To remove just libpdl-io-hdf5-perl package itself from Debian 9 (Stretch) execute on terminal:
sudo apt-get remove libpdl-io-hdf5-perl
Uninstall libpdl-io-hdf5-perl and it's dependent packages
To remove the libpdl-io-hdf5-perl package and any other dependant package which are no longer needed from Debian Stretch.
sudo apt-get remove --auto-remove libpdl-io-hdf5-perl
If you also want to delete configuration and/or data files of libpdl-io-hdf5-perl from Debian Stretch then this will work:
sudo apt-get purge libpdl-io-hdf5-perl
To delete configuration and/or data files of libpdl-io-hdf5-perl and it's dependencies from Debian Stretch then execute:
sudo apt-get purge --auto-remove libpdl-io-hdf5-perl
More information about apt-get remove
apt-get remove is identical to install except that packages are removed instead of installed. Note that removing a package leaves its configuration files on the system. If a plus sign is appended to the package name (with no intervening space), the identified package will be installed instead of removed.