Problems during the firedrake-check "installation" step

[96mat]

Hi devs, the title is more or less self-explanatory. Basically, I followed the whole process described in the installation page of Firedrake website, no errors with it no problems at all, but when typing the following command (virtual env activated):

firedrake-check

I get the following message:

Traceback (most recent call last):
  File "/home/orion/FireDrakeFEM/venv-firedrake/bin/firedrake-check", line 5, in <module>
    from firedrake._check import main
  File "/home/orion/FireDrakeFEM/venv-firedrake/lib/python3.11/site-packages/firedrake/__init__.py", line 45, in <module>
    from firedrake.checkpointing import *
  File "/home/orion/FireDrakeFEM/venv-firedrake/lib/python3.11/site-packages/firedrake/checkpointing.py", line 7, in <module>
    from firedrake.cython import hdf5interface as h5i
  File "firedrake/cython/hdf5interface.pyx", line 2, in init firedrake.cython.hdf5interface
  File "/home/orion/FireDrakeFEM/venv-firedrake/lib/python3.11/site-packages/h5py/__init__.py", line 33, in <module>
    from . import version
  File "/home/orion/FireDrakeFEM/venv-firedrake/lib/python3.11/site-packages/h5py/version.py", line 15, in <module>
    from . import h5 as _h5
  File "h5py/h5.pyx", line 1, in init h5py.h5
ImportError: /home/orion/FireDrakeFEM/venv-firedrake/lib/python3.11/site-packages/h5py/defs.cpython-311-x86_64-linux-gnu.so: undefined symbol: H5Sencode

indeed when calling the from firedrake import * i get the same error, instead Petsc4py can be imported no problems. Therefore i would ask to you what could be the issue in my installation? (my Python version: Python 3.11.7)

[96mat]

EDIT: I forgot to mention: installation on the WSL (Ubuntu)

[connorjward]

Missing symbols errors are usually caused by using compiled extensions that have been compiled against a different library to the one now on your system. For instance I recently had a very similar error when I upgraded the system HDF5 but did not recompile the extensions. I have a number of questions:

1. Did you recently update your system?
2. Did you install Firedrake previously?
3. Did you run pip cache purge?

[96mat]

Thanks for your answer.

1. I didn't update my system

2. Yes I did, I tried a couple of times before installing Firedrake but always in a virtual environment, but at the end of the process I recursively removed the whole folder because it wasn't successful :/

3. Yes I did it and after that the following commands

pip cache remove mpi4py
pip cache remove petsc4py
pip cache remove h5py
pip cache remove slepc4py
pip cache remove libsupermesh
pip cache remove firedrake

• From your answer I just got in my mind the possibility to use -no-pakage version of

python3 ../firedrake-configure --no-package-manager --show-petsc-configure-options | xargs -L1 ./configure

Since I was doing it without the -no-package flag

What do you think?

[connorjward]

If you have a successful install apart from this issue then I think it should be possible to debug things without deleting everything. I don't recommend passing --no-package-manager as that will just make things more confusing. It should work fine without.

1. What does ldd /home/orion/FireDrakeFEM/venv-firedrake/lib/python3.11/site-packages/h5py/defs.cpython-311-x86_64-linux-gnu.so give you?
2. Do you have the HDF5_DIR environment variable set (you shouldn't)?

My first guess to fix it would be

$ pip uninstall -y h5py
$ pip cache remove h5py
$ HDF5_MPI=ON pip install -v --no-binary h5py h5py
$ python -c "from h5py import *"  # to test it

[96mat]

Thanks I solved the problem, now I can import everything, Firedrake's checks are ok. The issue was from another source not related to the procedure described in the Firedrake web page.. an interference of environments with conda that by default imposes in the bashrc an "hard activation" of its base environment