HDF5 Troubleshooting - I2PC/xmipp GitHub Wiki

We sometimes see issues regarding the HDF5 dependency. We recommend removing all hdf5 versions and install just hdf5-devel. To do that (Ubuntu-Debian systems):

sudo apt remove hdf5
sudo apt remove hdf5-devel
pip uninstall h5py

Remove all files related to hdf5 in:

• _/usr/lib64/libhdf5*_
• _/usr/include/hdf5*_
• _/usr/lib/x86_64-linux-gnu/hdf5_*
• _.../anaconda3/include/H5*.h_
• _.../anaconda3/include/hdf5*.h_
• _.../anaconda3/lib/libhdf5*_
• _.../anaconda3/envs/.../libhdf5*_

We strongy recommend you to install it via your default package manager: sudo apt-get install libhdf5-dev If you install it using other package management system (such as Conda), it might lead to compile/link time issues caused by incompatible version being fetched. Other option is to run"scipion3 installb xmippSrc" to force the xmipp install its own HDF5 into its desired directory.