Error at installation

[madalina-phys]

My installation gets the following error when running pip install --no-binary h5py 'firedrake[check]':

pip install --no-binary h5py 'firedrake[check]'
Collecting firedrake[check]
Using cached firedrake-2025.4.0.tar.gz (1.7 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [24 lines of output]
Traceback (most recent call last):
File "/home/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/home/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/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/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-hd1j76h2/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-hd1j76h2/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-hd1j76h2/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 317, in run_setup
exec(code, locals())
File "", line 286, in
File "", line 275, in make_firedrake_check_package
File "/usr/lib/python3.12/shutil.py", line 435, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/lib/python3.12/shutil.py", line 260, in copyfile
with open(src, 'rb') as fsrc:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'Makefile'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

The installation procedure was followed step-by-step.
I am running on Ubuntu 24. Can somebody help me debug? Thank you!

[connorjward]

Ahh. Looks like the PyPI package doesn't work properly (we released it for the first time yesterday). I will fix that tomorrow but for now you can avoid this by running

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

[madalina-phys]

Thank you! It works now!

[madalina-phys]

Hi! I encountered an error when writing .h5 files (see below)
Is it related to the installation error that I mentioned in this thread?
What should I do to fix the problem?

Thank you!

========================================================================================================

Saving checkpoint for restart at t=0.0100 to Files/checkpoint__trials4_flow_A.h5

Traceback (most recent call last):

  File "/home/madalinaphys/Documents/STRASSE_LH2_Simulation/Thermosiphon_2D/simulation.py", line 399, in

    with CheckpointFile(save_path, 'w') as chk:

         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/site-packages/firedrake/checkpointing.py", line 538, in init

    self.set_attr_byte_string("/", "dmplex_storage_version", version)

  File "/home/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/site-packages/firedrake/checkpointing.py", line 1700, in set_attr_byte_string

    grp = self.require_group(path)

          ^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/site-packages/firedrake/checkpointing.py", line 1780, in require_group

    _self = self.h5pyfile

            ^^^^^^^^^^^^^

  File "/home/madalinaphys/Software/Firedrake/venv-firedrake/lib/python3.12/site-packages/firedrake/checkpointing.py", line 1653, in h5pyfile

    self._h5pyfile = h5i.get_h5py_file(self.viewer)

                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "firedrake/cython/hdf5interface.pyx", line 35, in firedrake.cython.hdf5interface.get_h5py_file

  File "h5py/h5i.pyx", line 34, in h5py.h5i.wrap_identifier

  File "h5py/h5i.pyx", line 39, in h5py.h5i.wrap_identifier

  File "h5py/defs.pyx", line 1222, in h5py.defs.H5Iget_type

RuntimeError: Unspecified error in H5Iget_type (return value <0)

[dham]

Doesn't look immediately obviously related. Please open a new discussion providing a minimal failing example.