Linking stage issues with google protobuf

[fbonnet08]

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Issue summary

I having some issues at compilation time, and it seems to fail at linking time at the same place in different systems. The neccessary software has been installed such as protobuf-dev, atlas and the like following the caffe instruction.

The summary of the error is given as follows:

[ 81%] Building CXX object src/caffe/CMakeFiles/caffe.dir/common.cpp.o [ 81%] Linking CXX shared library ../../lib/libcaffe.so [ 81%] Built target caffe Scanning dependencies of target compute_image_mean [ 81%] Building CXX object tools/CMakeFiles/compute_image_mean.dir/compute_image_mean.cpp.o [ 83%] Linking CXX executable compute_image_mean CMakeFiles/compute_image_mean.dir/compute_image_mean.cpp.o: In functionstd::string* google::MakeCheckOpString<int, int>(int const&, int const&, char const*)':
compute_image_mean.cpp:(.text._ZN6google17MakeCheckOpStringIiiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringIiiEEPSsRKT_RKT0_PKc]+0x50): undefined reference to google::base::CheckOpMessageBuilder::NewString()' CMakeFiles/compute_image_mean.dir/compute_image_mean.cpp.o: In functionstd::string* google::MakeCheckOpString<unsigned long, int>(unsigned long const&, int const&, char const*)':
compute_image_mean.cpp:(.text._ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc[ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc]+0x50): undefined reference to google::base::CheckOpMessageBuilder::NewString()' CMakeFiles/compute_image_mean.dir/compute_image_mean.cpp.o: In functionmain':
compute_image_mean.cpp:(.text.startup+0x172): undefined reference to google::SetUsageMessage(std::string const&)' compute_image_mean.cpp:(.text.startup+0x2ab): undefined reference togoogle::protobuf::MessageLite::ParseFromString(std::string const&)'
compute_image_mean.cpp:(.text.startup+0x499): undefined reference to google::protobuf::MessageLite::ParseFromString(std::string const&)' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::Message::InitializationErrorString() const'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::string*)' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::Message::GetTypeName() const'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::Message::DebugString() const' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::internal::empty_string'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)' ../lib/libcaffe.so.1.0.0: undefined reference tocv::imread(std::string const&, int)'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::DescriptorPool::FindFileByName(std::string const&) const' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::internal::StringTypeHandlerBase::Delete(std::string*)' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void ()(std::string const&))'
../lib/libcaffe.so.1.0.0: undefined reference to leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)' ../lib/libcaffe.so.1.0.0: undefined reference tocv::imencode(std::string const&, cv::_InputArray const&, std::vector<unsigned char, std::allocator >&, std::vector<int, std::allocator > const&)'
../lib/libcaffe.so.1.0.0: undefined reference to google::protobuf::internal::StringTypeHandlerBase::New()' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream)'
../lib/libcaffe.so.1.0.0: undefined reference to leveldb::Status::ToString() const' ../lib/libcaffe.so.1.0.0: undefined reference togoogle::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
collect2: error: ld returned 1 exit status
tools/CMakeFiles/compute_image_mean.dir/build.make:134: recipe for target 'tools/compute_image_mean' failed
make[2]: *** [tools/compute_image_mean] Error 1
CMakeFiles/Makefile2:467: recipe for target 'tools/CMakeFiles/compute_image_mean.dir/all' failed
make[1]: *** [tools/CMakeFiles/compute_image_mean.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2
`

Steps to reproduce

If you are having difficulty building Caffe or training a model, please ask the caffe-users mailing list. If you are reporting a build error that seems to be due to a bug in Caffe, please attach your build configuration (either Makefile.config or CMakeCache.txt) and the output of the make (or cmake) command.

Your system configuration

Operating system: linux-x86_64
Compiler: gnu chain tool gcc,g++, gfortran--> 4.9.3
CUDA version: cuda-8.0 driver version 375.39
CUDNN version (if applicable): v5
BLAS: atlas, built in blas
Python or MATLAB version (for pycaffe and matcaffe respectively): python3

[ou525]

i I encountered the same problem, how can you solve?

[akorzh]

same problem for me.
Looks like the problem is that i had gcc 7.1.1 in my system and system protobuf was built with that one.
But CUDA is not supporting gcc >5, so using devtoolset i installed gcc 5.3.1 and used this one to build caffe, but it wont link with protobuf....
And building with gcc 7.1.1 works fine and links to protobuf but CPU only version as CUDA wont compile.
So i am building protobuf from sources using gcc 5.3.1 so it would link to caffe....

hope it helps, folks

[akorzh]

actually wasnt anough. i had recompiled both protobuf (3.2.0) and glog(HEAD) from git with -fPIC ( ./configure --enable-shared --with-pic). NB: protobuf 3.3.0 gave errors for some goooglish reasons.
Also with caffe, edited makefile: removed protobuf and glog from LIBRARIES and added as static to LDFLAGS