h5py configuration: HDF5 dir versus specification of HDF5 lib and include directories

[Brad Aagaard]

The user can specify the HDF5 directory when configuring h5py via the --hdf5 argument or the HDF5_DIR environment variable, but cannot specify the include and lib directories separately. Package managers often install parallel HDF5 into lower level directories like /usr/include/hdf5/openmpi and /usr/lib/x86_64-linux-gnu/hdf5/openmpi. As a result, they cannot be found through specification of an HDF5 directory. Although slightly less convenient, user specification of the HDF5 include and lib directories provides a much more flexible and robust approach.

Is there a reason why the h5py configuration doesn't do this? Would you be willing to accept a pull request that adds this feature?

[Thomas Kluyver]

Hi Brad,

In fact, I believe there's already a pull request open that would allow this: https://github.com/h5py/h5py/pull/1414 . It's been on hold because I wanted to confirm that it was actually necessary, and we weren't just adding configurability for the sake of it. It sounds like it is useful, so I'll go back and review it.

Thanks,

Thomas

On Tue, 21 Apr 2020 at 17:23, Brad Aagaard <baagaa...@gmail.com> wrote:

The user can specify the HDF5 directory when configuring h5py via the --hdf5 argument or the HDF5_DIR environment variable, but cannot specify the include and lib directories separately. Package managers often install parallel HDF5 into lower level directories like /usr/include/hdf5/openmpi and /usr/lib/x86_64-linux-gnu/hdf5/openmpi. As a result, they cannot be found through specification of an HDF5 directory. Although slightly less convenient, user specification of the HDF5 include and lib directories provides a much more flexible and robust approach.

Is there a reason why the h5py configuration doesn't do this? Would you be willing to accept a pull request that adds this feature?

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[Brad Aagaard]

Thanks for pointing me to the PR. This includes the features I want, and I added my use case as a comment.

 

Thanks,

Brad

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