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POshared library locations for matlab mex files:
 

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    <p>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, provides a libhdf5.so from the 1.6 release. (Matlab <code>.mat</code> files bootstrap hdf5, evidently). When I compile the mex, it segfaults in Matlab. If I downgrade my version of libhdf5 to 1.6 (not a long-term option), the code compiles and runs fine.</p> <p>question: how do I solve this problem? how do I tell the mex compilation process to link against /usr/lib64/libhdf5.so.6 instead of /opt/matlab/bin/glnxa64/libhdf5.so.0 ? When I try to do this using <code>-Wl,-rpath-link,/usr/lib64</code> in my compilation, I get errors like:</p> <pre><code>/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libhdf5.so.0, needed by /opt/matlab/matlab75/bin/glnxa64/libmat.so, may conflict with libhdf5.so.6 /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status mex: link of 'hdf5_read_strings.mexa64' failed. make: *** [hdf5_read_strings.mexa64] Error 1 </code></pre> <p>ack. the last resort would be to download a local copy of the hdf5-1.6.5 headers and be done with it, but this is not future proof (a Matlab version upgrade is in my future.). any ideas?</p> <p>EDIT: per Ramashalanka's excellent suggestions, I </p> <p>A) called <code>mex -v</code> to get the 3 <code>gcc</code> commands; the last is the linker command;</p> <p>B) called that linker command with a <code>-v</code> to get the <code>collect</code> command;</p> <p>C) called that <code>collect2 -v -t</code> and the rest of the flags.</p> <p>The relevant parts of my output:</p> <pre><code>/usr/bin/ld: mode elf_x86_64 /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/crtbeginS.o hdf5_read_strings.o mexversion.o -lmx (/opt/matlab/matlab75/bin/glnxa64/libmx.so) -lmex (/opt/matlab/matlab75/bin/glnxa64/libmex.so) -lhdf5 (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/libhdf5.so) /lib64/libz.so -lm (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/libm.so) -lstdc++ (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libstdc++.so) -lgcc_s (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libgcc_s.so) /lib64/libpthread.so.0 /lib64/libc.so.6 /lib64/ld-linux-x86-64.so.2 -lgcc_s (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libgcc_s.so) /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crtn.o </code></pre> <p>So, in fact the <code>libhdf5.so</code> from <code>/usr/lib64</code> is being referenced. However, this is being overriden, I believe, by the environment variable <code>LD_LIBRARY_PATH</code>, which my version of Matlab automagically sets at run-time so it can locate its own versions of e.g. <code>libmex.so</code>, etc.</p> <p>I am thinking that the <code>crt_file.c</code> example works either b/c it does not use the functions I am using (<code>H5DOpen</code>, which had a signature change in the move from 1.6 to 1.8 (yes, I am using <code>-DH5_USE_16_API</code>)), or, less likely, b/c it does not hit the parts of Matlab internals that need hdf5. ack.</p>
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    1. COIn your output I see `lib64/libhdf5.so` which is a dynamic library. You need to specify the explicit path for the static library (with a .o suffix) and not use `-lhdf5`. Then post new linker output if it's still not working. If the `.so` file is the only one in the listing then that is the only one included. `LD_LIBRARY_PATH` or any other path, such as in `-L` shouldn't matter if you don't have `-lhdf5` as an option and you specify the path to the static library explicitly (see below). I agree with your comments on `h5_crtfile.c`, but all the information we need is in your linker output above.
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    2. COI don't have a `libhdf5.o` file; gentoo's hdf5 package provides `libhdf5.so`, `libhdf5.a`, `libhdf5.la`, and some fortran and cpp files. Do I have to compile libhdf5 myself? this is an option...
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    3. COSorry, I meant `.a`, not `.o`. You can check that the `libhdf5.a` file you have is the correct version by e.g. `strings libhdf5.a`. I see `HDF5 Version: 1.8.4` in mine. If you can't get the right static library as a binary, it is easy to compile. See my comments to your other query below.
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