PyPartMC failing to build on Keeling #292

leeanne2 · 2023-09-27T21:17:46Z

leeanne2
Sep 27, 2023

(base) bash-4.2$ pip install PyPartMC
Collecting PyPartMC
  Using cached PyPartMC-0.6.3.tar.gz (2.2 MB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages (from PyPartMC) (1.25.2)
Building wheels for collected packages: PyPartMC
  Building wheel for PyPartMC (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [112 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-311
      creating build/lib.linux-x86_64-cpython-311/PyPartMC
      copying PyPartMC/__init__.py -> build/lib.linux-x86_64-cpython-311/PyPartMC
      running build_ext
      -- The C compiler identification is GNU 4.8.5
      -- The CXX compiler identification is GNU 4.8.5
      -- The Fortran compiler identification is GNU 4.8.5
      -- Check for working C compiler: /usr/bin/cc
      -- Check for working C compiler: /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: /usr/bin/c++
      -- Check for working CXX compiler: /usr/bin/c++ - works
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      -- Check for working Fortran compiler: /usr/bin/gfortran
      -- Check for working Fortran compiler: /usr/bin/gfortran - works
      -- Detecting Fortran compiler ABI info
      -- Detecting Fortran compiler ABI info - done
      -- Checking whether /usr/bin/gfortran supports Fortran 90
      -- Checking whether /usr/bin/gfortran supports Fortran 90 - yes
      -- Found PythonInterp: /data/keeling/a/leeanne2/miniconda3/bin/python (found version "3.11.4")
      Appending C RELEASE flags
      -- Added CVODE module
      -- Added SUNMATRIX_BAND module
      -- Added SUNMATRIX_DENSE module
      -- Added SUNMATRIX_SPARSE module
      -- Added SUNLINSOL_BAND module
      -- Added SUNLINSOL_DENSE module
      -- Added SUNLINSOL_PCG module
      -- Added SUNLINSOL_SPBCGS module
      -- Added SUNLINSOL_SPFGMR module
      -- Added SUNLINSOL_SPGMR module
      -- Added SUNLINSOL_SPTFQMR module
      -- Added SUNNONLINSOL_NEWTON module
      -- Added SUNNONLINSOL_FIXEDPOINT module
      -- Added NVECTOR_SERIAL module
      -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
      CMake Error in /tmp/pip-install-zth7vlih/pypartmc_45d09924a0544607a3bf3c26f1d37bdd/build/temp.linux-x86_64-cpython-311/_PyPartMC/CMakeFiles/CMakeTmp/CMakeLists.txt:
        Target "cmTC_76168" requires the language dialect "CXX17" , but CMake does
        not know the compile flags to use to enable it.
      
      
      CMake Error at /usr/share/cmake3/Modules/CheckCXXSourceCompiles.cmake:110 (try_compile):
        Failed to generate test project build system.
      Call Stack (most recent call first):
        /usr/share/cmake3/Modules/CheckCXXCompilerFlag.cmake:49 (check_cxx_source_compiles)
        /usr/share/cmake3/Modules/GenerateExportHeader.cmake:226 (check_cxx_compiler_flag)
        /usr/share/cmake3/Modules/GenerateExportHeader.cmake:407 (_test_compiler_hidden_visibility)
        gitmodules/sundials/src/sundials/CMakeLists.txt:102 (generate_export_header)
      
      
      -- Configuring incomplete, errors occurred!
      See also "/tmp/pip-install-zth7vlih/pypartmc_45d09924a0544607a3bf3c26f1d37bdd/build/temp.linux-x86_64-cpython-311/_PyPartMC/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-zth7vlih/pypartmc_45d09924a0544607a3bf3c26f1d37bdd/setup.py", line 125, in <module>
          setup(
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
          self.run_command(cmd)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 325, in run
          self.run_command("build")
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/command/build.py", line 33, in run
          super().run()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 84, in run
          _build_ext.run(self)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 346, in run
          self.build_extensions()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 466, in build_extensions
          self._build_extensions_serial()
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 492, in _build_extensions_serial
          self.build_extension(ext)
        File "/tmp/pip-install-zth7vlih/pypartmc_45d09924a0544607a3bf3c26f1d37bdd/setup.py", line 119, in build_extension
          subprocess.check_call(["cmake", ext.sourcedir] + cmake_args, cwd=build_temp)
        File "/data/keeling/a/leeanne2/miniconda3/lib/python3.11/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-zth7vlih/pypartmc_45d09924a0544607a3bf3c26f1d37bdd', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-zth7vlih/pypartmc_45d09924a0544607a3bf3c26f1d37bdd/build/lib.linux-x86_64-cpython-311/', '-DPYTHON_EXECUTABLE=/data/keeling/a/leeanne2/miniconda3/bin/python', '-DCMAKE_BUILD_TYPE=Release', '-DVERSION_INFO=0.6.3']' returned non-zero exit status 1.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for PyPartMC
  Running setup.py clean for PyPartMC
Failed to build PyPartMC
ERROR: Could not build wheels for PyPartMC, which is required to install pyproject.toml-based projects

leeanne2 · 2023-09-27T21:17:56Z

leeanne2
Sep 27, 2023
Author

:(

0 replies

slayoo · 2023-09-27T21:54:13Z

slayoo
Sep 27, 2023
Maintainer

Thank you for the report, @leeanne2 !

First, pip is not picking up the binary package, and tries to build from source. This seems to be caused by newer Python (3.11), if you try with Python 3.10, it should work with a binary package - without building. The reason is that the virtual machines we use for building for old glibc (in particular, for keeling) only support Python <=3.10.

Second, the compilation does not even start as CMake complains about being too old to know what C++17 is. The docs suggest that this will happen if your CMake is <= 3.8. Could you confirm if you CMake is indeed <=3.8 and try with a newer one?

I've just added a PR that should make the error message more understandable in such case: #285

Thanks!

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PyPartMC failing to build on Keeling #292

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PyPartMC failing to build on Keeling #292

leeanne2 Sep 27, 2023

Replies: 2 comments

leeanne2 Sep 27, 2023 Author

slayoo Sep 27, 2023 Maintainer

leeanne2
Sep 27, 2023

leeanne2
Sep 27, 2023
Author

slayoo
Sep 27, 2023
Maintainer