runtest fails on ubuntu because of libhdf5

[Victor Zhong]

I've managed to install Caffe on my Ubuntu machine, however `make runtest` is failing with the following message:

.build_release/test/test_all.testbin 0 --gtest_shuffle 

.build_release/test/test_all.testbin: error while loading shared libraries: libhdf5_hl.so.8: cannot open shared object file: No such file or directory

The thing is, when I lookup the files associated with a freshly installed libhdf5-serial-dev, I cannot find livhdf5_hl.so.8:

victor@boxy:/usr/lib$ dpkg -L libhdf5-serial-dev | grep hdf5

/usr/include/hdf5.h

/usr/include/hdf5.mod

/usr/include/hdf5_hl.h

/usr/lib/libhdf5.settings

/usr/lib/libhdf5.la

/usr/lib/libhdf5_cpp.la

/usr/lib/libhdf5_fortran.la

/usr/lib/libhdf5_hl.la

/usr/lib/libhdf5_hl_cpp.la

/usr/lib/libhdf5hl_fortran.la

/usr/lib/libhdf5.a

/usr/lib/libhdf5_cpp.a

/usr/lib/libhdf5_fortran.a

/usr/lib/libhdf5_hl.a

/usr/lib/libhdf5_hl_cpp.a

/usr/lib/libhdf5hl_fortran.a

/usr/share/doc/libhdf5-serial-dev

/usr/share/doc/libhdf5-serial-dev/copyright

/usr/lib/libhdf5.so

/usr/lib/libhdf5_cpp.so

/usr/lib/libhdf5_fortran.so

/usr/lib/libhdf5_hl.so

/usr/lib/libhdf5_hl_cpp.so

/usr/lib/libhdf5hl_fortran.so

/usr/share/doc/libhdf5-serial-dev/RELEASE.txt.gz

/usr/share/doc/libhdf5-serial-dev/changelog.Debian.gz

Has anybody seen this before? How do I get around this? We'd like to run some experiments where the data is given in HDF5 format.

Thanks!

[SK]

Hi,

I had a similar issue. I am using Ubuntu 12.04. I installed opencv 2.4.10 and Anaconda Python 2.7.8.  Here's what I did to address this issue.

1) Download  hdf5-1.8.13 from  http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/bin/linux-x86_64/. Note that using 1.8.12 resulted in mismatch error between the header and library. So I used 1.8.13. 

2) tar -xvzf to unpack and  browse the lib folder in this distribution  make sure it has libhdf5.so.8.  Then copy the lib folder in this distribution to /usr/lib/hdf5_libs  (you dont need to copy as long as you can point the LD_LIBRARY_PATH to the right folder)

3) Add  /usr/lib/hdf5_libs (change this to your folder where the libhdf5.so.8 libraries are ) to /etc/ld.so.conf. Then run  "sudo  ldconfig"

4) Add  /usr/lib/hdf5_libs to LD_LIBRARY_PATH  in your ~/.bashrc file and source this file.

5) Add  /usr/lib/hdf5_libs to the LIBRARY_DIRS variable in caffe/Makefile.config.   

6) Now run make all, make test, followed by make runtest.

Hope this helps.