[Fedora 28] hdf5 fails to load #105
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mightybigcar
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Feb 22, 2019
…e on system path. Issue google-deepmind#105.
iskra-vitaly
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…tion * origin/master: Added return code checking to header parsing. Throw error if the operation failed. Pass includePath to gcc so it can find include files that might not be on system path. Issue google-deepmind#105. Fix undefined behavior by not casting -1 to unsigned int directly Remove test for threads as it requries threads to be installed and hdf5 compiled with --enable-threadsafety Add torch serialization so hdf5files can be read from multiple threads Prevent H5Dget_space from being called twice
iskra-vitaly
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Merges master from upstream * fix-nullable-annotation: Added return code checking to header parsing. Throw error if the operation failed. Pass includePath to gcc so it can find include files that might not be on system path. Issue google-deepmind#105. Fix undefined behavior by not casting -1 to unsigned int directly Remove test for threads as it requries threads to be installed and hdf5 compiled with --enable-threadsafety Add torch serialization so hdf5files can be read from multiple threads
iskra-vitaly
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* origin/master: Added return code checking to header parsing. Throw error if the operation failed. Pass includePath to gcc so it can find include files that might not be on system path. Issue google-deepmind#105. Fix undefined behavior by not casting -1 to unsigned int directly Remove test for threads as it requries threads to be installed and hdf5 compiled with --enable-threadsafety Add torch serialization so hdf5files can be read from multiple threads
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HDF5 fails to load on Fedora 28 as follows:
$ luajit -e "local hdf5 = require('hdf5'); In file included from /usr/include/openmpi-x86_64/hdf5.h:22: /usr/include/openmpi-x86_64/H5public.h:59:13: fatal error: mpi.h: No such file or directory # include <mpi.h> ^~~~~~~ compilation terminated. /brewpub/tools/torch/bin/luajit: /brewpub/tools/torch/share/lua/5.1/trepl/init.lua:389: /brewpub/tools/torch/share/lua/5.1/hdf5/ffi.lua:63: missing declaration for symbol 'H5open' stack traceback: [C]: in function 'error' /brewpub/tools/torch/share/lua/5.1/trepl/init.lua:389: in function 'require' main_test_realsense.lua:13: in main chunk [C]: in function 'dofile' /brewpub/tools/torch/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk [C]: at 0x004059f0This is because
mpi.his in the same place ashdf5.h, but that directory is not in the system include paths. As indicated by the comments in the code, the fix is to passincludePathto gcc using the-Iswitch inloadHDF5Header()inffi.lua. I've made this change, which resolves the issue, and will submit a pull request shortly.Thanks,
Chris
PS Sorry for the repeated edits. I'm not at all familiar with Markdown.
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