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    <p>I am accepting Ramashalanka's answer because it led me to the exact solution which I will post here for completeness only:</p> <ol> <li>download the hdf5-1.6.5 library from the hdf5 website, and install the header files in a local directory;</li> <li>tell mex to look for "hdf5.h" in this local directory, rather than in the standard location (e.g. <code>/usr/include</code>.)</li> <li>tell mex to compile my code <em>and the shared object library provided by matlab</em>, and do <em>not</em> use the <code>-ldfh5</code> flag in <code>LDFLAGS</code>.</li> </ol> <p>the command I used is, essentially:</p> <pre><code>/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 </code></pre> <p>this gets translated by mex into the commands:</p> <pre><code>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++ </code></pre> <p>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. </p> <p>Note this would all have been trivial if Mathworks had provided a set of the header files with the Matlab distribution...</p>
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    1. POshared library locations for matlab mex files:
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    1. COThis is how I handled multithreaded mex files that needed to link boost-thread. But there MUST be some way to get it to link to the system library instead of the one inside Matlab and avoid the segfaults that way. Being stuck with whatever boost is inside Matlab is not very nice.
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    2. CORegarding Ramashalanka's helpful suggestions, I can also say that with my boost-thread linking situation I had to do this workaround in Linux but not in Mac; in Mac it seems that the mex command does not link in the internal versions as it does in Linux.
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    3. COSomething like the answer here: http://stackoverflow.com/questions/9927568/compiling-c11-code-as-part-of-a-matlab-mex-file might work (although the question is for something somewhat different). I'll report back if I get it working.
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