Caffe 1.0.0-rc3 make failed on Ubuntu 16.04 / CUDA 8.0

[jianghaitao]

I am trying to build caffe based on the update to date version in the Github. I have installed

• Base OS: Ubuntu 16.04
• CUDA 8.0 / cuDDN 5.05
• Caffe 1.0.0-rc3 (rc3-216-g42cd785-dirty)
• C++ 4.9.3

cmake . runs fine and found / confirmed all dependencies.

make failed with following error

[ 83%] Linking CXX executable caffe
CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `train()':
caffe.cpp:(.text+0x286a): undefined reference to `google::protobuf::internal::StringTypeHandlerBase::New()'
CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `std::string* google::MakeCheckOpString<cudaError, cudaError>(cudaError const&, cudaError const&, char const*)':
caffe.cpp:(.text._ZN6google17MakeCheckOpStringI9cudaErrorS1_EEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringI9cudaErrorS1_EEPSsRKT_RKT0_PKc]+0x50): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `std::string* google::MakeCheckOpString<unsigned long, int>(unsigned long const&, int const&, char const*)':
caffe.cpp:(.text._ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc]+0x50): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `main':
caffe.cpp:(.text.startup+0x53): undefined reference to `google::SetVersionString(std::string const&)'
caffe.cpp:(.text.startup+0x86): undefined reference to `google::SetUsageMessage(std::string const&)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::Message::InitializationErrorString() const'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::string*)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::Message::GetTypeName() const'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::Message::DebugString() const'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::empty_string_'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `cv::imread(std::string const&, int)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::DescriptorPool::FindFileByName(std::string const&) const'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::StringTypeHandlerBase::Delete(std::string*)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `cv::imencode(std::string const&, cv::_InputArray const&, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<int, std::allocator<int> > const&)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `leveldb::Status::ToString() const'
../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
collect2: error: ld returned 1 exit status
tools/CMakeFiles/caffe.bin.dir/build.make:133: recipe for target 'tools/caffe' failed
make[2]: *** [tools/caffe] Error 1
CMakeFiles/Makefile2:435: recipe for target 'tools/CMakeFiles/caffe.bin.dir/all' failed
make[1]: *** [tools/CMakeFiles/caffe.bin.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

Would appreciate any help on this.

[Solomon1588]

Your compiler is GCC 4.9 but the libraries in Ubuntu 15.10 ,16.04 repository is compiled with higher version(e.g. 5.2), so the protobuf lib is not compatible with your caffe.
You can recompile CUDA and Caffe with GCC5.2，
in addition, you can compile the protobuf, glog, gflags and boost .etc(maybe include levledb , lmdb?) manually.
If you want to learn more information, you can browse my post:
#4499 ubuntu 15.10 /16.04 runtest : Segmentation fault (core dumped)—— Be sure to link with compatible libraries

[shelhamer]

For 16.04 compile Caffe master and see #4046.

From https://github.com/BVLC/caffe/blob/master/CONTRIBUTING.md:

Please do not post usage, installation, or modeling questions, or other requests for help to Issues.
Use the caffe-users list instead. This helps developers maintain a clear, uncluttered, and efficient view of the state of Caffe.

[internetcoffeephone]

I had a similar error which was not caused by an old GCC, but by an old protobuf version in my Anaconda install.
It was solved with conda install protobuf, which updated the install.

[hszhoushen]

I successfully solve the problem by recompile the protof with changed gcc ( I changed gcc from gcc5.4 to gcc4.8.5)

[danfouer]

[ 76%] Linking CXX executable ../bin/batch_matmul_op_gpu_test

../lib/libcaffe2.so: undefined reference to google::SetUsageMessage(std::string const&)' ../lib/libcaffe2.so: undefined reference to leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'
../lib/libcaffe2_gpu.so: undefined reference to google::base::CheckOpMessageBuilder::NewString()' ../lib/libcaffe2.so: undefined reference to leveldb::Status::ToString() const'

[danfouer]

I changed gcc from gcc5.4 to gcc4.8.5), then I got：

[ 76%] Linking CXX executable ../bin/batch_matmul_op_gpu_test
/usr/bin/cmake: /home/danfouer/anaconda3/envs/PY27/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
/usr/bin/cmake: /home/danfouer/anaconda3/envs/PY27/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
/usr/bin/cmake: /home/danfouer/anaconda3/envs/PY27/lib/libssl.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
/usr/bin/cmake: /home/danfouer/anaconda3/envs/PY27/lib/libcrypto.so.1.0.0: no version information available (required by /usr/lib/x86_64-linux-gnu/libcurl.so.4)
CMakeFiles/batch_matmul_op_gpu_test.dir/operators/batch_matmul_op_gpu_test.cc.o: In function caffe2::(anonymous namespace)::BatchMatMulOpGPUTest::SetUp()': batch_matmul_op_gpu_test.cc:(.text+0x9ca): undefined reference to google::protobuf::internal::fixed_address_empty_string'
CMakeFiles/batch_matmul_op_gpu_test.dir/operators/batch_matmul_op_gpu_test.cc.o: In function caffe2::(anonymous namespace)::BatchMatMulOpGPUTest_BatchMatMulOpGPUBroadcastTest_Test::TestBody()': batch_matmul_op_gpu_test.cc:(.text+0x2c7f): undefined reference to google::protobuf::internal::fixed_address_empty_string'
../lib/libcaffe2.so: undefined reference to google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)' ../lib/libcaffe2.so: undefined reference to google::SetUsageMessage(std::string const&)'
../lib/libcaffe2.so: undefined reference to google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)' ../lib/libcaffe2.so: undefined reference to google::protobuf::internal::AssignDescriptors(std::string const&, google::protobuf::internal::MigrationSchema const*, google::protobuf::Message const* const*, unsigned int const*, google::protobuf::MessageFactory*, google::protobuf::Metadata*, google::protobuf::EnumDescriptor const**, google::protobuf::ServiceDescriptor const**)'
../lib/libcaffe2.so: undefined reference to google::protobuf::Message::GetTypeName() const' ../lib/libcaffe2.so: undefined reference to google::protobuf::MessageLite::SerializeToString(std::string*) const'
../lib/libcaffe2.so: undefined reference to google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))' ../lib/libcaffe2.so: undefined reference to leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'
../lib/libcaffe2.so: undefined reference to google::protobuf::TextFormat::ParseFromString(std::string const&, google::protobuf::Message*)' ../lib/libcaffe2.so: undefined reference to google::protobuf::Message::DebugString() const'
../lib/libcaffe2_gpu.so: undefined reference to google::base::CheckOpMessageBuilder::NewString()' ../lib/libcaffe2.so: undefined reference to google::protobuf::internal::WireFormatLite::WriteBytes(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
../lib/libcaffe2.so: undefined reference to google::protobuf::internal::OnShutdownDestroyString(std::string const*)' ../lib/libcaffe2.so: undefined reference to google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
../lib/libcaffe2_gpu.so: undefined reference to google::protobuf::Message::ShortDebugString() const' ../lib/libcaffe2_gpu.so: undefined reference to google::protobuf::MessageLite::ParseFromString(std::string const&)'
../lib/libcaffe2.so: undefined reference to google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)' ../lib/libcaffe2_gpu.so: undefined reference to google::protobuf::internal::ParseNamedEnum(google::protobuf::EnumDescriptor const*, std::string const&, int*)'
../lib/libcaffe2.so: undefined reference to leveldb::Status::ToString() const' ../lib/libcaffe2_gpu.so: undefined reference to google::protobuf::MessageLite::SerializeAsString() const'
../lib/libcaffe2.so: undefined reference to google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)' ../lib/libcaffe2.so: undefined reference to google::protobuf::Message::InitializationErrorString() const'
collect2: error: ld returned 1 exit status

[metalaman]

Ubuntu 16.04, Caffe with CPU Only.
Getting g++5 and having this CUSTOM_CXX := /usr/bin/g++-5 in my Makefile.config, then building solved the issue for me. Also, follow steps in this.
I didn't compile any Google library manually.

[hana9090]

@internetcoffeephone How you make caffe consider this protobuf from conda?

[internetcoffeephone]

@hana9090 It did this automatically, I made no effort to do it. I don't know how caffe found my Anaconda installation and decided it was the default python installation (it wasn't), sorry.

[sunbinbin1991]

use this commad and show your g++ version, switch g++ version 5 works for me
sudo update-alternatives --config gcc

[mrgloom]

What if I want to compile on Ubuntu 16 with gcc 4.8 for some reason, how to understand which versions of libs I need and which libs should be compiled from source?

[toby5box]

gcc 5 isn't a viable avenue if you hit this: #6010 (which is why I am using gcc-4.8 and hit the OP's issue today).

Also rebuilding selected libraries with a different gcc may cause runtime issues with previously installed software? (e.g. other ML frameworks)

[adataylor]

@toby5box did you ever find a solution for this? I'm hitting the same

[toby5box]

Sorry @adataylor I do not think I did.