Error when writing h5 file

[madalina-phys]

I get an error when trying to write .h5 files.
Please see below an example of code and the error that I get.
Thank you!

Example of code:

# test_save.py
from firedrake import *
import os
import traceback

filename = f"test_checkpoint_save.h5"

mesh = UnitSquareMesh(10, 10)
V = FunctionSpace(mesh, "P", 1)
f = Function(V, name="my_function")
f.interpolate(SpatialCoordinate(mesh)[0])

print(f"Attempting to save to {filename}...")

try:
    with CheckpointFile(filename, 'w') as chk:
        chk.save_function(f)
    print(f"SUCCESS: Checkpoint file saved.")
except Exception as e:
    print(f"ERROR: Failed to save checkpoint file.")
    traceback.print_exc()

---

Error:

python3 test_save.py 
Attempting to save to test_checkpoint_save.h5...
ERROR: Failed to save checkpoint file.
Traceback (most recent call last):
  File "/home/madalinaphys/Documents/STRASSE_LH2_Simulation/Thermosiphon_2D/test_save.py", line 16, in <module>
    with CheckpointFile(filename, '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)

---

[connorjward]

There is clearly something wrong with your HDF5/h5py. How recent was your installation? What OS are you installing with?

[madalina-phys]

My Firedrake installation was done on 30.04.2025.
It all went well/normal except for the issue reported in the Discussion "Error at installation #4273". After following your instructions back then, the installation was completed.
I am running on Ubuntu 24.

Indeed it seems like an installation problem. I am not sure how I should 'fix' the installation without causing more damage instead so I am asking for help. Thank you!

[connorjward]

I would recommend a from-scratch installation as things have changed a little since then. In particular the install should be much faster for you.

[connorjward]

And please run pip cache purge beforehand too

[madalina-phys]

ok, thank you!

[connorjward]

Has this worked for you?

[madalina-phys]

Yes, thank you very much, after re-installation it worked!