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pip install amuse-framework fails on Alma Linux 9 (CentOS) #1091

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aatrani opened this issue Nov 5, 2024 · 5 comments
Open

pip install amuse-framework fails on Alma Linux 9 (CentOS) #1091

aatrani opened this issue Nov 5, 2024 · 5 comments
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@aatrani
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aatrani commented Nov 5, 2024 •
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I recently had to switch to an old laptop because of a hardware failure.

I tried reinstalling amuse on Alma Linux (formely CentOS, free equivalment of RHEL9), but I can't get around this error.

I am on Python 3.9.18. I also tried installing different versions of setuptools, to no avail.

Defaulting to user installation because normal site-packages is not writeable
Collecting amuse-framework
  Using cached amuse_framework-2024.6.0.tar.gz (679 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [82 lines of output]
      WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
      Traceback (most recent call last):
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject
          section = defn.get("tool", {})[tool_name]
      KeyError: 'setuptools_scm'
      running dist_info
      creating /tmp/pip-modern-metadata-koi7l6lp/amuse_framework.egg-info
      writing /tmp/pip-modern-metadata-koi7l6lp/amuse_framework.egg-info/PKG-INFO
      writing dependency_links to /tmp/pip-modern-metadata-koi7l6lp/amuse_framework.egg-info/dependency_links.txt
      writing requirements to /tmp/pip-modern-metadata-koi7l6lp/amuse_framework.egg-info/requires.txt
      writing top-level names to /tmp/pip-modern-metadata-koi7l6lp/amuse_framework.egg-info/top_level.txt
      writing manifest file '/tmp/pip-modern-metadata-koi7l6lp/amuse_framework.egg-info/SOURCES.txt'
      INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']'
      Traceback (most recent call last):
        File "/home/lex/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/lex/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/lex/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 376, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 521, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 319, in run_setup
          exec(code, locals())
        File "<string>", line 49, in <module>
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 183, in setup
          return run_commands(dist)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/dist_info.py", line 93, in run
          self.egg_info.run()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 312, in run
          self.find_sources()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 320, in find_sources
          mm.run()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 541, in run
          self.add_defaults()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 579, in add_defaults
          sdist.add_defaults(self)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 110, in add_defaults
          self._add_defaults_build_sub_commands()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 130, in _add_defaults_build_sub_commands
          self.filelist.extend(chain.from_iterable(files))
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 484, in extend
          self.files.extend(filter(self._safe_path, paths))
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 129, in <genexpr>
          files = (c.get_source_files() for c in cmds if hasattr(c, "get_source_files"))
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 128, in <genexpr>
          cmds = (self.get_finalized_command(c) for c in missing_cmds)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 303, in get_finalized_command
          cmd_obj.ensure_finalized()
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 111, in ensure_finalized
          self.finalize_options()
        File "/tmp/pip-install-_kwi4_ih/amuse-framework_e6190ba8b8794f429b6ee2adf4322878/support/setup_codes.py", line 814, in finalize_options
          CodeCommand.finalize_options(self)
        File "/tmp/pip-install-_kwi4_ih/amuse-framework_e6190ba8b8794f429b6ee2adf4322878/support/setup_codes.py", line 284, in finalize_options
          self.set_fortran_variables()
        File "/tmp/pip-install-_kwi4_ih/amuse-framework_e6190ba8b8794f429b6ee2adf4322878/support/setup_codes.py", line 360, in set_fortran_variables
          compiler = fcompiler.new_fcompiler(requiref90=True)
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib64/python3.9/site-packages/numpy/distutils/fcompiler/__init__.py", line 892, in new_fcompiler
          compiler = get_default_fcompiler(plat, requiref90=requiref90,
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib64/python3.9/site-packages/numpy/distutils/fcompiler/__init__.py", line 863, in get_default_fcompiler
          compiler_type =  _find_existing_fcompiler(matching_compiler_types,
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib64/python3.9/site-packages/numpy/distutils/fcompiler/__init__.py", line 807, in _find_existing_fcompiler
          from numpy.distutils.core import get_distribution
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib64/python3.9/site-packages/numpy/distutils/core.py", line 24, in <module>
          from numpy.distutils.command import config, config_compiler, \
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib64/python3.9/site-packages/numpy/distutils/command/config.py", line 19, in <module>
          from numpy.distutils.mingw32ccompiler import generate_manifest
        File "/tmp/pip-build-env-ics9_i8y/overlay/lib64/python3.9/site-packages/numpy/distutils/mingw32ccompiler.py", line 27, in <module>
          from distutils.msvccompiler import get_build_version as get_build_msvc_version
      ModuleNotFoundError: No module named 'distutils.msvccompiler'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
@aatrani aatrani added the bug label Nov 5, 2024
@aatrani aatrani changed the title Can pip install amuse-framework fails on Alma Linux 9 (CentOS) Nov 5, 2024
@rieder
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rieder commented Nov 5, 2024

Could you add which version of setuptools you are using?

@aatrani
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aatrani commented Nov 5, 2024

Could you add which version of setuptools you are using?

setuptools.version
'75.3.0'

@rieder
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rieder commented Nov 5, 2024

Could you try installing an older setuptools (< 65)?

@aatrani
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aatrani commented Nov 5, 2024

No luck with setuptools 64

lex@tpx1c:~/Work/tsunami/nospinbuild/python (master)$ pip install "setuptools<65"
Defaulting to user installation because normal site-packages is not writeable
Collecting setuptools<65
  Using cached setuptools-64.0.3-py3-none-any.whl.metadata (6.2 kB)
Using cached setuptools-64.0.3-py3-none-any.whl (1.2 MB)
Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 75.3.0
    Uninstalling setuptools-75.3.0:
      Successfully uninstalled setuptools-75.3.0
Successfully installed setuptools-64.0.3
lex@tpx1c:~/Work/tsunami/nospinbuild/python (master)$ pip install amuse-framework
Defaulting to user installation because normal site-packages is not writeable
Collecting amuse-framework
  Using cached amuse_framework-2024.6.0.tar.gz (679 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [82 lines of output]
      WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
      Traceback (most recent call last):
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject
          section = defn.get("tool", {})[tool_name]
      KeyError: 'setuptools_scm'
      running dist_info
      creating /tmp/pip-modern-metadata-3uxm0oct/amuse_framework.egg-info
      writing /tmp/pip-modern-metadata-3uxm0oct/amuse_framework.egg-info/PKG-INFO
      writing dependency_links to /tmp/pip-modern-metadata-3uxm0oct/amuse_framework.egg-info/dependency_links.txt
      writing requirements to /tmp/pip-modern-metadata-3uxm0oct/amuse_framework.egg-info/requires.txt
      writing top-level names to /tmp/pip-modern-metadata-3uxm0oct/amuse_framework.egg-info/top_level.txt
      writing manifest file '/tmp/pip-modern-metadata-3uxm0oct/amuse_framework.egg-info/SOURCES.txt'
      INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']'
      Traceback (most recent call last):
        File "/home/lex/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/lex/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/lex/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 376, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 521, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 319, in run_setup
          exec(code, locals())
        File "<string>", line 49, in <module>
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 183, in setup
          return run_commands(dist)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/dist_info.py", line 93, in run
          self.egg_info.run()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 312, in run
          self.find_sources()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 320, in find_sources
          mm.run()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 541, in run
          self.add_defaults()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 579, in add_defaults
          sdist.add_defaults(self)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 110, in add_defaults
          self._add_defaults_build_sub_commands()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 130, in _add_defaults_build_sub_commands
          self.filelist.extend(chain.from_iterable(files))
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py", line 484, in extend
          self.files.extend(filter(self._safe_path, paths))
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 129, in <genexpr>
          files = (c.get_source_files() for c in cmds if hasattr(c, "get_source_files"))
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py", line 128, in <genexpr>
          cmds = (self.get_finalized_command(c) for c in missing_cmds)
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 303, in get_finalized_command
          cmd_obj.ensure_finalized()
        File "/tmp/pip-build-env-faz87xem/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 111, in ensure_finalized
          self.finalize_options()
        File "/tmp/pip-install-diwv_qvd/amuse-framework_adb4c22a479b4bc5a89fd7ae3cc057d1/support/setup_codes.py", line 814, in finalize_options
          CodeCommand.finalize_options(self)
        File "/tmp/pip-install-diwv_qvd/amuse-framework_adb4c22a479b4bc5a89fd7ae3cc057d1/support/setup_codes.py", line 284, in finalize_options
          self.set_fortran_variables()
        File "/tmp/pip-install-diwv_qvd/amuse-framework_adb4c22a479b4bc5a89fd7ae3cc057d1/support/setup_codes.py", line 360, in set_fortran_variables
          compiler = fcompiler.new_fcompiler(requiref90=True)
        File "/tmp/pip-build-env-faz87xem/overlay/lib64/python3.9/site-packages/numpy/distutils/fcompiler/__init__.py", line 892, in new_fcompiler
          compiler = get_default_fcompiler(plat, requiref90=requiref90,
        File "/tmp/pip-build-env-faz87xem/overlay/lib64/python3.9/site-packages/numpy/distutils/fcompiler/__init__.py", line 863, in get_default_fcompiler
          compiler_type =  _find_existing_fcompiler(matching_compiler_types,
        File "/tmp/pip-build-env-faz87xem/overlay/lib64/python3.9/site-packages/numpy/distutils/fcompiler/__init__.py", line 807, in _find_existing_fcompiler
          from numpy.distutils.core import get_distribution
        File "/tmp/pip-build-env-faz87xem/overlay/lib64/python3.9/site-packages/numpy/distutils/core.py", line 24, in <module>
          from numpy.distutils.command import config, config_compiler, \
        File "/tmp/pip-build-env-faz87xem/overlay/lib64/python3.9/site-packages/numpy/distutils/command/config.py", line 19, in <module>
          from numpy.distutils.mingw32ccompiler import generate_manifest
        File "/tmp/pip-build-env-faz87xem/overlay/lib64/python3.9/site-packages/numpy/distutils/mingw32ccompiler.py", line 27, in <module>
          from distutils.msvccompiler import get_build_version as get_build_msvc_version
      ModuleNotFoundError: No module named 'distutils.msvccompiler'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

@LourensVeen
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I think you may need a newer version of NumPy here. At any rate, installing AMUSE via the instructions on the website is unfortunately broken. We're working on a brand new installer that doesn't use distutils or any of the other old Python packaging stuff, but it's not quite there yet.

I've recently made some alternative installation instructions for an AMUSE course in Leiden. Perhaps you could give them a try instead?

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@rieder @LourensVeen @aatrani