HDF5 Compiler Problems

Symptom: ​HDF5 programs written in C return 'undefined reference to `function_name' messages for all ​HDF5 functions when compiled on ​GNU or ​Intel compilers.

Problem: ​HDF5 compilation requires a pretty complicated tangle of linking options. They were all sorted out in ​Fortran on AstroBEAR a long time ago, but starting a new project using gcc or ifc is a tricky prospect.

Affects: Anyone trying to compile a C module that uses ​HDF5. The problem may even extend to ​Fortran users attempting to compile new ​HDF5 projects independent of the AstroBEAR makefile framework.

Solution: Most newer ​HDF5 distributions (verifiably as far back as 1.6.2) come with the h5cc compilation script. This essentially wraps currently-installed compilers with the required inclusions and linking options to compile an ​HDF5 project in C. The script can be found in the HDF_DIR/bin/ directory, and can be incorporated into a make file (replacing gcc or icc under the COMPILER option) or used in the command line using gcc-like syntax:

/usr/local/hdf5/bin/h5cc foo.c -o foo