After a reading around for a bit it looks like this serial/parallel problem for HDF5 may need to be addressed. Basically HDF5 appears to support both single node (serial) and parallel (mpi) implementations, and Linux distros based on Debian (like mine) all have both packages available. To avoid naming conflicts, the file libhdf5.so does not exist by default, and the libraries and headers are either in subdirectories or have a suffix indicating which package they belong to. Hence libhdf5_serial.so is identical to libhdf5.so, which is why libhdf5.so doesn't exist by default.
It may be worthwhile adding some condition into configure.ac that tries to find HDF5 with the explicit serial labelling if it can't find it with the generic file names/paths.
After a reading around for a bit it looks like this serial/parallel problem for HDF5 may need to be addressed. Basically HDF5 appears to support both single node (serial) and parallel (mpi) implementations, and Linux distros based on Debian (like mine) all have both packages available. To avoid naming conflicts, the file libhdf5.so does not exist by default, and the libraries and headers are either in subdirectories or have a suffix indicating which package they belong to. Hence libhdf5_serial.so is identical to libhdf5.so, which is why libhdf5.so doesn't exist by default.
It may be worthwhile adding some condition into configure.ac that tries to find HDF5 with the explicit serial labelling if it can't find it with the generic file names/paths.