Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

pip install from source fails due to internal compiler error with gcc 13.2.0 (only on x86-64) #1665

Open
BenWibking opened this issue Aug 28, 2024 · 1 comment
Open

pip install from source fails due to internal compiler error with gcc 13.2.0 (only on x86-64) #1665

BenWibking opened this issue Aug 28, 2024 · 1 comment
Labels
install

Comments

@BenWibking
Copy link

Performed steps
Building this Dockerfile (https://github.com/parthenon-hpc-lab/parthenon/blob/ebe3f9bc020073aa262045233b1c17ce04a2d759/scripts/docker/Dockerfile.nvcc) with

docker build --file Dockerfile.nvcc --tag parthenon-hpc-lab/new-ci-image --platform linux/amd64 .

led to the following output/problem during install

15.80 Building wheels for collected packages: openpmd-api, mpi4py
15.80   Building wheel for openpmd-api (pyproject.toml): started
87.63   Building wheel for openpmd-api (pyproject.toml): still running...
148.0   Building wheel for openpmd-api (pyproject.toml): still running...
208.6   Building wheel for openpmd-api (pyproject.toml): still running...
237.0   Building wheel for openpmd-api (pyproject.toml): finished with status 'error'
237.0   error: subprocess-exited-with-error
237.0
237.0   × Building wheel for openpmd-api (pyproject.toml) did not run successfully.
237.0   │ exit code: 1
237.0   ╰─> [241 lines of output]
237.0       running bdist_wheel
237.0       running build
237.0       running build_ext
237.0       <string>:28: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
237.0       -- The C compiler identification is GNU 13.2.0
237.0       -- The CXX compiler identification is GNU 13.2.0
237.0       -- Detecting C compiler ABI info
237.0       -- Detecting C compiler ABI info - done
237.0       -- Check for working C compiler: /usr/bin/cc - skipped
237.0       -- Detecting C compile features
237.0       -- Detecting C compile features - done
237.0       -- Detecting CXX compiler ABI info
237.0       -- Detecting CXX compiler ABI info - done
237.0       -- Check for working CXX compiler: /usr/bin/c++ - skipped
237.0       -- Detecting CXX compile features
237.0       -- Detecting CXX compile features - done
237.0       -- Found MPI_CXX: /opt/openmpi/lib/libmpi.so (found version "3.1")
237.0       -- Found MPI: TRUE (found version "3.1") found components: CXX
237.0       CMake Deprecation Warning at share/openPMD/thirdParty/json/CMakeLists.txt:1 (cmake_minimum_required):
237.0         Compatibility with CMake < 3.5 will be removed from a future version of
237.0         CMake.
237.0
237.0         Update the VERSION argument <min> value or use a ...<max> suffix to tell
237.0         CMake that the project does not need compatibility with older versions.
237.0
237.0
237.0       -- Using the single-header code from /tmp/pip-install-ta16014x/openpmd-api_9c05105b422c4f5fab8485e5103983fa/share/openPMD/thirdParty/json/single_include/
237.0       -- nlohmann-json: Using INTERNAL version '3.9.1'
237.0       CMake Deprecation Warning at share/openPMD/thirdParty/toml11/CMakeLists.txt:1 (cmake_minimum_required):
237.0         Compatibility with CMake < 3.5 will be removed from a future version of
237.0         CMake.
237.0
237.0         Update the VERSION argument <min> value or use a ...<max> suffix to tell
237.0         CMake that the project does not need compatibility with older versions.
237.0
237.0
237.0       -- toml11: Using INTERNAL version '3.7.1'
237.0       -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
237.0       CMake Deprecation Warning at share/openPMD/cmake/FindADIOS.cmake:91 (cmake_minimum_required):
237.0         Compatibility with CMake < 3.5 will be removed from a future version of
237.0         CMake.
237.0
237.0         Update the VERSION argument <min> value or use a ...<max> suffix to tell
237.0         CMake that the project does not need compatibility with older versions.
237.0       Call Stack (most recent call first):
237.0         CMakeLists.txt:384 (find_package)
237.0
237.0
237.0       -- Found MPI_C: /opt/openmpi/lib/libmpi.so (found version "3.1")
237.0       -- Found MPI: TRUE (found version "3.1")
237.0       -- Found ADIOS2: /usr/local/lib/cmake/adios2/adios2-config.cmake (found suitable version "2.10.0.393", minimum required is "2.7.0") found components: C CXX MPI
237.0       -- Found Python: /usr/bin/python3 (found version "3.12.3") found components: Interpreter Development.Module
237.0       CMake Deprecation Warning at share/openPMD/thirdParty/pybind11/CMakeLists.txt:8 (cmake_minimum_required):
237.0         Compatibility with CMake < 3.5 will be removed from a future version of
237.0         CMake.
237.0
237.0         Update the VERSION argument <min> value or use a ...<max> suffix to tell
237.0         CMake that the project does not need compatibility with older versions.
237.0
237.0
237.0       -- pybind11 v2.10.1
237.0       -- Performing Test HAS_FLTO
237.0       -- Performing Test HAS_FLTO - Success
237.0       -- pybind11: Using INTERNAL version 2.10.1
237.0       -- Python LTO/IPO: ON
237.0
237.0       openPMD build configuration:
237.0         library Version: 0.15.2
237.0         openPMD Standard: 1.1.0
237.0         C++ Compiler: GNU 13.2.0
237.0           /usr/bin/c++
237.0
237.0         Install with RPATHs: ON
237.0         Installation prefix: /usr/local
237.0               bin: bin
237.0               lib: lib
237.0           include: include
237.0             cmake: lib/cmake/openPMD
237.0            python: lib/python3.12/site-packages
237.0
237.0         Build Type: Release
237.0         Library: static
237.0         CLI Tools: OFF
237.0         Examples: OFF
237.0         Testing: OFF
237.0         Invasive Tests: OFF
237.0         Internal VERIFY: ON
237.0         Build Options:
237.0           MPI: ON
237.0           HDF5: OFF
237.0           ADIOS1: OFF
237.0           ADIOS2: ON
237.0           PYTHON: ON
237.0           CUDA_EXAMPLES: OFF
237.0
237.0       -- Configuring done (6.3s)
237.0       -- Generating done (0.0s)
237.0       -- Build files have been written to: /tmp/pip-install-ta16014x/openpmd-api_9c05105b422c4f5fab8485e5103983fa/build/temp.linux-x86_64-cpython-312
237.0       [  1%] Building CXX object CMakeFiles/openPMD.dir/src/config.cpp.o
237.0       [  2%] Building CXX object CMakeFiles/openPMD.dir/src/ChunkInfo.cpp.o
237.0       [  4%] Building CXX object CMakeFiles/openPMD.dir/src/Dataset.cpp.o
237.0       [  5%] Building CXX object CMakeFiles/openPMD.dir/src/Datatype.cpp.o
237.0       [  6%] Building CXX object CMakeFiles/openPMD.dir/src/Error.cpp.o
237.0       [  8%] Building CXX object CMakeFiles/openPMD.dir/src/Format.cpp.o
237.0       [  9%] Building CXX object CMakeFiles/openPMD.dir/src/Iteration.cpp.o
237.0       [ 10%] Building CXX object CMakeFiles/openPMD.dir/src/IterationEncoding.cpp.o
237.0       [ 12%] Building CXX object CMakeFiles/openPMD.dir/src/Mesh.cpp.o
237.0       [ 13%] Building CXX object CMakeFiles/openPMD.dir/src/ParticlePatches.cpp.o
237.0       [ 15%] Building CXX object CMakeFiles/openPMD.dir/src/ParticleSpecies.cpp.o
237.0       [ 16%] Building CXX object CMakeFiles/openPMD.dir/src/ReadIterations.cpp.o
237.0       [ 17%] Building CXX object CMakeFiles/openPMD.dir/src/Record.cpp.o
237.0       [ 19%] Building CXX object CMakeFiles/openPMD.dir/src/RecordComponent.cpp.o
237.0       [ 20%] Building CXX object CMakeFiles/openPMD.dir/src/Series.cpp.o
237.0       [ 21%] Building CXX object CMakeFiles/openPMD.dir/src/version.cpp.o
237.0       [ 23%] Building CXX object CMakeFiles/openPMD.dir/src/WriteIterations.cpp.o
237.0       [ 24%] Building CXX object CMakeFiles/openPMD.dir/src/auxiliary/Date.cpp.o
237.0       [ 26%] Building CXX object CMakeFiles/openPMD.dir/src/auxiliary/Filesystem.cpp.o
237.0       [ 27%] Building CXX object CMakeFiles/openPMD.dir/src/auxiliary/JSON.cpp.o
237.0       [ 28%] Building CXX object CMakeFiles/openPMD.dir/src/backend/Attributable.cpp.o
237.0       [ 30%] Building CXX object CMakeFiles/openPMD.dir/src/backend/BaseRecordComponent.cpp.o
237.0       [ 31%] Building CXX object CMakeFiles/openPMD.dir/src/backend/Container.cpp.o
237.0       [ 32%] Building CXX object CMakeFiles/openPMD.dir/src/backend/MeshRecordComponent.cpp.o
237.0       [ 34%] Building CXX object CMakeFiles/openPMD.dir/src/backend/PatchRecord.cpp.o
237.0       [ 35%] Building CXX object CMakeFiles/openPMD.dir/src/backend/PatchRecordComponent.cpp.o
237.0       [ 36%] Building CXX object CMakeFiles/openPMD.dir/src/backend/Writable.cpp.o
237.0       [ 38%] Building CXX object CMakeFiles/openPMD.dir/src/benchmark/mpi/OneDimensionalBlockSlicer.cpp.o
237.0       [ 39%] Building CXX object CMakeFiles/openPMD.dir/src/helper/list_series.cpp.o
237.0       [ 41%] Building CXX object CMakeFiles/openPMD.dir/src/IO/AbstractIOHandler.cpp.o
237.0       [ 42%] Building CXX object CMakeFiles/openPMD.dir/src/IO/AbstractIOHandlerImpl.cpp.o
237.0       [ 43%] Building CXX object CMakeFiles/openPMD.dir/src/IO/AbstractIOHandlerHelper.cpp.o
237.0       [ 45%] Building CXX object CMakeFiles/openPMD.dir/src/IO/DummyIOHandler.cpp.o
237.0       [ 46%] Building CXX object CMakeFiles/openPMD.dir/src/IO/IOTask.cpp.o
237.0       [ 47%] Building CXX object CMakeFiles/openPMD.dir/src/IO/FlushParams.cpp.o
237.0       [ 49%] Building CXX object CMakeFiles/openPMD.dir/src/IO/HDF5/HDF5IOHandler.cpp.o
237.0       [ 50%] Building CXX object CMakeFiles/openPMD.dir/src/IO/HDF5/ParallelHDF5IOHandler.cpp.o
237.0       [ 52%] Building CXX object CMakeFiles/openPMD.dir/src/IO/HDF5/HDF5Auxiliary.cpp.o
237.0       [ 53%] Building CXX object CMakeFiles/openPMD.dir/src/IO/JSON/JSONIOHandler.cpp.o
237.0       [ 54%] Building CXX object CMakeFiles/openPMD.dir/src/IO/JSON/JSONIOHandlerImpl.cpp.o
237.0       [ 56%] Building CXX object CMakeFiles/openPMD.dir/src/IO/JSON/JSONFilePosition.cpp.o
237.0       [ 57%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/ADIOS2IOHandler.cpp.o
237.0       [ 58%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/ADIOS2Auxiliary.cpp.o
237.0       [ 60%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/ADIOS2PreloadAttributes.cpp.o
237.0       [ 61%] Building CXX object CMakeFiles/openPMD.dir/src/IO/InvalidatableFile.cpp.o
237.0       [ 63%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/CommonADIOS1IOHandler.cpp.o
237.0       [ 64%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/ADIOS1IOHandler.cpp.o
237.0       [ 65%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/ParallelADIOS1IOHandler.cpp.o
237.0       [ 67%] Linking CXX static library lib/libopenPMD.a
237.0       [ 67%] Built target openPMD
237.0       [ 68%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/openPMD.cpp.o
237.0       [ 69%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Access.cpp.o
237.0       [ 71%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Attributable.cpp.o
237.0       [ 72%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/BaseRecord.cpp.o
237.0       [ 73%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/BaseRecordComponent.cpp.o
237.0       [ 75%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/ChunkInfo.cpp.o
237.0       [ 76%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Container.cpp.o
237.0       [ 78%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Dataset.cpp.o
237.0       [ 79%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Datatype.cpp.o
237.0       [ 80%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Error.cpp.o
237.0       [ 82%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Helper.cpp.o
237.0       [ 83%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Iteration.cpp.o
237.0       [ 84%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/IterationEncoding.cpp.o
237.0       [ 86%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Mesh.cpp.o
237.0       [ 87%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/ParticlePatches.cpp.o
237.0       [ 89%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/ParticleSpecies.cpp.o
237.0       [ 90%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/PatchRecord.cpp.o
237.0       [ 91%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/PatchRecordComponent.cpp.o
237.0       [ 93%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Record.cpp.o
237.0       [ 94%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/RecordComponent.cpp.o
237.0       [ 95%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/MeshRecordComponent.cpp.o
237.0       [ 97%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/Series.cpp.o
237.0       [ 98%] Building CXX object CMakeFiles/openPMD.py.dir/src/binding/python/UnitDimension.cpp.o
237.0       [100%] Linking CXX shared module /tmp/pip-install-ta16014x/openpmd-api_9c05105b422c4f5fab8485e5103983fa/build/lib.linux-x86_64-cpython-312/openpmd_api/openpmd_api_cxx.cpython-312-x86_64-linux-gnu.so
237.0       lto1: internal compiler error: in return_token, at opts-common.cc:2135
237.0       0x19bb73a internal_error(char const*, ...)
237.0           ???:0
237.0       0x683a32 fancy_abort(char const*, int, char const*)
237.0           ???:0
237.0       0x6ba314 lto_main()
237.0           ???:0
237.0       Please submit a full bug report, with preprocessed source (by using -freport-bug).
237.0       Please include the complete backtrace with any bug report.
237.0       See <file:///usr/share/doc/gcc-13/README.Bugs> for instructions.
237.0       lto-wrapper: fatal error: /usr/bin/c++ returned 1 exit status
237.0       compilation terminated.
237.0       /usr/bin/ld: error: lto-wrapper failed
237.0       collect2: error: ld returned 1 exit status
237.0       gmake[2]: *** [CMakeFiles/openPMD.py.dir/build.make:453: /tmp/pip-install-ta16014x/openpmd-api_9c05105b422c4f5fab8485e5103983fa/build/lib.linux-x86_64-cpython-312/openpmd_api/openpmd_api_cxx.cpython-312-x86_64-linux-gnu.so] Error 1
237.0       gmake[1]: *** [CMakeFiles/Makefile2:920: CMakeFiles/openPMD.py.dir/all] Error 2
237.0       gmake: *** [Makefile:146: all] Error 2
237.0       Traceback (most recent call last):
237.0         File "/usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
237.0           main()
237.0         File "/usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
237.0           json_out['return_val'] = hook(**hook_input['kwargs'])
237.0                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
237.0         File "/usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
237.0           return _build_backend().build_wheel(wheel_directory, config_settings,
237.0                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 421, in build_wheel
237.0           return self._build_with_temp_dir(
237.0                  ^^^^^^^^^^^^^^^^^^^^^^^^^^
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 403, in _build_with_temp_dir
237.0           self.run_setup()
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/build_meta.py", line 318, in run_setup
237.0           exec(code, locals())
237.0         File "<string>", line 170, in <module>
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/__init__.py", line 117, in setup
237.0           return distutils.core.setup(**attrs)
237.0                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/core.py", line 184, in setup
237.0           return run_commands(dist)
237.0                  ^^^^^^^^^^^^^^^^^^
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/core.py", line 200, in run_commands
237.0           dist.run_commands()
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/dist.py", line 953, in run_commands
237.0           self.run_command(cmd)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/dist.py", line 950, in run_command
237.0           super().run_command(command)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/dist.py", line 972, in run_command
237.0           cmd_obj.run()
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/command/bdist_wheel.py", line 384, in run
237.0           self.run_command("build")
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/cmd.py", line 316, in run_command
237.0           self.distribution.run_command(command)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/dist.py", line 950, in run_command
237.0           super().run_command(command)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/dist.py", line 972, in run_command
237.0           cmd_obj.run()
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/command/build.py", line 135, in run
237.0           self.run_command(cmd_name)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/cmd.py", line 316, in run_command
237.0           self.distribution.run_command(command)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/dist.py", line 950, in run_command
237.0           super().run_command(command)
237.0         File "/tmp/pip-build-env-al2hbpy9/overlay/local/lib/python3.12/dist-packages/setuptools/_distutils/dist.py", line 972, in run_command
237.0           cmd_obj.run()
237.0         File "<string>", line 36, in run
237.0         File "<string>", line 115, in build_extension
237.0         File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
237.0           raise CalledProcessError(retcode, cmd)
237.0       subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
237.0       [end of output]
237.0
237.0   note: This error originates from a subprocess, and is likely not a problem with pip.
237.0   ERROR: Failed building wheel for openpmd-api

You can also add images such as screenshots :-)

System environment

  • operating system: Ubuntu 24.04 (see Dockerfile)
  • machine: Docker VM
  • name and version of Python implementation: see Dockerfile

Additional context
MPI is enabled in the Dockerfile:
https://github.com/parthenon-hpc-lab/parthenon/blob/ebe3f9bc020073aa262045233b1c17ce04a2d759/scripts/docker/Dockerfile.nvcc#L48
@BenWibking
Copy link
Author

Strangely, building the Dockerfile on arm64 works perfectly fine:

docker build --file Dockerfile.nvcc --tag parthenon-hpc-lab/new-ci-image --platform linux/arm64 .

@BenWibking BenWibking mentioned this issue Aug 28, 2024
Draft
12 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
install
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@BenWibking