, 2024, 4:40am

Hi @rheller, nice to hear from you!

That’s indeed interesting - is there any way you can squeeze out from your Clang that it in fact is an AppleClang derivative or poses as such? I’d then amend the compiler checks so the right version is picked in your scenario.

Best,
Simon

rheller · May 8, 2024, 11:47pm

Hmm, as a Clang novice, I was able to figure out a couple options that work for our environments, but not sure how well they generalize.

Right now, cmake/compiler-flag-checks.cmake is checking CMAKE_CXX_COMPILER_ID to detect apple (and for us, this gives simply Clang instead of AppleClang.)
We can also check CMAKE_CXX_COMPILER, and for both Hyeyeun and I, this gives a string containing “apple”, e.g. arm64-apple-darwin20.0.0-clang++. So you could add another condition to L31 like IF(CMAKE_CXX_COMPILER MATCHES "apple") to capture this case.

However, I noticed I have another version of the clang executable from Conda that is simply named Clang for both CXX_COMPILER and CXX_COMPILER_ID, AND despite this, it still requires the Apple version of this flag. To catch this one inside cmake, they only way I found was to check CMAKE_SYSTEM_NAME STREQUAL "Darwin". This is just checking that the OS is based on Darwin (= MacOS). It’s possible that this condition is too general—maybe someone has a Clang that behaves like Linux but runs on Apple (though that kind of user can maybe figure this out themselves).

simonspa · May 13, 2024, 2:44pm

Hi @rheller

does this work for you?

Best,
Simon

rheller · May 13, 2024, 6:02pm

Hi @simonspa,

Oops, I realized I gave you bad advice. The new check works, but it is also still passing the original check for regular clang, so it ends up with both the linux and the apple flags.

This works for me to make the two checks exclusive:

IF((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") OR (CMAKE_SYSTEM_NAME STREQUAL "Darwin"))
    SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Wl,-undefined,error")
ELSEIF((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))
    SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Wl,--no-undefined")
ENDIF()

(Sorry, my gitlab.cern.ch account is not active now, or I would make a pull request.)

simonspa · May 13, 2024, 6:47pm

If you like, you can open a PR over at our GitHub repo!

GitHub - allpix-squared/allpix-squared

rheller · May 14, 2024, 6:21pm

Great, I made a PR at github.