hdf5 v1.10 upgrade/installation instruction for using single-write-multiple-read (SWMR) in h5py.

Upgrading HDF5 and h5py to use SWMR with h5 files.md

The new 1.10 version of hdf5 library is stable. You can now install from the source to use this new capability.

The installation process has a few caveats, so here is how to do it.

Note:

1. you need to first remove the hdf5 libraries currently installed in ubuntu.
2. Then you need to reinstall h5py.
3. when you reinstall h5py via pip, use the --no-binary flag. This is because the h5py wheel comes with its own hdf5 binary.

Instructions:

First search for hdf5 libraries, and then remove all of them.

# do this, to show the list of packages you need to remove
dpkg --get-selections | grep -v deinstall | grep hdf5

# now remove all of then
sudo apt-get uninstall <name of these libraries, should be four of them>

Then install from hdf5 source.

Note: although it says 'patch', it is actually not a patch.

reference

wget https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0-patch1/src/hdf5-1.10.0-patch1.tar.gz
tar -xzf hdf5-1.10.0-patch1.tar.gz
cd hdf5-1.10.0-patch1
./configure --prefix=/usr/local --enable-cxx --enable-build-mode=production 
sudo make install

Now reinstall h5py with the --no-binary option.

sudo pip install h5py --no-binary --force-reinstall

Acknowledgement

Thanks to @tacaswell for helping me!