Adding the installation of h5py==3.11.0 in the dockerfile

[mikibonacci]

Only if architecture is arm64. Otherwise the aiidalab-qe-vibroscopy plugin will fail to install. The reason is that we cannot install easily h5py via pip, for arm64.

This should solve issue aiidalab/aiidalab-qe#745 and mikibonacci/aiidalab-qe-vibroscopy#52

[mikibonacci]

@unkcpz , @AndresOrtegaGuerrero
not entirely sure that I placed the h5py mamba installation in the optimal place (because we just run the apt-get there), but at least is in the arm64 specific block of instructions.

[danielhollas]

Can I ask, why is this only needed for arm64?

[mikibonacci]

Hi @danielhollas, the reason is that for arm64 the h5py package has no wheel support, and this breaks the installation of the phonon plugin for the QE app. It seems that for a pyproject-based package you always need a wheel for each dependency package which is not yet installed.

[danielhollas]

If the wheel is not available than pip will attempt to install from source distribution (sdist), which presumably involves some compilation. What is the exact error that you're seeing? Perhaps instead of installing this package to the base image, we should instead install the missing dependencies? Since those might be useful to other packages in the future.

For example, with @AndresOrtegaGuerrero we've been discussing adding cmake recently.
https://aiida.discourse.group/t/installing-cmake-in-aiidalab-container/387

Am I missing something?

[mikibonacci]

The error is this one: mikibonacci/aiidalab-qe-vibroscopy#52. Mainly, the problem is that we don't have HDF5 already compiled and installed:

Building h5py requires pkg-config unless the HDF5 path is explicitly specified using the environment variable HDF5_DIR.

So we can try to install via apt-get the hdf5 library, then setup the HDF5_DIR env variable. I will give it a try

[danielhollas]

I think installing hdf5 via apt (or conda for that matter) is preferable since then you can choose which h5py version you install when the plugin is installed.

[mikibonacci]

I completely agree. I'll modify my PR in respect of this

[mikibonacci]

I added the installation of two packages: libhdf5-serial-dev and pkg-config. I tried to install just the first package and set up the HDF5_DIR env var, but it was not sufficient to allow the afterwards pip installation of h5py.

Now h5py will be installed without issues when the aiidalab-qe-vibroscopy plugin is installed.

[danielhollas]

Thanks @mikibonacci, can you please push your branch into origin repo (aiidalab/aiidalab-docker-stack/) and open a new PR from it? This will allow the build and tests to run (they currently don't run from forks). LMK in case you don't have write access to this repo (but I believe you should).

[mikibonacci]

Hi @danielhollas, I tried and I have no permission to write in the origin repo, but as soon as you give me permission I will push! Thanks a lot for the help

[danielhollas]

@mikibonacci can you try now?

@unkcpz FYI I've added write permissions to the internal-maintainers team LMK if that is not desired

[unkcpz]

@unkcpz FYI I've added write permissions to the internal-maintainers team LMK if that is not desired

The internal-maintainers team was create to do such things (for qeapp originally), it is desired. Thanks for adding it here.

[mikibonacci]

@danielhollas , it works now, I just created the PR. thanks!

[mikibonacci]

replaced by #468