Exception: This version of h5py requires HDF5 >= 1.10.6 (got version (1, 10, 4) from environment variable or library) #4200

time-less-ness · 2025-04-04T15:14:50Z

time-less-ness
Apr 4, 2025

Installing Firedrake on Ubuntu in AWS.

Linux hostname 5.15.0-1049-aws #54~20.04.1-Ubuntu SMP Fri Oct 6 22:04:33 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

I am doing

pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git#[test]"

And there seems to be no firedrake-install.log as mentioned in the reporting FAQ. I even searched for it and there are no results.

$ find . -name '*.log'
./petsc/configure.log
./petsc/make.log
./petsc/RDict.log
./petsc/arch-linux-c-debug/externalpackages/git.sowing/config.log
./petsc/arch-linux-c-debug/lib/petsc/conf/configure.log
./petsc/arch-linux-c-debug/lib/petsc/conf/make.log
./petsc/arch-linux-c-debug/lib/petsc/conf/gmake.log
./petsc/arch-linux-c-debug/lib/petsc/conf/error.log
./hdf5-1.10.6/config.log

But I'm guessing the results from the terminal while trying to install it would be informative.

(venv-firedrake) (base) ubuntu@ip-172-31-43-51:~$ pip install --no-binary h5py "firedrake @ git+https://github.com/firedrakeproject/firedrake.git#[test]"
DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
Collecting firedrake@ git+https://github.com/firedrakeproject/firedrake.git#[test]
  Cloning https://github.com/firedrakeproject/firedrake.git to /tmp/pip-install-zwk8gi5r/firedrake_a4e3c8fa7eb14b59b07dd0559a422215
  Running command git clone --filter=blob:none --quiet https://github.com/firedrakeproject/firedrake.git /tmp/pip-install-zwk8gi5r/firedrake_a4e3c8fa7eb14b59b07dd0559a422215
  Resolved https://github.com/firedrakeproject/firedrake.git to commit 73d63aa95d4a9f6a454254840b95367600434a5f
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting fenics-fiat@ git+https://github.com/firedrakeproject/fiat.git
  Cloning https://github.com/firedrakeproject/fiat.git to /tmp/pip-install-zwk8gi5r/fenics-fiat_972c7c86fa3445f29c53d1800e142762
  Running command git clone --filter=blob:none --quiet https://github.com/firedrakeproject/fiat.git /tmp/pip-install-zwk8gi5r/fenics-fiat_972c7c86fa3445f29c53d1800e142762
  Resolved https://github.com/firedrakeproject/fiat.git to commit 4ca4d68a378e60f706a87ee257e2d069372cc09e
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pyadjoint-ad@ git+https://github.com/dolfin-adjoint/pyadjoint.git
  Cloning https://github.com/dolfin-adjoint/pyadjoint.git to /tmp/pip-install-zwk8gi5r/pyadjoint-ad_3ac213c6647944cda772755da4a3822f
  Running command git clone --filter=blob:none --quiet https://github.com/dolfin-adjoint/pyadjoint.git /tmp/pip-install-zwk8gi5r/pyadjoint-ad_3ac213c6647944cda772755da4a3822f
  Resolved https://github.com/dolfin-adjoint/pyadjoint.git to commit 0b1348021fb3bc69504e3e7ec4f90f21ba1b3822
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting fenics-ufl@ git+https://github.com/firedrakeproject/ufl.git
  Cloning https://github.com/firedrakeproject/ufl.git to /tmp/pip-install-zwk8gi5r/fenics-ufl_5f499e3448824b92a1bdcd3e03318417
  Running command git clone --filter=blob:none --quiet https://github.com/firedrakeproject/ufl.git /tmp/pip-install-zwk8gi5r/fenics-ufl_5f499e3448824b92a1bdcd3e03318417
  Resolved https://github.com/firedrakeproject/ufl.git to commit 07d8a76efc1f8d6075fb33d8c55eff0b2999eaca
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting loopy@ git+https://github.com/firedrakeproject/loopy.git@main
  Cloning https://github.com/firedrakeproject/loopy.git (to revision main) to /tmp/pip-install-zwk8gi5r/loopy_5964135ff43f49daa2de831db058d079
  Running command git clone --filter=blob:none --quiet https://github.com/firedrakeproject/loopy.git /tmp/pip-install-zwk8gi5r/loopy_5964135ff43f49daa2de831db058d079
  Resolved https://github.com/firedrakeproject/loopy.git to commit 27aead574b5188de8e0d98518c93f1863951fc4b
  Running command git submodule update --init --recursive -q
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting mpi4py
  Using cached mpi4py-4.0.3-cp310-cp310-linux_x86_64.whl
Collecting libsupermesh
  Using cached libsupermesh-2025.3.0-cp310-cp310-linux_x86_64.whl
Collecting progress
  Using cached progress-1.6.tar.gz (7.8 kB)
  Preparing metadata (setup.py) ... done
Collecting petsc4py==3.22.2
  Using cached petsc4py-3.22.2-cp310-cp310-linux_x86_64.whl
Collecting decorator<=4.4.2
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting scipy
  Using cached scipy-1.15.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (37.6 MB)
Collecting packaging
  Using cached packaging-24.2-py3-none-any.whl (65 kB)
Collecting requests
  Using cached requests-2.32.3-py3-none-any.whl (64 kB)
Collecting rtree>=1.2
  Using cached rtree-1.4.0-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (541 kB)
Collecting sympy
  Using cached sympy-1.13.3-py3-none-any.whl (6.2 MB)
Collecting h5py>3.12.1
  Using cached h5py-3.13.0.tar.gz (414 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pytools[siphash]
  Using cached pytools-2025.1.2-py3-none-any.whl (92 kB)
Collecting pkgconfig
  Using cached pkgconfig-1.5.5-py3-none-any.whl (6.7 kB)
Collecting cachetools
  Using cached cachetools-5.5.2-py3-none-any.whl (10 kB)
Collecting pycparser
  Using cached pycparser-2.22-py3-none-any.whl (117 kB)
Collecting numpy
  Using cached numpy-2.2.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.4 MB)
Collecting pytest
  Using cached pytest-8.3.5-py3-none-any.whl (343 kB)
Collecting mpi-pytest
  Using cached mpi_pytest-2025.4.0-py3-none-any.whl (32 kB)
Collecting symengine
  Using cached symengine-0.14.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (50.3 MB)
Collecting recursivenodes
  Using cached recursivenodes-0.2.0-py3-none-any.whl (42 kB)
Collecting mako
  Using cached Mako-1.3.9-py3-none-any.whl (78 kB)
Collecting islpy>=2019.1
  Using cached islpy-2025.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.8 MB)
Collecting constantdict
  Using cached constantdict-2025.1.1-py3-none-any.whl (7.3 kB)
Collecting colorama
  Using cached colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting cgen>=2016.1
  Using cached cgen-2020.1.tar.gz (19 kB)
  Preparing metadata (setup.py) ... done
Collecting genpy>=2016.1.2
  Using cached genpy-2022.1.tar.gz (6.7 kB)
  Preparing metadata (setup.py) ... done
Collecting typing-extensions>=4
  Using cached typing_extensions-4.13.1-py3-none-any.whl (45 kB)
Collecting pymbolic>=2024.2.2
  Using cached pymbolic-2024.2.2-py3-none-any.whl (135 kB)
Collecting codepy>=2017.1
  Using cached codepy-2023.1.tar.gz (21 kB)
  Preparing metadata (setup.py) ... done
Collecting checkpoint_schedules
  Using cached checkpoint_schedules-1.0.4-py3-none-any.whl (41 kB)
Collecting pluggy<2,>=1.5
  Using cached pluggy-1.5.0-py3-none-any.whl (20 kB)
Collecting iniconfig
  Using cached iniconfig-2.1.0-py3-none-any.whl (6.0 kB)
Collecting exceptiongroup>=1.0.0rc8
  Using cached exceptiongroup-1.2.2-py3-none-any.whl (16 kB)
Collecting tomli>=1
  Using cached tomli-2.2.1-py3-none-any.whl (14 kB)
Collecting platformdirs>=2.2
  Using cached platformdirs-4.3.7-py3-none-any.whl (18 kB)
Collecting siphash24>=1.6
  Using cached siphash24-1.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (106 kB)
Collecting urllib3<3,>=1.21.1
  Using cached urllib3-2.3.0-py3-none-any.whl (128 kB)
Collecting charset-normalizer<4,>=2
  Using cached charset_normalizer-3.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (146 kB)
Collecting certifi>=2017.4.17
  Using cached certifi-2025.1.31-py3-none-any.whl (166 kB)
Collecting idna<4,>=2.5
  Using cached idna-3.10-py3-none-any.whl (70 kB)
Collecting mpmath<1.4,>=1.1.0
  Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)
Collecting immutabledict
  Using cached immutabledict-4.2.1-py3-none-any.whl (4.7 kB)
Collecting MarkupSafe>=0.9.2
  Using cached MarkupSafe-3.0.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB)
Building wheels for collected packages: h5py, fenics-fiat, fenics-ufl, firedrake, loopy, pyadjoint-ad
  Building wheel for h5py (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for h5py (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [179 lines of output]
      /tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
      !!

              ********************************************************************************
              Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

              By 2026-Feb-18, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        corresp(dist, value, root_dir)
      /tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!

              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:

              License :: OSI Approved :: BSD License

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        dist._finalize_license_expression()
      /tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!

              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:

              License :: OSI Approved :: BSD License

              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************

      !!
        self._finalize_license_expression()
      running bdist_wheel
      running build
      running build_py
      creating build/lib.linux-x86_64-cpython-310/h5py
      copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-cpython-310/h5py
      copying h5py/ipy_completer.py -> build/lib.linux-x86_64-cpython-310/h5py
      copying h5py/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py
      copying h5py/version.py -> build/lib.linux-x86_64-cpython-310/h5py
      creating build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/selections.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/compat.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/vds.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/group.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/base.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/files.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/filters.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      copying h5py/_hl/dims.py -> build/lib.linux-x86_64-cpython-310/h5py/_hl
      creating build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_big_endian_file.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_group.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_completions.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_file.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_attribute_create.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_dtype.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/common.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_base.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_errors.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5o.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_ros3.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5s.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_filters.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_file_alignment.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5z.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5pl.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_file_image.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/conftest.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_file2.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-cpython-310/h5py/tests
      creating build/lib.linux-x86_64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/data_files
      creating build/lib.linux-x86_64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/__init__.py -> build/lib.linux-x86_64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-x86_64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-x86_64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-x86_64-cpython-310/h5py/tests/data_files
      running build_ext
      Loading library to get build settings and version: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so
      ********************************************************************************
                             Summary of the h5py configuration

        HDF5 include dirs: [
        '/usr/include/openmpi'
        '/usr/include/hdf5/openmpi'
      ]
        HDF5 library dirs: [
        '/usr/lib/x86_64-linux-gnu/hdf5/openmpi'
        '/usr/lib/openmpi/lib'
      ]
             HDF5 Version: (1, 10, 4)
              MPI Enabled: True
         ROS3 VFD Enabled: False
       DIRECT VFD Enabled: False
         Rebuild Required: True
           MS-MPI Enabled: False
      MS-MPI include dirs: []
      MS-MPI library dirs: []

      ********************************************************************************
      Traceback (most recent call last):
        File "/home/ubuntu/venv-firedrake/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
          main()
        File "/home/ubuntu/venv-firedrake/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/ubuntu/venv-firedrake/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 249, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 438, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 426, in _build
          return self._build_with_temp_dir(
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
          self.run_setup()
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 70, in <module>
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1104, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
          self.run_command("build")
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
          self.distribution.run_command(command)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1104, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
          self.distribution.run_command(command)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1104, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-yiv0l_0m/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-zwk8gi5r/h5py_6a04b8a9c23e47ce9bc2419939c27ccd/setup_build.py", line 146, in run
          raise Exception(
      Exception: This version of h5py requires HDF5 >= 1.10.6 (got version (1, 10, 4) from environment variable or library)
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for h5py

  Building wheel for fenics-fiat (pyproject.toml) ... done
  Created wheel for fenics-fiat: filename=fenics_fiat-2024.0.0-py3-none-any.whl size=468903 sha256=5b467e545042100400b839b8c1eedd92b2a38b69b9d1cf60274c194b6d246707
  Stored in directory: /tmp/pip-ephem-wheel-cache-959pkq1y/wheels/78/1c/11/12139478e7e1eaf19d13a91e7cb6388a58a9429adc044f4f74
  Building wheel for fenics-ufl (pyproject.toml) ... done
  Created wheel for fenics-ufl: filename=fenics_ufl-2024.3.0.dev0-py3-none-any.whl size=251590 sha256=2bb212a053e5c2a9e463048542b89fadb47469cfc30c9a7294297867c5f07cdc
  Stored in directory: /tmp/pip-ephem-wheel-cache-959pkq1y/wheels/55/88/f5/2ae3baeca020844cf73dabe26166f5953d7a6b39b6e6995149
  Building wheel for firedrake (pyproject.toml) ... -^done
  Created wheel for firedrake: filename=firedrake-0.14.dev0-cp310-cp310-linux_x86_64.whl size=2750130 sha256=46c0dc1ba47a3b923ef51f37f17e31bf8bc9a82fd51ec21a78366f6ae1108234
  Stored in directory: /tmp/pip-ephem-wheel-cache-959pkq1y/wheels/af/1b/fd/376ad736e7885175a7593d72819acecae9f3c5dd8d7835c160
  Building wheel for loopy (pyproject.toml) ... done
  Created wheel for loopy: filename=loopy-2024.1-py3-none-any.whl size=529599 sha256=c64bb9e2060ad4c06aec8a65b4b167f0393587b07d9032258334f24dcd08e10d
  Stored in directory: /tmp/pip-ephem-wheel-cache-959pkq1y/wheels/55/df/ab/2b87d3f00d4a0dbb14516377f44208498cae4f7438246fa5ec
  Building wheel for pyadjoint-ad (pyproject.toml) ... done
  Created wheel for pyadjoint-ad: filename=pyadjoint_ad-2023.0.0-py3-none-any.whl size=66593 sha256=21d5e290ebe3f351cab59b5ea068f963e8a98335d1e0fbe1ae60e4c6049ccbe7
  Stored in directory: /tmp/pip-ephem-wheel-cache-959pkq1y/wheels/00/30/91/e7fa2c3a839e031928e65c46dca28f4713ebee1408ce6f91cf
Successfully built fenics-fiat fenics-ufl firedrake loopy pyadjoint-ad
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects

The PETSC log is quite large.
petsc-configure.log
Here's the make.log.
petsc-make.log

I have tried installing HDF5 but 1.10.4 is the latest the Ubuntu version supplies. So I tried installing 1.10.6 from source and removing the system package of 1.10.4, but this does not change the error at all.

I have searched for issues like this and found nothing yet. I will continue searching, but also appreciate any pointers if anyone has solved this.

Answered by dham

Apr 4, 2025

Alternatively, it appears that the Ubuntu 22.04 and 24.04 (the last two lts releases) have new enough hdf 5 versions. You are using 20.04 which is rather long in the tooth. You should be able to specify a newer Ubuntu to AWS.

View full answer

dham · 2025-04-04T15:25:58Z

dham
Apr 4, 2025
Maintainer

That seems to be an h5py issue rather than a Firedrake one. It appears that h5py increased their hdf5 version between 3.12 and 3.13: h5py/h5py@0b8e21e

If you only have 1.10.4 then you probably need to install h5py version 3.12.1 or earlier.

2 replies

dham Apr 4, 2025
Maintainer

Alternatively, it appears that the Ubuntu 22.04 and 24.04 (the last two lts releases) have new enough hdf 5 versions. You are using 20.04 which is rather long in the tooth. You should be able to specify a newer Ubuntu to AWS.

Answer selected by time-less-ness

time-less-ness Apr 4, 2025
Author

Thanks for the help! I'll start by trying Ubuntu 24.04.

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Exception: This version of h5py requires HDF5 >= 1.10.6 (got version (1, 10, 4) from environment variable or library) #4200

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