shared library locations for matlab mex files:

Question

I am trying to write a matlab mex function which uses libhdf5; My Linux install provides libhdf5-1.8 shared libraries and headers. However, my version of Matlab, r2007b, pro

Answer 1

The following worked on my system:

1. Install hdf5 version 1.8.4 (you've already done this: I installed the source and compiled to ensure it is compatible with my system, that I get gcc versions and that I get the static libraries - e.g. the binaries offered for my system are icc specific).

2. Make a target file. You already have your own file. I used the simple h5_crtfile.c from here (a good idea to start with this simple file first a look for warnings). I changed main to mexFunction with the usual args and included mex.h.

3. Specify the static 1.8.4 library you want to load explicitly (the full path with no -L for it necessary) and don't include -lhdf5 in the LDFLAGS. Include a -t option so you can ensure that there is no dynamic hdf5 library being loaded. You also need -lz, with zlib installed. For darwin we also need a -bundle in LDFLAGS:

   mex CFLAGS='-I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -bundle' h5_crtfile.c -v
   

   For linux, you need an equivalent position-independent call, e.g. fPIC and maybe -shared, but I don't have a linux system with a matlab license, so I can't check:

   mex CFLAGS='-fPIC -I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -shared' h5_crtfile.c -v
   

4. Run the h5_crtfile mex file. This runs without problems on my machine. It just does a H5Fcreate and H5Fclose to create "file.h5" in the current directory, and when I call file file.h5 I get file.h5: Hierarchical Data Format (version 5) data.

Note that if I include a -lhdf5 above in step 3, then matlab aborts when I try to run the executable (because it then uses matlab's dynamic libraries which for me are version 1.6.5), so this is definitely solving the problem on my system.

Thanks for the question. My solution above is definitely much easier for me than what I was doing before. Hopefully the above works for you.

Answer 2

I am accepting Ramashalanka's answer because it led me to the exact solution which I will post here for completeness only:

1. download the hdf5-1.6.5 library from the hdf5 website, and install the header files in a local directory;
2. tell mex to look for "hdf5.h" in this local directory, rather than in the standard location (e.g. /usr/include.)
3. tell mex to compile my code and the shared object library provided by matlab, and do not use the -ldfh5 flag in LDFLAGS.

the command I used is, essentially:

/opt/matlab/matlab_default/bin/mex -v CC#gcc CXX#g++ CFLAGS#"-Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include" CXXFLAGS#"-Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include " -O -lmwblas -largeArrayDims -L/usr/lib64 hdf5_read_strings.c /opt/matlab/matlab_default/bin/glnxa64/libhdf5.so.0

this gets translated by mex into the commands:

gcc -c -I/opt/matlab/matlab75/extern/include -DMATLAB_MEX_FILE -Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include -O -DNDEBUG hdf5_read_strings.c
gcc -c -I/opt/matlab/matlab75/extern/include -DMATLAB_MEX_FILE -Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include -O -DNDEBUG /opt/matlab/matlab75/extern/src/mexversion.c
gcc -O -pthread -shared -Wl,--version-script,/opt/matlab/matlab75/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -o hdf5_read_strings.mexa64  hdf5_read_strings.o mexversion.o  -lmwblas -L/usr/lib64 /opt/matlab/matlab_default/bin/glnxa64/libhdf5.so.0 -Wl,-rpath-link,/opt/matlab/matlab_default/bin/glnxa64 -L/opt/matlab/matlab_default/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++

this solution should work on all my various target machines and at least until I upgrade to matlab r2009a, which I believe uses hdf5-1.8. thanks for all the help, sorry for being so dense with this--I think I was overly-committed to using the packaged version of hdf5, rather than a local set of header files.

Note this would all have been trivial if Mathworks had provided a set of the header files with the Matlab distribution...