kmsmith137 / sp_hdf5

Header-only C++ library with "thin" wrappers around libhdf5_cpp

sp_hdf5

Header-only C++ library containing "thin" wrappers around libhdf5_cpp.

For documentation, it's easiest to start by looking at the example programs sp_hdf5/example_read.cpp and sp_hdf5/example_write.cpp.

For further details, I suggest reading the sp_hdf5.hpp source file, which should be pretty digestible (I hope!)

Installing an out-of-date HDF5 (!!)

Note: to use sp_hdf5, you'll need to install an out-of-date version of the HDF5 library! This is getting to be a big nuisance issue, and and I hope to fix it soon! In the meantime you'll need to download an old version of HDF5 (I recommend 1.8.20) and install it in your user directory as follows:

cd ~
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.20/src/hdf5-1.8.20.tar.gz
tar zxvf hdf5-1.8.20.tar.gz
cd hdf5-1.8.20/
./configure --enable-cxx --prefix=$HOME
make -j 20
make install

You may want to create an hdf5.pc file. so that pkg-config can find hdf5.
(This is not always necessary, but I needed to do this to install Kiyo Masui's bitshuffle plugin.) See instructions in README_pc.md.

Installing sp_hdf5

• The sp_hdf5 Makefile assumes the existence of a file Makefile.local which defines the Makefile variables:

  INCDIR     Installation directory for C++ header files
  CPP        C++ compiler executable + flags
  

  You can probably use one of the example Makefile.locals in site/.

• To build and install, do make all install.

• For a quick test, you should get no errors when you run the pair of example programs back-to-back:

  ./example-write
  ./example-read
  

To do list

• Error messages could be improved

• Not very feature-complete. Some missing features offhand:

  • Retrieve list of datasets/groups/etc
  • Partial reads/writes
  • String-valued datasets

• Minor loose ends

  • Remove copy in hdf5_read_attribute(), N-dimensional string case (see FIXME in sp_hdf5_implementation.hpp)