undefined reference to google protobuf error when compiling 3D-Caffe

[DarcyHu]

Hi, I'm trying to compile 3D-Caffe.

my Makefile.config(lines begin with # are removed):

OPENCV_VERSION := 3

CUSTOM_CXX := g++-4.9

CUDA_DIR := /opt/cuda

CUDA_ARCH := -gencode arch=compute_20,code=sm_20 \

  -gencode arch=compute_20,code=sm_21 \

  -gencode arch=compute_30,code=sm_30 \

  -gencode arch=compute_35,code=sm_35 \

  -gencode arch=compute_50,code=sm_50 \

  -gencode arch=compute_50,code=compute_50

BLAS := open

MATLAB_DIR := /usr/local/MATLAB/R2017a

PYTHON_INCLUDE := /usr/include/python2.7 \

  /usr/lib/python2.7/dist-packages/numpy/core/include

PYTHON_LIB := /usr/lib

INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include

LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib

BUILD_DIR := build

DISTRIBUTE_DIR := distribute

TEST_GPUID := 0

Q ?= @

make -j 8 log:

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/upgrade_net_proto_text.bin] Error 1

make: *** Waiting for unfinished jobs....

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'make: *** [Makefile:617: .build_release/tools/finetune_net.bin] Error 1

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/train_net.bin] Error 1

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/upgrade_net_proto_binary.bin] Error 1

.build_release/tools/convert_imageset.o: In function `std::string* google::MakeCheckOpString<unsigned long, int>(unsigned long const&, int const&, char const*)':

convert_imageset.cpp:(.text._ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc]+0x40): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/tools/convert_imageset.o: In function `_GLOBAL__sub_I_convert_imageset.cpp':

convert_imageset.cpp:(.text.startup+0x113): undefined reference to `google::FlagRegisterer::FlagRegisterer<std::string>(char const*, char const*, char const*, std::string*, std::string*)'

convert_imageset.cpp:(.text.startup+0x274): undefined reference to `google::FlagRegisterer::FlagRegisterer<std::string>(char const*, char const*, char const*, std::string*, std::string*)'

.build_release/tools/convert_imageset.o: In function `main':

convert_imageset.cpp:(.text.startup+0x328): undefined reference to `google::SetUsageMessage(std::string const&)'

convert_imageset.cpp:(.text.startup+0xbdb): undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/convert_imageset.bin] Error 1

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/net_speed_benchmark.bin] Error 1

.build_release/tools/compute_image_mean.o: In function `std::string* google::MakeCheckOpString<int, int>(int const&, int const&, char const*)':

compute_image_mean.cpp:(.text._ZN6google17MakeCheckOpStringIiiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringIiiEEPSsRKT_RKT0_PKc]+0x40): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/tools/compute_image_mean.o: In function `std::string* google::MakeCheckOpString<unsigned long, int>(unsigned long const&, int const&, char const*)':

compute_image_mean.cpp:(.text._ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc]+0x40): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/tools/compute_image_mean.o: In function `_GLOBAL__sub_I_compute_image_mean.cpp':

compute_image_mean.cpp:(.text.startup+0xaf): undefined reference to `google::FlagRegisterer::FlagRegisterer<std::string>(char const*, char const*, char const*, std::string*, std::string*)'

.build_release/tools/compute_image_mean.o: In function `main':

compute_image_mean.cpp:(.text.startup+0x155): undefined reference to `google::SetUsageMessage(std::string const&)'

compute_image_mean.cpp:(.text.startup+0x259): undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

compute_image_mean.cpp:(.text.startup+0x3ee): undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::fixed_address_empty_string'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/compute_image_mean.bin] Error 1

.build_release/tools/extract_features.o: In function `std::string* google::MakeCheckOpString<int, int>(int const&, int const&, char const*)':

extract_features.cpp:(.text._ZN6google17MakeCheckOpStringIiiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringIiiEEPSsRKT_RKT0_PKc]+0x40): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/tools/extract_features.o: In function `std::string* google::MakeCheckOpString<unsigned long, unsigned long>(unsigned long const&, unsigned long const&, char const*)':

extract_features.cpp:(.text._ZN6google17MakeCheckOpStringImmEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImmEEPSsRKT_RKT0_PKc]+0x41): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'

.build_release/tools/extract_features.o: In function `int feature_extraction_pipeline<float>(int, char**)':

extract_features.cpp:(.text._Z27feature_extraction_pipelineIfEiiPPc[_Z27feature_extraction_pipelineIfEiiPPc]+0xc6a): undefined reference to `google::protobuf::internal::fixed_address_empty_string'

extract_features.cpp:(.text._Z27feature_extraction_pipelineIfEiiPPc[_Z27feature_extraction_pipelineIfEiiPPc]+0x127d): undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::InitializationErrorString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::io::CodedOutputStream::WriteStringWithSizeToArray(std::string const&, unsigned char*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() const'

.build_release/lib/libcaffe.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**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::DebugString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::NameOfEnum(google::protobuf::EnumDescriptor const*, int)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::ReadBytes(google::protobuf::io::CodedInputStream*, std::string*)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageFactory::InternalRegisterGeneratedFile(char const*, void (*)(std::string const&))'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::string const&, leveldb::DB**)'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteBytesMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

.build_release/lib/libcaffe.so: undefined reference to `leveldb::Status::ToString() const'

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'

collect2: error: ld returned 1 exit status

make: *** [Makefile:617: .build_release/tools/extract_features.bin] Error 1

ldd .build_release/lib/libcaffe.so gives me:

linux-vdso.so.1 (0x00007ffd14bd3000)

libcudart.so.8.0 => /opt/cuda/lib64/libcudart.so.8.0 (0x00007f5236d0c000)

libcublas.so.8.0 => /opt/cuda/lib64/libcublas.so.8.0 (0x00007f5234274000)

libcurand.so.8.0 => /opt/cuda/lib64/libcurand.so.8.0 (0x00007f52302fe000)

libglog.so.0 => /usr/lib/libglog.so.0 (0x00007f52300cd000)

libgflags.so.2.2 => /usr/lib/libgflags.so.2.2 (0x00007f522fea8000)

libprotobuf.so.13 => /usr/lib/libprotobuf.so.13 (0x00007f522fa13000)

libboost_system.so.1.65.1 => /usr/lib/libboost_system.so.1.65.1 (0x00007f522f80e000)

libboost_filesystem.so.1.65.1 => /usr/lib/libboost_filesystem.so.1.65.1 (0x00007f522f5f3000)

libhdf5_hl.so.100 => /usr/lib/libhdf5_hl.so.100 (0x00007f522f3d0000)

libhdf5.so.101 => /usr/lib/libhdf5.so.101 (0x00007f522ee4d000)

libleveldb.so.1 => /usr/lib/libleveldb.so.1 (0x00007f522ebee000)

libsnappy.so.1 => /usr/lib/libsnappy.so.1 (0x00007f522e9e6000)

liblmdb.so => /usr/lib/liblmdb.so (0x00007f522e7d1000)

libopencv_core.so.3.3 => /usr/lib/libopencv_core.so.3.3 (0x00007f522d48b000)

libopencv_highgui.so.3.3 => /usr/lib/libopencv_highgui.so.3.3 (0x00007f522d278000)

libopencv_imgproc.so.3.3 => /usr/lib/libopencv_imgproc.so.3.3 (0x00007f522957b000)

libopencv_imgcodecs.so.3.3 => /usr/lib/libopencv_imgcodecs.so.3.3 (0x00007f5228fd5000)

libboost_thread.so.1.65.1 => /usr/lib/libboost_thread.so.1.65.1 (0x00007f5228daf000)

libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f5228a28000)

libopenblas.so.3 => /usr/lib/libopenblas.so.3 (0x00007f52264a6000)

libm.so.6 => /usr/lib/libm.so.6 (0x00007f522615a000)

libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f5225f43000)

libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007f5225d25000)

libc.so.6 => /usr/lib/libc.so.6 (0x00007f522596e000)

libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f522576a000)

librt.so.1 => /usr/lib/librt.so.1 (0x00007f5225562000)

libz.so.1 => /usr/lib/libz.so.1 (0x00007f522534b000)

/usr/lib64/ld-linux-x86-64.so.2 (0x00007f5237a64000)

libtcmalloc.so.4 => /usr/lib/libtcmalloc.so.4 (0x00007f52250d7000)

libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f5224e33000)

libtbb.so.2 => /usr/lib/libtbb.so.2 (0x00007f5224bf7000)

libgtk-x11-2.0.so.0 => /usr/lib/libgtk-x11-2.0.so.0 (0x00007f52245b7000)

libgdk-x11-2.0.so.0 => /usr/lib/libgdk-x11-2.0.so.0 (0x00007f5224302000)

libcairo.so.2 => /usr/lib/libcairo.so.2 (0x00007f5223fe4000)

libgdk_pixbuf-2.0.so.0 => /usr/lib/libgdk_pixbuf-2.0.so.0 (0x00007f5223dc0000)

libgobject-2.0.so.0 => /usr/lib/libgobject-2.0.so.0 (0x00007f5223b6d000)

libglib-2.0.so.0 => /usr/lib/libglib-2.0.so.0 (0x00007f522385a000)

libgtkglext-x11-1.0.so.0 => /usr/lib/libgtkglext-x11-1.0.so.0 (0x00007f5223656000)

libgdkglext-x11-1.0.so.0 => /usr/lib/libgdkglext-x11-1.0.so.0 (0x00007f52233f2000)

libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0x00007f5223189000)

libwebp.so.7 => /usr/lib/libwebp.so.7 (0x00007f5222f20000)

libpng16.so.16 => /usr/lib/libpng16.so.16 (0x00007f5222ce9000)

libtiff.so.5 => /usr/lib/libtiff.so.5 (0x00007f5222a62000)

libjasper.so.4 => /usr/lib/libjasper.so.4 (0x00007f52227ed000)

libIlmImf-2_2.so.22 => /usr/lib/libIlmImf-2_2.so.22 (0x00007f5222314000)

libHalf.so.12 => /usr/lib/libHalf.so.12 (0x00007f52220d1000)

libgfortran.so.4 => /usr/lib/libgfortran.so.4 (0x00007f5221cf5000)

libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007f5221ac7000)

libGLX.so.0 => /usr/lib/libGLX.so.0 (0x00007f5221897000)

libGLdispatch.so.0 => /usr/lib/libGLdispatch.so.0 (0x00007f52215c9000)

libgmodule-2.0.so.0 => /usr/lib/libgmodule-2.0.so.0 (0x00007f52213c5000)

libpangocairo-1.0.so.0 => /usr/lib/libpangocairo-1.0.so.0 (0x00007f52211b8000)

libX11.so.6 => /usr/lib/libX11.so.6 (0x00007f5220e79000)

libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f5220c73000)

libatk-1.0.so.0 => /usr/lib/libatk-1.0.so.0 (0x00007f5220a4d000)

libgio-2.0.so.0 => /usr/lib/libgio-2.0.so.0 (0x00007f52206b2000)

libpangoft2-1.0.so.0 => /usr/lib/libpangoft2-1.0.so.0 (0x00007f522049c000)

libpango-1.0.so.0 => /usr/lib/libpango-1.0.so.0 (0x00007f522024d000)

libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x00007f5220008000)

libXrender.so.1 => /usr/lib/libXrender.so.1 (0x00007f521fdfd000)

libXinerama.so.1 => /usr/lib/libXinerama.so.1 (0x00007f521fbfa000)

libXi.so.6 => /usr/lib/libXi.so.6 (0x00007f521f9e9000)

libXrandr.so.2 => /usr/lib/libXrandr.so.2 (0x00007f521f7de000)

libXcursor.so.1 => /usr/lib/libXcursor.so.1 (0x00007f521f5d3000)

libXcomposite.so.1 => /usr/lib/libXcomposite.so.1 (0x00007f521f3d0000)

libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f521f1cd000)

libXext.so.6 => /usr/lib/libXext.so.6 (0x00007f521efbb000)

libpixman-1.so.0 => /usr/lib/libpixman-1.so.0 (0x00007f521ed13000)

libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x00007f521ea4d000)

libxcb-shm.so.0 => /usr/lib/libxcb-shm.so.0 (0x00007f521e849000)

libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f521e620000)

libxcb-render.so.0 => /usr/lib/libxcb-render.so.0 (0x00007f521e412000)

libffi.so.6 => /usr/lib/libffi.so.6 (0x00007f521e209000)

libpcre.so.1 => /usr/lib/libpcre.so.1 (0x00007f521df96000)

libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f521dd16000)

libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00007f521dafb000)

libXt.so.6 => /usr/lib/libXt.so.6 (0x00007f521d892000)

libpangox-1.0.so.0 => /usr/lib/libpangox-1.0.so.0 (0x00007f521d672000)

liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007f521d44c000)

libImath-2_2.so.12 => /usr/lib/libImath-2_2.so.12 (0x00007f521d23a000)

libIex-2_2.so.12 => /usr/lib/libIex-2_2.so.12 (0x00007f521d01a000)

libIlmThread-2_2.so.12 => /usr/lib/libIlmThread-2_2.so.12 (0x00007f521ce13000)

libquadmath.so.0 => /usr/lib/../lib/libquadmath.so.0 (0x00007f521cbd3000)

libresolv.so.2 => /usr/lib/libresolv.so.2 (0x00007f521c9bc000)

libmount.so.1 => /usr/lib/libmount.so.1 (0x00007f521c768000)

libharfbuzz.so.0 => /usr/lib/libharfbuzz.so.0 (0x00007f521c4cf000)

libthai.so.0 => /usr/lib/libthai.so.0 (0x00007f521c2c5000)

libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00007f521c093000)

libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x00007f521be83000)

libXau.so.6 => /usr/lib/libXau.so.6 (0x00007f521bc7f000)

libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007f521ba79000)

libSM.so.6 => /usr/lib/libSM.so.6 (0x00007f521b871000)

libICE.so.6 => /usr/lib/libICE.so.6 (0x00007f521b654000)

libblkid.so.1 => /usr/lib/libblkid.so.1 (0x00007f521b409000)

libuuid.so.1 => /usr/lib/libuuid.so.1 (0x00007f521b204000)

libgraphite2.so.3 => /usr/lib/libgraphite2.so.3 (0x00007f521afd8000)

libdatrie.so.1 => /usr/lib/libdatrie.so.1 (0x00007f521add0000)

It shows that libprotobuf is founded. 

I have to use gcc 4.9.4, because I will need to make matcaffe, which MATLAB mex compiler only support gcc 4.9.x.

OS: Arch Linux

Compiler: gcc-4.9.4

CUDA: 8.0.61

protobuf: 3.3.2

MATLAB: 2017b

[DarcyHu]

Actually, MATLAB did not support gcc > 4.9.x as mex compiler officially, one could still use gcc > 4.9.x. And caffe suggests gcc > 4.9.x to compile caffe. So, I changed the Makefile.config, set CUSTOM_CXX := g++-5, finally I succeed to compile and build 3D-Caffe. make all & make matcaffe with no error.

However, when I use matcaffe, I got this error:

Invalid MEX-file '~/3D-FCNN-code/Automatic

3D Cardiovascular MR Segmentation with Densely-Connected Volumetric

ConvNets/HeartSeg/3D-Caffe/matlab/+caffe/private/caffe_.mexa64':

'~/3D-FCNN-code/Automatic 3D

Cardiovascular MR Segmentation with Densely-Connected Volumetric

ConvNets/HeartSeg/3D-Caffe/matlab/+caffe/private/caffe_.mexa64' is not a valid

shared library..

Error in caffe.reset_all (line 5)

caffe_('reset');

Error in test_model (line 36)

caffe.reset_all

 Test code is available here.

!ldd ../3D-Caffe/matlab/+caffe/private/caffe_.mexa64 gives me:

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ../3D-Caffe/matlab/+caffe/private/caffe_.mexa64)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libglog.so.0)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libglog.so.0)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libgflags.so.2.2)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libgflags.so.2.2)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libprotobuf.so.13)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libboost_system.so.1.65.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libboost_system.so.1.65.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libboost_filesystem.so.1.65.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libboost_filesystem.so.1.65.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libleveldb.so.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libsnappy.so.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libsnappy.so.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libopencv_core.so.3.3)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libopencv_core.so.3.3)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libopencv_imgproc.so.3.3)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libopencv_imgcodecs.so.3.3)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libopencv_imgcodecs.so.3.3)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /usr/lib/libboost_thread.so.1.65.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libboost_thread.so.1.65.1)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libtcmalloc.so.4)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libIlmImf-2_2.so.22)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libIex-2_2.so.12)

../3D-Caffe/matlab/+caffe/private/caffe_.mexa64: /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/libIlmThread-2_2.so.12)

It seems that the libstdc++ version ship with MATLAB 2017a is not compatible with the system lib, which is linked with while building matcaffe. So I create a soft link to the system's libstdc++, and try again, MATLAB still complained that caffe_.mexa64 is invalid.

Any suggestion?

[DarcyHu]

Ok, just to mentioned that it's solved. The libfreetype shipped with MATLAB is too old, use the system one instead.

env LD_PRELOAD=/usr/lib/libstdc++.so.6:/usr/lib/libfreetype.so.6 MATLAB_SHELL=bash optirun matlab -desktop