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HDF5 is a file format used for large quantities of numerical data. libhdf5 is a library that can access files in HDF5 format. There are also some commandline tools for manipulating HDF5 files.

Instructions for users: 

The Ubuntu workstations come with a pre-built libhdf5 and utilities. However it was built against GNU compilers (this matters because not all Fortran compilers are compatible) and doesn't contain the Fortran 2003 bindings. Consequently we also have a couple of locally built versions available as modules. If you aren't using Fortran, stick with the Ubuntu packages as you don't need to do anything special to access those. If you are using Fortran, load the appropriate module.

Try to use the shared library when possible. If you use the static library you may run into problems when using szipped files. The HDF5_USE_SHLIB variable is set.

Licence Details: 

This is Free Software. The licence is BSD-like.

Admin notes: 

Ubuntu provide a perfectly good package of this, but it doesn't have the Fortran 2003 bindings so we also provide our own versions via modules which do. We do need the Ubuntu package installed as it is a dependency of some important packages like grace and cdo.

 module purge 
module add szlib # not needed on 18.04; install libsz2 package instead
./configure --prefix=/usr/local/shared/ubuntu-18.04/x86_64/hdf5/gnu/serial/1.8.12 --enable-fortran --enable-fortran2003 --with-szlib
make check 
make install 
module add icc # not 14.0, it fails make check 
CC=icc FC=ifort ./configure --prefix=/usr/local/shared/ubuntu-18.04/x86_64/hdf5/intel/serial/1.8.12 --enable-fortran --enable-fortran2003 --with-szlib 
make check 
make install 

Our copy of szip isn't on the standard library search path, so if you link an app that needs the szip functionality with libhdf5.a rather than you won't find szip at runtime if using GNU compilers because we do not wrap them to set RPATH.

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