[Erros in compiling Caffe in Ubuntu 14.04 LTS]

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Yongjin Cho

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Dec 29, 2015, 9:33:10 PM12/29/15
to Caffe Users
When I try to 'make all -j', 

I get the following error message : 

CXX/LD -o .build_release/tools/net_speed_benchmark.bin
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/test_net.bin] Error 1
make: *** Waiting for unfinished jobs....
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/net_speed_benchmark.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/train_net.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_encoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_lzma_preset@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_memusage@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_code@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/upgrade_net_proto_text.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_encoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_lzma_preset@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_memusage@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_code@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/upgrade_solver_proto_text.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_encoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_lzma_preset@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_memusage@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_code@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/upgrade_net_proto_binary.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_encoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_lzma_preset@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_memusage@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_code@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/compute_image_mean.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_encoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_lzma_preset@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_memusage@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_code@XZ_5.0'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/extract_features.bin] Error 1
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_decoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_footer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_uncompressed_size@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_stream_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_stream_encoder@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_lzma_preset@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_buffer_decode@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libunwind.so.8: undefined reference to `lzma_index_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_end@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_memusage@XZ_5.0'
//usr/lib/x86_64-linux-gnu/libtiff.so.5: undefined reference to `lzma_code@XZ_5.0'

I followed the instructions on this link https://github.com/tiangolo/caffe/blob/ubuntu-tutorial-b/docs/install_apt2.md, and when I looked at the result of 'ldconfig -p | grep lzma', it shows that there is only one ( not shadowed by the one in the anaconda library).
Are there any people who are aware of this issue in compiling? 

Thanks

Neil Nelson

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Dec 30, 2015, 1:01:08 AM12/30/15
to Caffe Users
I compiled three different sets of caffe, including a just obtained caffe-master, on Ubuntu 14.04 yesterday without error.

I used the installation instructions on http://caffe.berkeleyvision.org/installation.html.

I have Python 2.7.6 from the Ubuntu Software Center. There are a lot of packages for hdf5 there also.

ldconfig -p | grep lzma
    liblzma.so.5 (libc6,x86-64) => /lib/x86_64-linux-gnu/liblzma.so.5
    liblzma.so.5 (libc6) => /lib/i386-linux-gnu/liblzma.so.5
    liblzma.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/liblzma.so

Yongjin Cho

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Dec 30, 2015, 1:19:10 AM12/30/15
to Caffe Users
Hey Neil, 

thanks a lot. I got the hint from the line "    liblzma.so.5 (libc6,x86-64) => /lib/x86_64-linux-gnu/liblzma.so.5". Obviously, my linkages were to /usr/lib/ . And I think I mistakenly overwrote on the $LD_LIBRARY_PATH myself while doodling in installation process. 
So I just added "/lib/x86_64-linux-gnu/" to $LD_LIBRARY_PATH and it successfully compiled! 

Thanks!

Shine Leo

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Aug 11, 2016, 9:02:18 AM8/11/16
to Caffe Users
If that still doesn't hold, this is worth to try:

In ~/.bashrc file :  comment out export PATH="/home/jackie/anaconda2/bin:$PATH".  
      Explain: Sometime cmake will try to find library dependency base on python execute (/home/jackie/anaconda2/bin/). This will cause some ananconda's 3-rd library sneak in while linking.

P.S. It is also good to use "make VERBOSE=1" to make the cmake project, which can show the gcc compiling command line.


在 2015年12月30日星期三 UTC+1上午7:19:10，Yongjin Cho写道：
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