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    <p>The following worked on my system:</p> <ol> <li><p>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 <code>icc</code> specific).</p></li> <li><p>Make a target file. You already have your own file. I used the simple <code>h5_crtfile.c</code> from <a href="http://www.hdfgroup.org/HDF5/Tutor/examples/C/h5_crtfile.c" rel="noreferrer">here</a> (a good idea to start with this simple file first a look for warnings). I changed <code>main</code> to <code>mexFunction</code> with the usual args and included <code>mex.h</code>.</p></li> <li><p>Specify the <em>static</em> 1.8.4 library you want to load explicitly (the full path with no -L for it necessary) and don't include <code>-lhdf5</code> in the <code>LDFLAGS</code>. Include a <code>-t</code> option so you can ensure that there is no dynamic hdf5 library being loaded. You also need <code>-lz</code>, with <code>zlib</code> installed. For darwin we also need a <code>-bundle</code> in <code>LDFLAGS</code>:</p> <pre><code>mex CFLAGS='-I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -bundle' h5_crtfile.c -v </code></pre> <p>For linux, you need an equivalent position-independent call, e.g. <code>fPIC</code> and maybe <code>-shared</code>, but I don't have a linux system with a matlab license, so I can't check:</p> <pre><code>mex CFLAGS='-fPIC -I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -shared' h5_crtfile.c -v </code></pre></li> <li><p>Run the <code>h5_crtfile</code> 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 <code>file file.h5</code> I get <code>file.h5: Hierarchical Data Format (version 5) data</code>.</p></li> </ol> <p>Note that if I include a <code>-lhdf5</code> 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. </p> <p>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.</p>
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    1. POshared library locations for matlab mex files:
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    1. COhmmm. when I try this, the compilation fails b/c `libmat.so` relies on `libhdf5.so`. something strange there. unfortunately, I cannot include `mex.h` without also pulling in Mathworks' hdf5; regrettably, the header files distributed by Mathworks does not include `hdf5.h`.
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    2. COOK, I've rewritten the post, see how that goes.
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    3. COI compile in shell with gcc commands spit out by mex. So I tried your solution, skipping steps 2 & 3; (`-bundle` is Darwin-specific, BTW) using `h5_crtfile.c`, I get "Warning! The HDF5 header files included by this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. 'HDF5_DISABLE_VERSION_CHECK' environment variable set, application will continue. Headers are 1.8.4, library is 1.6.5" however, `file.h5` is created! BUT, with this trick on my mex, it still segfaults.
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