BUG: CheckpointFile mesh saving crash about firedrake

[ksagiyam]

As suggested on Slack, this might be an issue of HDF5. I would first try using the older HDF5 on the HPC, and see if it fixes.

cd /your/path
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.bz2
export PETSC_CONFIGURE_OPTIONS="--download-hdf5=/your/path/hdf5-1.12.2.tar.bz2"
python3 firedrake-install

Note that due to this issue #3514 you might need to put petsc_options.discard("--download-hdf5") at

firedrake/scripts/firedrake-install

Line 823 in cb77d32

"to have PETSc built against $HDF5_DIR.")

in the script before running firedrake-install.

[Ainlina]

I am using the Docker image to avoid any potential install weirdness; is a correct HDF5 supposed to be bundled in there? I don't have root on these machines so can only run firedrake-install inside an Apptainer sandbox which tends to be quite janky and often fail.

[ksagiyam]

The docker image contains the latest HDF5 (1.14). 1.14 seems to work mostly fine, but some users have had to downgrade to 1.12 in their settings for some reason.

[Ainlina]

It appears that this is to do with network file systems; saving to /tmp seems to work, so as a workaround I'll do that then move the file - I don't have access to any local disk storage on my machine because of how my organisation has set it up.