Building n2h5 on OS X

[sdangi]

Even though I have hdf5 installed (with homebrew) on Mac OS X Mavericks, I get the following error when I run "cmake .":

sdangi$ cmake .
-- checking for module 'python-2.7'
--   package 'python-2.7' not found
-- Found Python executable: /usr/local/bin/python
-- Found Python version: 2.7.6
-- Found Python library: -F/usr/local/Frameworks -framework Python
-- Search mex libraries at MATLAB_INCLUDE_DIR-NOTFOUND/../lib/osx64
-- Add cbpy build target using Python found at /usr/local/bin/python
-- Add n2h5 utility build target
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
HDF5_HL_LIBRARIES
    linked by target "n2h5" in directory /Users/sdangi/code/CereLink/build

-- Configuring incomplete, errors occurred!
See also "/Users/sdangi/code/CereLink/build/CMakeFiles/CMakeOutput.log".
See also "/Users/sdangi/code/CereLink/build/CMakeFiles/CMakeError.log".
sdangi$ brew install hdf5
Warning: hdf5-1.8.12 already installed

(Up until now, I've just been commenting out the n2h5 part of CMakeLists.txt in order to avoid this error, but now I want to actually use n2h5.)

[sdangi]

In OS X, the HDF5 shared libraries (installed into /usr/local/lib by homebrew) have a .dylib extension instead of .so:

sdangi$ cd /usr/local/lib
sdangi$ ls -l | grep hdf5
lrwxr-xr-x   1 sdangi  admin      41 Jan 21 17:57 libhdf5.8.dylib -> ../Cellar/hdf5/1.8.12/lib/libhdf5.8.dylib
lrwxr-xr-x   1 sdangi  admin      35 Jan 21 17:57 libhdf5.a -> ../Cellar/hdf5/1.8.12/lib/libhdf5.a
lrwxr-xr-x   1 sdangi  admin      39 Jan 21 17:57 libhdf5.dylib -> ../Cellar/hdf5/1.8.12/lib/libhdf5.dylib
lrwxr-xr-x   1 sdangi  admin      42 Jan 21 17:57 libhdf5.settings -> ../Cellar/hdf5/1.8.12/lib/libhdf5.settings
lrwxr-xr-x   1 sdangi  admin      44 Jan 21 17:57 libhdf5_hl.8.dylib -> ../Cellar/hdf5/1.8.12/lib/libhdf5_hl.8.dylib
lrwxr-xr-x   1 sdangi  admin      38 Jan 21 17:57 libhdf5_hl.a -> ../Cellar/hdf5/1.8.12/lib/libhdf5_hl.a
lrwxr-xr-x   1 sdangi  admin      42 Jan 21 17:57 libhdf5_hl.dylib -> ../Cellar/hdf5/1.8.12/lib/libhdf5_hl.dylib

However, for target n2h5, CMakeLists.txt looks specifically for libhdf5_hl.so:

        FIND_LIBRARY (HDF5_HL_LIBRARIES libhdf5_hl.so

A fix to this issue is achieved by either:

1. Changing the ".so" in the line above to "*"
2. Detecting with the OS is mac, linux, etc., and searching specifically for libhdf5_hl.dylib, .so, etc. based on that

[dashesy]

I did a small commit (removed .so extension), it works still on Linux, if it works on OSX we can close this

[sdangi]

Yup, with .so removed, it builds fine on OS X. I'm closing the issue.

[sdangi]

Oops -- with .so removed, it actually doesn't work on linux (n2h5 build target is not added when running cmake .). Maybe change it to .* ?

FIND_LIBRARY (HDF5_HL_LIBRARIES libhdf5_hl.*

[dashesy]

sure, I tried it once, perhaps my CMake cache was not refreshed then, or maybe it is distro specific.

[dashesy]

This should work now