Issue with linking

[eugeny-stoyka]

Hello, i installed caffe without any problem but when i'm trying to build caffe-lstm i have next issues:

[ 86%] Linking CXX executable train_net
../lib/libcaffe.so: undefined reference to `H5LTget_dataset_ndims'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_int'
../lib/libcaffe.so: undefined reference to `H5LTfind_dataset'
../lib/libcaffe.so: undefined reference to `caffe::BlockingQueue<caffe::Batch<double>*>::pop(std::string const&)'
../lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_double'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_int'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_float'
../lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_float'
../lib/libcaffe.so: undefined reference to `H5LTget_dataset_info'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_string'
../lib/libcaffe.so: undefined reference to `caffe::BlockingQueue<caffe::Batch<float>*>::pop(std::string const&)'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_double'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_string'
collect2: error: ld returned 1 exit status
make[2]: *** [tools/CMakeFiles/test_net.dir/build.make:127: tools/test_net] Error 1
make[1]: *** [CMakeFiles/Makefile2:510: tools/CMakeFiles/test_net.dir/all] Error 2
../lib/libcaffe.so: undefined reference to `H5LTget_dataset_ndims'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_int'
../lib/libcaffe.so: undefined reference to `H5LTfind_dataset'
../lib/libcaffe.so: undefined reference to `caffe::BlockingQueue<caffe::Batch<double>*>::pop(std::string const&)'
../lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_double'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_int'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_float'
../lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_float'
../lib/libcaffe.so: undefined reference to `H5LTget_dataset_info'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_string'
../lib/libcaffe.so: undefined reference to `caffe::BlockingQueue<caffe::Batch<float>*>::pop(std::string const&)'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_double'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_string'
collect2: error: ld returned 1 exit status
make[2]: *** [tools/CMakeFiles/train_net.dir/build.make:127: tools/train_net] Error 1
make[1]: *** [CMakeFiles/Makefile2:548: tools/CMakeFiles/train_net.dir/all] Error 2
In file included from /usr/include/boost/type_traits/ice.hpp:15:0,
                 from /usr/include/boost/python/detail/def_helper.hpp:9,
                 from /usr/include/boost/python/class.hpp:29,
                 from /usr/include/boost/python.hpp:18,
                 from /home/standnail/Git/caffe-lstm/tools/caffe.cpp:2:
/usr/include/boost/type_traits/detail/ice_or.hpp:17:71: note: #pragma message: NOTE: Use of this header (ice_or.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
                                                                       ^
In file included from /usr/include/boost/type_traits/ice.hpp:16:0,
                 from /usr/include/boost/python/detail/def_helper.hpp:9,
                 from /usr/include/boost/python/class.hpp:29,
                 from /usr/include/boost/python.hpp:18,
                 from /home/standnail/Git/caffe-lstm/tools/caffe.cpp:2:
/usr/include/boost/type_traits/detail/ice_and.hpp:18:72: note: #pragma message: NOTE: Use of this header (ice_and.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
                                                                        ^
In file included from /usr/include/boost/type_traits/ice.hpp:17:0,
                 from /usr/include/boost/python/detail/def_helper.hpp:9,
                 from /usr/include/boost/python/class.hpp:29,
                 from /usr/include/boost/python.hpp:18,
                 from /home/standnail/Git/caffe-lstm/tools/caffe.cpp:2:
/usr/include/boost/type_traits/detail/ice_not.hpp:17:72: note: #pragma message: NOTE: Use of this header (ice_not.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
                                                                        ^
In file included from /usr/include/boost/type_traits/ice.hpp:18:0,
                 from /usr/include/boost/python/detail/def_helper.hpp:9,
                 from /usr/include/boost/python/class.hpp:29,
                 from /usr/include/boost/python.hpp:18,
                 from /home/standnail/Git/caffe-lstm/tools/caffe.cpp:2:
/usr/include/boost/type_traits/detail/ice_eq.hpp:17:71: note: #pragma message: NOTE: Use of this header (ice_eq.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
                                                                       ^
[ 86%] Linking CXX executable caffe
../lib/libcaffe.so: undefined reference to `H5LTget_dataset_ndims'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_int'
../lib/libcaffe.so: undefined reference to `H5LTfind_dataset'
../lib/libcaffe.so: undefined reference to `caffe::BlockingQueue<caffe::Batch<double>*>::pop(std::string const&)'
../lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_double'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_int'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_float'
../lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_float'
../lib/libcaffe.so: undefined reference to `H5LTget_dataset_info'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_string'
../lib/libcaffe.so: undefined reference to `caffe::BlockingQueue<caffe::Batch<float>*>::pop(std::string const&)'
../lib/libcaffe.so: undefined reference to `H5LTread_dataset_double'
../lib/libcaffe.so: undefined reference to `H5LTmake_dataset_string'
collect2: error: ld returned 1 exit status
make[2]: *** [tools/CMakeFiles/caffe.bin.dir/build.make:127: tools/caffe] Error 1
make[1]: *** [CMakeFiles/Makefile2:472: tools/CMakeFiles/caffe.bin.dir/all] Error 2
make: *** [Makefile:128: all] Error 2

I set blas to openblas like cmake -DBLAS=open ../caffe-lstm/ and fixed in make.config file BLAS := open
Doing it on archlinux
any solution?

[ra1995]

Whats the solution??
Compiling on windows MSVC 2015 64bit

[eugeny-stoyka]

I just used gcc5.3 and cuda from official repository. All works well.

[ra1995]

Thanks, all works now

[athiselvam]

Hi @ra1995 what is the change you have made?
i'm also getting the same error. please tell me the changes. I'm using gg5.4

[ra1995]

I don't remember the exact solution, but it had something to do with hdf5 library. I use the bvlc caffe master branch now, it has the necessary lstm layers. You can try building that, didn't give any errors for me.