Standardise makefiles

[aniabrown]

Between Project, Examples, Tests, and GPU/CPU versions, there are 7 different Makefiles which have been updated to build with HDF5. These are currently slightly different, for different systems -- some for Iridis, some for local ubuntu etc. Should standardise and include instructions for what needs to be tweaked to work on each system.

[IanHawke]

Agreed. More documentation decisions for the next meeting.

[aniabrown]

I've standardised makefiles in Project, Tests, and Examples/KelvinHelmholtz:

• added options to use MPI/HDF5 or not where appropriate
• clearly separated out vars which users were likely to need to edit, with hints for how to set them on different systems
• created Makefile.template in KelvinHelmholtz which works with small tweaks for all the KH examples, with instructions in the template for where to edit when new source files are added to METHOD
• for GPU, added option to change gpu compute capability

The CPU makefiles are updated in dev_hdf5, commit d1bb0c6
The GPU makefiles are updated in gpu, commit 7717aee

Not done:

• Compilation with support for OpenMP threading is not implemented in all makefiles and is not properly controlled by USE_OMP -- the code might fail to compile on systems without OpenMP installed (macs)
• non-KelvinHelmholtz examples