When running
make pycaffe
We are ending up with missing hdf5 libraries.
CXX/LD -o python/caffe/_caffe.so python/caffe/_caffe.cpp
/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: error: ld returned 1 exit status
Makefile:502: recipe for target 'python/caffe/_caffe.so' failed
make: *** [python/caffe/_caffe.so] Error 1
Note that every conceivable combination of these libraries has been installed on this ubuntu 15.10 system.
$ dpkg --get-selections | grep hdf5
hdf5-helpers install
libhdf5-10:amd64 install
libhdf5-cpp-10:amd64 install
libhdf5-dev install
libhdf5-mpi-dev install
libhdf5-mpich-10:amd64 install
libhdf5-mpich-dev install
libhdf5-openmpi-10:amd64 install
libhdf5-openmpi-dev install
libhdf5-serial-dev install
Now I realize that is overkill .. but they were added one at a time - and then we retried the make pycaffe before adding another.. We just wanted to be sure missing hdf5 libs were not the core issue.
Update In response to the supplied answer from @jon
dpkg -L libhdf5-dev | grep so
/usr/lib/x86_64-linux-gnu/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_fortran.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5hl_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.so
And in the Makefile.config:
LIBRARY_DIRS := /usr/opt/libsr $(PYTHON_LIB)
/usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu
run dpkg -L libhdf5-dev | grep so should output:
/usr/lib/x86_64-linux-gnu/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5hl_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5.so
Make sure the path /usr/lib/x86_64-linux-gnu (which contains libhdf5.so and libhdf5_hl.so) is in Makefile.config's LIBRARY_DIRS