caffe build on ubuntu 15.10

[Алексей Филимонов]

CXX/LD -o .build_release/tools/extract_features.bin
CXX/LD -o .build_release/tools/compute_image_mean.bin
CXX/LD -o .build_release/tools/test_net.bin
CXX/LD -o .build_release/tools/caffe.bin
CXX/LD -o .build_release/tools/device_query.bin
CXX/LD -o .build_release/tools/convert_imageset.bin
.build_release/tools/extract_features.o: In function `caffe::db::LevelDBTransaction::Commit()':
extract_features.cpp:(.text._ZN5caffe2db18LevelDBTransaction6CommitEv[_ZN5caffe2db18LevelDBTransaction6CommitEv]+0x71): undefined reference to `leveldb::Status::ToString() const'
.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]+0x50): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
.build_release/tools/extract_features.o: In function `std::string* google::MakeCheckOpString<unsigned int, int>(unsigned int const&, int const&, char const*)':
extract_features.cpp:(.text._ZN6google17MakeCheckOpStringIjiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringIjiEEPSsRKT_RKT0_PKc]+0x50): 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]+0x51): 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]+0xca4): undefined reference to `google::protobuf::internal::empty_string_'
extract_features.cpp:(.text._Z27feature_extraction_pipelineIfEiiPPc[_Z27feature_extraction_pipelineIfEiiPPc]+0x105e): undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'
extract_features.cpp:(.text._Z27feature_extraction_pipelineIfEiiPPc[_Z27feature_extraction_pipelineIfEiiPPc]+0x2081): undefined reference to `leveldb::Status::ToString() 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::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::string*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() 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 `cv::imread(std::string const&, int)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::DescriptorPool::FindFileByName(std::string const&) const'
.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::internal::StringTypeHandlerBase::Delete(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 `cv::imencode(std::string const&, cv::_InputArray const&, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<int, std::allocator<int> > const&)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::StringTypeHandlerBase::New()'
.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::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
collect2: error: ld returned 1 exit status
Makefile:596: recipe for target '.build_release/tools/extract_features.bin' failed
make: *** [.build_release/tools/extract_features.bin] Error 1
.build_release/tools/compute_image_mean.o: Inmake: *** Waiting for unfinished jobs....
 function `std::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()'
.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]+0x50): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
.build_release/tools/compute_image_mean.o: In function `main':
compute_image_mean.cpp:(.text.startup+0x148): undefined reference to `google::SetUsageMessage(std::string const&)'
compute_image_mean.cpp:(.text.startup+0x281): undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'
compute_image_mean.cpp:(.text.startup+0x471): 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::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::string*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() 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::empty_string_'
.build_release/lib/libcaffe.so: undefined reference to `cv::imread(std::string const&, int)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::DescriptorPool::FindFileByName(std::string const&) const'
.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::internal::StringTypeHandlerBase::Delete(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 `cv::imencode(std::string const&, cv::_InputArray const&, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<int, std::allocator<int> > const&)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::StringTypeHandlerBase::New()'
.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
Makefile:596: recipe for target '.build_release/tools/compute_image_mean.bin' failed
make: *** [.build_release/tools/compute_image_mean.bin] Error 1
.build_release/tools/caffe.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()'
.build_release/tools/caffe.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()'
.build_release/tools/caffe.o: In function `main':
caffe.cpp:(.text.startup+0x50): undefined reference to `google::SetUsageMessage(std::string const&)'
.build_release/tools/caffe.o: In function `std::string* google::MakeCheckOpString<int, float>(int const&, float const&, char const*)':
caffe.cpp:(.text._ZN6google17MakeCheckOpStringIifEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringIifEEPSsRKT_RKT0_PKc]+0x56): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
.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::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::string*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() 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::empty_string_'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'
.build_release/lib/libcaffe.so: undefined reference to `cv::imread(std::string const&, int)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::DescriptorPool::FindFileByName(std::string const&) const'
.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::internal::StringTypeHandlerBase::Delete(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 `cv::imencode(std::string const&, cv::_InputArray const&, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<int, std::allocator<int> > const&)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::StringTypeHandlerBase::New()'
.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
Makefile:596: recipe for target '.build_release/tools/caffe.bin' failed
make: *** [.build_release/tools/caffe.bin] Error 1
.build_release/tools/convert_imageset.o: In function `caffe::db::LevelDBTransaction::Commit()':
convert_imageset.cpp:(.text._ZN5caffe2db18LevelDBTransaction6CommitEv[_ZN5caffe2db18LevelDBTransaction6CommitEv]+0x71): undefined reference to `leveldb::Status::ToString() const'
.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]+0x50): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
.build_release/tools/convert_imageset.o: In function `main':
convert_imageset.cpp:(.text.startup+0x31d): undefined reference to `google::SetUsageMessage(std::string const&)'
convert_imageset.cpp:(.text.startup+0x959): undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) const'
convert_imageset.cpp:(.text.startup+0x107e): undefined reference to `leveldb::Status::ToString() 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::internal::WireFormatLite::ReadString(google::protobuf::io::CodedInputStream*, std::string*)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::Message::GetTypeName() 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::empty_string_'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::MessageLite::ParseFromString(std::string const&)'
.build_release/lib/libcaffe.so: undefined reference to `cv::imread(std::string const&, int)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::DescriptorPool::FindFileByName(std::string const&) const'
.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::internal::StringTypeHandlerBase::Delete(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 `cv::imencode(std::string const&, cv::_InputArray const&, std::vector<unsigned char, std::allocator<unsigned char> >&, std::vector<int, std::allocator<int> > const&)'
.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::StringTypeHandlerBase::New()'
.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::WireFormatLite::WriteString(int, std::string const&, google::protobuf::io::CodedOutputStream*)'
collect2: error: ld returned 1 exit status
Makefile:596: recipe for target '.build_release/tools/convert_imageset.bin' failed
make: *** [.build_release/tools/convert_imageset.bin] Error 1

I install all dependencies and make pycaffe ok, but make all have some errors. I used gcc-4.9 because gcc-5.1 dont supported nvcc.

[Jan C Peters]

The error messages indicate that the problem is related to the protobuf lib dependency, i. e. it seems libprotobuf.so is not pulled in for some reason. You sure you installed libprotobuf-dev ?

However, you also cannot expect everything to work out-of-the-box on a new distro release that is only a few days old.

[Алексей Филимонов]

Yes, i am sure that install libprotobuf-dev, i try install another version, but it doesn`t work.

[Алексей Филимонов]

Yeah, you are right, but i will hope, that it will work, but i was wrong.

[Jan C Peters]

Well if you want to go deeper, the first step for me would be to run ldd on the caffe lib, e. g. ldd .build_release/lib/libcaffe.so, which gies you the libraries caffe depends on. libprotobuf.so should be listed there (quick check with ldd .build_release/lib/libcaffe.so | grep protobuf; if it doesn't output anything, libprotobuf is not in the list).

[Алексей Филимонов]

alexey@alexey-des:~/caffe$ sudo ldd .build_release/lib/libcaffe.so | grep protobuf
    libprotobuf.so.9 => /usr/lib/x86_64-linux-gnu/libprotobuf.so.9 (0x00007f060397d000)
 
libcaffe.so has reference for libprotobuf.

[Алексей Филимонов]

but, references of next libs didn`t found.
    libcudart.so.7.0 => not found
    libcublas.so.7.0 => not found
    libcurand.so.7.0 => not found
    libcudnn.so.7.0 => not found

[Jan C Peters]

The CUDA libs are not found because ld does not know about them, but they should exist in /usr/local/cuda-7.0/lib64. There are essentially two ways to inform ld about these libs, either setting LD_LIBRARY_PATH or adding a very short config file to /etc/ld.so.conf.d, both of which are explained here: http://askubuntu.com/questions/210884/setting-ld-library-path-for-cuda.

But that libprotobuf is actually in the list and the linker can't find these references puzzles me.

After having a closer look at the outputs, it is not only protobuf that is having problems, but also leveldb and opencv. Maybe it has something to do with the compiler you are using. You can try to use the standard gcc (5.1) and see if those errors still arise. To shut CUDA up about the compiler version you can edit /usr/local/cuda-7.0/include/host_config.h. Somewhere around line 104 there should be the GNUC version check. Just remove that #if ... #endif block altogether or change the checked version numbers so that 5.1 gets accepted. This is kind of a dirty hack, but it shouldn't be a problem (have done it myself).

[Алексей Филимонов]

I tried this method(change for gcc 5.1), but it didn't help for this problem, i had some errors for build .cu files.
For example errors.

/usr/include/c++/5/bits/locale_classes.tcc:271:23: error: template argument required for ‘class collate_byname’
/usr/include/c++/5/bits/locale_classes.tcc:273:23: error: ‘collate’ is not a template function
/usr/include/c++/5/bits/locale_classes.tcc:273:30: error: expected ‘;’ before ‘<’ token
/usr/include/c++/5/bits/locale_classes.tcc:277:22: error: parse error in template argument list
/usr/include/c++/5/bits/locale_classes.tcc:277:22: error: template-id ‘has_facet<<expression error> >’ for ‘bool std::has_facet(const std::locale&)’ does not match any template declaration
/usr/include/c++/5/bits/locale_classes.tcc:282:23: error: ‘collate’ is not a class template
   extern template class collate<wchar_t>;
                       ^
/usr/include/c++/5/bits/locale_classes.tcc:282:23: error: template argument required for ‘class collate’
/usr/include/c++/5/bits/locale_classes.tcc:283:23: error: ‘collate_byname’ is not a class template
   extern template class collate_byname<wchar_t>;
                       ^
/usr/include/c++/5/bits/locale_classes.tcc:283:23: error: template argument required for ‘class collate_byname’
/usr/include/c++/5/bits/locale_classes.tcc:285:23: error: ‘collate’ is not a template function
/usr/include/c++/5/bits/locale_classes.tcc:285:30: error: expected ‘;’ before ‘<’ token
/usr/include/c++/5/bits/locale_classes.tcc:289:22: error: parse error in template argument list
/usr/include/c++/5/bits/locale_classes.tcc:289:22: error: template-id ‘has_facet<<expression error> >’ for ‘bool std::has_facet(const std::locale&)’ does not match any template declaration
Makefile:565: recipe for target '.build_release/cuda/src/caffe/util/math_functions.o' failed
make: *** [.build_release/cuda/src/caffe/util/math_functions.o] Error 1


Do you have any advises for solution of this problem?

[Jan C Peters]

That may have something to do with the c++ standard that is used for compilation but I am entirely unsure about that. And sadly I don't have time to try and reproduce these errors. You will probably have to wait for the devs to fix that. But my guess is that they will probably only add support for the next LTS version of ubuntu (which would be 16.04), at least the only ubuntu versions they mention on the installation page (http://caffe.berkeleyvision.org/installation.html) as "tested on" are LTS versions.


Anyway, I just found this GitHub issue (https://github.com/BVLC/caffe/issues/2347) which may by chance be related to your problem, at least these guys seem to have gotten it to compile on ubuntu 15.04. Maybe that works for you too?

[Алексей Филимонов]

If i disable support CUDA(only CPU), caffe will build "make all" fine, 0 errors. May be this comment help you for understand my problem.

[Алексей Филимонов]

Ok, thank you for advices, i will try it, may be it help me.

[Darren Garvey]

Are you setting CUDA_HOST_COMPILER? I hacked around this issue last night and got caffe linking on Ubuntu 15.10.

The issue with linking to protobuf is down to c++ ABI changes between GCC 4.9 and GCC 5.x. The ABI for std::string has changed so you need to be sure to link with compatible libraries.

Since CUDA doesn't officially support GCC >= 4.9, I had initially set CUDA_HOST_COMPILER to get CUDA stuff compiled. The issue with doing just that is that caffe will build with the default GCC which is 5.2.

If you go ahead and build caffe with GCC 4.9 as well then you'll have link problems against the libprotobuf-dev package which is built with GCC 5.x as with all other Ubuntu packages in 15.10.

What I ended up doing is just hacking the header in CUDA that claims CUDA can't be built with GCC 5.x. I think it was host_config.h or something similar (don't have it here, sorry). Hacking that to make the version check accept GCC 5.2 made the problem go away and I've not had any issues with CUDA. I'm guessing it's just a defensive check, but YMMV!

The alternative meant too much building IMO so I went with a hack. You may want to build everything with GCC 4.9 but you'll also have to build protobuf and possibly also all other system packages that export c++ functions containing std::string, std::vector, etc.with GCC 4.9 (eg. glog, gflags, boost?).

It would be better if nvidia just updated CUDA to support GCC 5.x (I was using the latest 7.5 version btw). I've not checked yet if there's a ticket for that open.

I have one more outstanding issue with liblzma linking but that's related to using anaconda. I only mention it for posterity.

Hope that helps.

Cheers,
Darren

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[Jan C Peters]

Well, I got caffe to compile with gcc 5.x (on Fedora) and CUDA 7.5, so maybe just try to use CUDA 7.5 instead of 7.0, at least there is a chance that this solves your problem (without reverting to a gcc 4.x version)

[Алексей Филимонов]

I install  cuda 7.5 and caffe build with gcc 5, but need to comments strings about errors in cuda config.h

thanks for that advice, but i don't work with caffe after that, may be it is solution doesn't work.

[Jonathan Chappelow]

That hack is what the Arch Linux package has done.  The comment still says to support 4.9, but that is a relic from when the SDK didn't support 4.9.  :)

[Darren Garvey]

On 30 October 2015 at 00:02, Jonathan Chappelow <jonathan....@gmail.com> wrote:

That hack is what the Arch Linux package has done.  The comment still says to support 4.9, but that is a relic from when the SDK didn't support 4.9.  :)

Hehe, I see they've just blotted out the error entirely. Nothing to see here... *whistles* I just changed line 113 in /usr/local/cuda/include/host_config.h to this:

#if __GNUC__ > 5 || (__GNUC__ == 5 && __GNUC_MINOR__ > 2)

.. perhaps *slighly* more good-citizeny? ;)

Perhaps NVIDIA should just make this check issue a warning rather than a hard error and make their lives a bit easier.

I hope you got it working at least Aleksey as I've not had any further issues (so far).

Cheers,

Darren

[Julie Bernauer]

With no other change there will be issues with protobuf and other libs because of the C++ ABI change. One way to overcome this is to force GCC to use the old ABI version by using the flag -D_GLIBCXX_USE_CXX11_ABI=0 in the Makefile. While maybe not the best ideal way to do it, a change at line 245 in the Makefile works.

[Locke Lee]

Hi, may i keep asking you a question? i can use cuda, but i can't compile caffe, i have try a lot of ways to reduce error, and now i got this error that i have nothing to do with:

CXX src/caffe/net.cpp
PROTOC src/caffe/proto/caffe.proto
...fine...
CXX tools/net_speed_benchmark.cpp
CXX examples/mnist/convert_mnist_data.cpp
CXX examples/cifar10/convert_cifar_data.cpp
CXX examples/cpp_classification/classification.cpp
CXX examples/siamese/convert_mnist_siamese_data.cpp
CXX .build_release/src/caffe/proto/caffe.pb.cc
AR -o .build_release/lib/libcaffe.a
LD -o .build_release/lib/libcaffe.so
CXX/LD -o .build_release/tools/test_net.bin
CXX/LD -o .build_release/tools/upgrade_solver_proto_text.bin
CXX/LD -o .build_release/tools/extract_features.bin
.build_release/tools/extract_features.o: In function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >* google::MakeCheckOpString<int, int>(int const&, int const&, char const*)':
extract_features.cpp:(.text._ZN6google17MakeCheckOpStringIiiEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc[_ZN6google17MakeCheckOpStringIiiEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc]+0x50): undefined reference to `google::base::CheckOpMessageBuilder::NewString[abi:cxx11]()'
.build_release/tools/extract_features.o: In function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >* google::MakeCheckOpString<unsigned long, unsigned long>(unsigned long const&, unsigned long const&, char const*)':
extract_features.cpp:(.text._ZN6google17MakeCheckOpStringImmEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImmEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc]+0x51): undefined reference to `google::base::CheckOpMessageBuilder::NewString[abi:cxx11]()'

collect2: error: ld returned 1 exit status

Makefile:598: recipe for target '.build_release/tools/extract_features.bin' failed

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

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

.build_release/lib/libcaffe.so: undefined reference to `google::base::CheckOpMessageBuilder::NewString[abi:cxx11]()'

collect2: error: ld returned 1 exit status

Makefile:598: recipe for target '.build_release/tools/upgrade_solver_proto_text.bin' failed
make: *** [.build_release/tools/upgrade_solver_proto_text.bin] Error 1
---when--
CXXFLAGS += -D_GLIBCXX_USE_CXX11_ABI=1
*****************************************************************************************
CXX examples/siamese/convert_mnist_siamese_data.cpp
CXX .build_release/src/caffe/proto/caffe.pb.cc
AR -o .build_release/lib/libcaffe.a
LD -o .build_release/lib/libcaffe.so
CXX/LD -o .build_release/tools/test_net.bin
CXX/LD -o .build_release/tools/upgrade_solver_proto_text.bin
CXX/LD -o .build_release/tools/extract_features.bin

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

.build_release/lib/libcaffe.so: undefined reference to `google::protobuf::internal::StringTypeHandlerBase::Delete(std::string*)'

.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::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::Message::DebugString() const'

.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::StringTypeHandlerBase::New()'

.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::empty_string_'

.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::WriteString(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::DescriptorPool::FindFileByName(std::string const&) const'
.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::Message::InitializationErrorString() const'

collect2: error: ld returned 1 exit status

Makefile:596: recipe for target '.build_release/tools/upgrade_solver_proto_text.bin' failed
make: *** [.build_release/tools/upgrade_solver_proto_text.bin] Error 1

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

.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]+0xc80): undefined reference to `google::protobuf::internal::empty_string_'
extract_features.cpp:(.text._Z27feature_extraction_pipelineIfEiiPPc[_Z27feature_extraction_pipelineIfEiiPPc]+0x1313): undefined reference to `google::protobuf::MessageLite::SerializeToString(std::string*) 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

---when--
CXXFLAGS += -D_GLIBCXX_USE_CXX11_ABI=0
************************************************************************************

------------------------------------------------
My environment is:
  `Ubuntu 15.10 64bit mate
  `intel MKL
  `Cuda 7.5
  `g++/gcc 5.2.1
i had changed the host_config.h in cuda-7.5/include
you said the problem is about c++ ABI, i tried both methods but still failed. could you help? Thanks!



------------------------------------------------


在 2015年11月21日星期六 UTC+8下午3:14:31，Julie Bernauer写道：

[rswt...@gmail.com]

Have you solved this problem ? I have been solving this problem for a long time, but failed!

在 2015年10月27日星期二 UTC+8下午9:57:03，Алексей Филимонов写道：

[Khoi Tran]

Hi all,

Thanks for the thread.  I just install 15.10 and this saved me from a lot of troubles.
With the latest version 15.10.1, only hacking CUDA is not enough. The error is because google-glog got built with -D_GLIBCXX_USE_CXX11_ABI=0 while everything else use the default option!
This is also the cause of the error that Locke Lee have shown.

I have made a full guide, (feel free to correct my English :D)

///////////////////////////////////////////////////////
1. HACK CUDA
+As all other packages in ubuntu 15.10 is built with GCC 5(.2) but CUDA (7.5) not allow >4.9 gcc version!
+We would like to "hack" CUDA to compile cuda files with gcc-5 as follows:

a) sudo gedit /usr/local/cuda/include/host_config.h

b) change line 113 to #if __GNUC__ > 5 || (__GNUC__ == 5 && __GNUC_MINOR__ > 2)

///////////////////////////////////////////////////////
2. FIX google-glog
+Some bad guys build google-glog with wrong gcc abi config! And the wrong build is in
the official repository. Fack!
+i.e when all other package is built with -D_GLIBCXX_USE_CXX11_ABI=1 (default). They built it with
-D_GLIBCXX_USE_CXX11_ABI=0! We need to built it ourself!

a)
sudo apt-get remove libgoogle-glog-dev libgoogle-glog0v5
cd ~ //other folder is ok
apt-get source libgoogle-glog-dev
cd google-glog-0.3.4
./configure

b) The generated makefile have some mistakes (?)
- change line 613 to ACLOCAL=aclocal-1.15
- change line 619 to AUTOMAKE=automake-1.15

c)
make // this will have some errors, dont worry
automake --add-missing
make -j 16 //or 100,whatever
sudo make install

//////////////////////////////////////////////////////////
Now we can build caffe! Profit!

[Attilio Porchia]

Thanks for waste time for a useless answer...

[djeb mtwo]

Anyone managed to solve this ?

Thank you.

[Jurgen Meijer]

Got passed this by building glog manually as described by Giorno Sabato. I've fixed many compiler errors such as this today, currently working on a 16.04 system where I had to link allot of packages manually and build some from source, downgrade etc (GCC 5.4 to 4.9 for example to build CUDA 8)..

[Charles Shang]

Using "apt remove lib[glog | gflags | protobuf]-dev" to remove any error-related libs, then building them from source solved my problems! 

p.s. dont forget to run "rm -rf * " to  remove the old builds. 

I think the 16.04 version default libs is not compatible with caffe, so you need to re-install them. 

在 2015年10月27日星期二 UTC+8下午9:57:03，Алексей Филимонов写道：

CXX/LD -o .build_release/tools/extract_features.bin

[Bassel Safwat]

I am following these steps but now I gets an error in "automake --add-missing". 

configure.ac:13: error: version mismatch.  This is Automake 1.15,

configure.ac:13: but the definition used by this AM_INIT_AUTOMAKE

configure.ac:13: comes from Automake 1.14.1.  You should recreate

configure.ac:13: aclocal.m4 with aclocal and run automake again.

I tried to continue to the next step "make -j8" and I get error:

src/logging_unittest-logging_unittest.o: In function `__static_initialization_and_destruction_0(int, int)':

logging_unittest.cc:(.text+0xf082): undefined reference to `google::FlagRegisterer::FlagRegisterer<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(char const*, char const*, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)'

logging_unittest.cc:(.text+0xf145): undefined reference to `google::FlagRegisterer::FlagRegisterer<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(char const*, char const*, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)'

logging_unittest.cc:(.text+0xf1c2): undefined reference to `google::FlagRegisterer::FlagRegisterer<bool>(char const*, char const*, char const*, bool*, bool*)'

logging_unittest.cc:(.text+0xf1f7): undefined reference to `google::FlagRegisterer::FlagRegisterer<int>(char mv -f src/.deps/stacktrace_unittest-stacktrace_unittest.Tpo src/.deps/stacktrace_unittest-stacktrace_unittest.Po

const*, char const*, char const*, int*, int*)'

collect2: error: ld returned 1 exit status

Makefile:1079: recipe for target 'logging_unittest' failed

make: *** [logging_unittest] Error 1

[Dennis Mungai]

Do you have protobuf and its' developer packages installed?

--

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[Dennis Mungai]

And at the automake part, simply run:

autoreconf -ivf

To fix the error you encounter at that stage.

[Dennis Mungai]

And after installing (or compiling) protobuf packages, remember to run:

ldconfig

As sudo to reload your libraries into the environment, then proceed to compile caffe.

[Bassel Safwat]

I have the protobuf installed, I didn't run ldconfig by that time. I tried to run it now and re-make the caffe but it still fails with the same error (underfine)

I also  the autoreconf -ivf didnt fix the issue, it gives me the following output: 

autoreconf: Entering directory `.'

autoreconf: configure.ac: not using Gettext

autoreconf: running: aclocal --force -I m4

autoreconf: configure.ac: tracing

autoreconf: running: libtoolize --copy --force

libtoolize: putting auxiliary files in '.'.

libtoolize: copying file './ltmain.sh'

libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.

libtoolize: copying file 'm4/libtool.m4'

libtoolize: copying file 'm4/ltoptions.m4'

libtoolize: copying file 'm4/ltsugar.m4'

libtoolize: copying file 'm4/ltversion.m4'

libtoolize: copying file 'm4/lt~obsolete.m4'

autoreconf: running: /usr/bin/autoconf --force

autoreconf: running: /usr/bin/autoheader --force

autoreconf: running: automake --add-missing --copy --force-missing

configure.ac:19: installing './compile'

configure.ac:13: installing './missing'

Makefile.am: installing './depcomp'

autoreconf: Leaving directory `.'

but when i check the specified lines (613) in the makefile, this is moved into 623 and 629 

ACLOCAL = ${SHELL} /home/bassel/basselTMP/glog-0.3.4/missing aclocal-1.15
AUTOMAKE = ${SHELL} /home/bassel/basselTMP/glog-0.3.4/missing automake-1.15

and when runnig the make command, I get the following error: 

/bin/bash ./config.status --recheck

running CONFIG_SHELL=/bin/bash /bin/bash ./configure --no-create --no-recursion

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... no

checking for mawk... mawk

checking whether make sets $(MAKE)... yes

checking whether make supports nested variables... yes

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking whether gcc understands -c and -o together... yes

checking for style of include used by make... GNU

checking dependency style of gcc... gcc3

checking how to run the C preprocessor... gcc -E

checking for g++... g++

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking dependency style of g++... gcc3

checking build system type... x86_64-pc-linux-gnu

checking host system type... x86_64-pc-linux-gnu

checking how to print strings... printf

checking for a sed that does not truncate output... /bin/sed

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -E

checking for fgrep... /bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 1572864

checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop

checking for /usr/bin/ld option to reload object files... -r

checking for objdump... objdump

checking how to recognize dependent libraries... pass_all

checking for dlltool... no

checking how to associate runtime and link libraries... printf %s\n

checking for ar... ar

checking for archiver @FILE support... @

checking for strip... strip

checking for ranlib... ranlib

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /bin/dd

checking how to truncate binary pipes... /bin/dd bs=4096 count=1

checking for mt... mt

checking if mt is a manifest tool... no

checking for ANSI C header files... no

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... yes

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking whether -lc should be explicitly linked in... no

checking dynamic linker characteristics... GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking whether stripping libraries is possible... yes

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... yes

checking how to run the C++ preprocessor... g++ -E

checking for ld used by g++... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking for g++ option to produce PIC... -fPIC -DPIC

checking if g++ PIC flag -fPIC -DPIC works... yes

checking if g++ static flag -static works... yes

checking if g++ supports -c -o file.o... yes

checking if g++ supports -c -o file.o... (cached) yes

checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... (cached) GNU/Linux ld.so

checking how to hardcode library paths into programs... immediate

checking for ANSI C header files... (cached) no

checking for stdint.h... (cached) yes

checking for sys/types.h... (cached) yes

checking for inttypes.h... (cached) yes

checking for unistd.h... (cached) yes

checking syscall.h usability... yes

checking syscall.h presence... yes

checking for syscall.h... yes

checking sys/syscall.h usability... yes

checking sys/syscall.h presence... yes

checking for sys/syscall.h... yes

checking execinfo.h usability... yes

checking execinfo.h presence... yes

checking for execinfo.h... yes

checking libunwind.h usability... no

checking libunwind.h presence... no

checking for libunwind.h... no

checking ucontext.h usability... yes

checking ucontext.h presence... yes

checking for ucontext.h... yes

checking sys/utsname.h usability... yes

checking sys/utsname.h presence... yes

checking for sys/utsname.h... yes

checking pwd.h usability... yes

checking pwd.h presence... yes

checking for pwd.h... yes

checking syslog.h usability... yes

checking syslog.h presence... yes

checking for syslog.h... yes

checking sys/time.h usability... yes

checking sys/time.h presence... yes

checking for sys/time.h... yes

checking glob.h usability... yes

checking glob.h presence... yes

checking for glob.h... yes

checking unwind.h usability... yes

checking unwind.h presence... yes

checking for unwind.h... yes

checking windows.h usability... no

checking windows.h presence... no

checking for windows.h... no

checking size of void *... 8

checking for uint16_t... yes

checking for u_int16_t... yes

checking for __uint16... no

checking for sigaltstack... yes

checking for sigaction... yes

checking for dladdr... no

checking for fcntl... yes

checking for pread... yes

checking for pwrite... yes

checking for __attribute__... yes

checking for __builtin_expect... yes

checking for __sync_val_compare_and_swap... yes

checking for the pthreads library -lpthreads... no

checking whether pthreads work without any flags... no

checking whether pthreads work with -Kthread... no

checking whether pthreads work with -kthread... no

checking for the pthreads library -llthread... no

checking whether pthreads work with -pthread... yes

checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE

checking if more special flags are required for pthreads... no

checking whether to check for GCC pthread/shared inconsistencies... yes

checking whether -pthread is sufficient with -shared... yes

checking for pthread_self in -lpthread... yes

checking for main in -lgflags... yes

checking for gtest-config... no

checking for main in -lgtest... no

checking support for pthread_rwlock_* functions... yes

checking whether the compiler implements namespaces... yes

checking what namespace STL code is in... std

checking whether compiler supports using ::operator<<... 1

checking for ucontext.h... (cached) yes

checking sys/ucontext.h usability... yes

checking sys/ucontext.h presence... yes

checking for sys/ucontext.h... yes

checking how to access the program counter from a struct ucontext... uc_mcontext.gregs[REG_RIP]

checking that generated files are newer than configure... done

configure: creating ./config.status

 /bin/bash ./config.status

config.status: creating Makefile

config.status: creating src/glog/logging.h

config.status: creating src/glog/raw_logging.h

config.status: creating src/glog/vlog_is_on.h

config.status: creating src/glog/stl_logging.h

config.status: creating libglog.pc

config.status: creating src/config.h

config.status: src/config.h is unchanged

config.status: executing depfiles commands

config.status: executing libtool commands

/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src  -I./src     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2 -MT src/libglog_la-logging.lo -MD -MP -MF src/.deps/libglog_la-logging.Tpo -c -o src/libglog_la-logging.lo `test -f 'src/logging.cc' || echo './'`src/logging.cc

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-logging.lo -MD -MP -MF src/.deps/libglog_la-logging.Tpo -c src/logging.cc  -fPIC -DPIC -o src/.libs/libglog_la-logging.o

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-logging.lo -MD -MP -MF src/.deps/libglog_la-logging.Tpo -c src/logging.cc -o src/libglog_la-logging.o >/dev/null 2>&1

mv -f src/.deps/libglog_la-logging.Tpo src/.deps/libglog_la-logging.Plo

/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src  -I./src     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2 -MT src/libglog_la-raw_logging.lo -MD -MP -MF src/.deps/libglog_la-raw_logging.Tpo -c -o src/libglog_la-raw_logging.lo `test -f 'src/raw_logging.cc' || echo './'`src/raw_logging.cc

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-raw_logging.lo -MD -MP -MF src/.deps/libglog_la-raw_logging.Tpo -c src/raw_logging.cc  -fPIC -DPIC -o src/.libs/libglog_la-raw_logging.o

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-raw_logging.lo -MD -MP -MF src/.deps/libglog_la-raw_logging.Tpo -c src/raw_logging.cc -o src/libglog_la-raw_logging.o >/dev/null 2>&1

mv -f src/.deps/libglog_la-raw_logging.Tpo src/.deps/libglog_la-raw_logging.Plo

/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src  -I./src     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2 -MT src/libglog_la-vlog_is_on.lo -MD -MP -MF src/.deps/libglog_la-vlog_is_on.Tpo -c -o src/libglog_la-vlog_is_on.lo `test -f 'src/vlog_is_on.cc' || echo './'`src/vlog_is_on.cc

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-vlog_is_on.lo -MD -MP -MF src/.deps/libglog_la-vlog_is_on.Tpo -c src/vlog_is_on.cc  -fPIC -DPIC -o src/.libs/libglog_la-vlog_is_on.o

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-vlog_is_on.lo -MD -MP -MF src/.deps/libglog_la-vlog_is_on.Tpo -c src/vlog_is_on.cc -o src/libglog_la-vlog_is_on.o >/dev/null 2>&1

mv -f src/.deps/libglog_la-vlog_is_on.Tpo src/.deps/libglog_la-vlog_is_on.Plo

/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src  -I./src     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2 -MT src/libglog_la-utilities.lo -MD -MP -MF src/.deps/libglog_la-utilities.Tpo -c -o src/libglog_la-utilities.lo `test -f 'src/utilities.cc' || echo './'`src/utilities.cc

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-utilities.lo -MD -MP -MF src/.deps/libglog_la-utilities.Tpo -c src/utilities.cc  -fPIC -DPIC -o src/.libs/libglog_la-utilities.o

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-utilities.lo -MD -MP -MF src/.deps/libglog_la-utilities.Tpo -c src/utilities.cc -o src/libglog_la-utilities.o >/dev/null 2>&1

mv -f src/.deps/libglog_la-utilities.Tpo src/.deps/libglog_la-utilities.Plo

/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src  -I./src     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2 -MT src/libglog_la-symbolize.lo -MD -MP -MF src/.deps/libglog_la-symbolize.Tpo -c -o src/libglog_la-symbolize.lo `test -f 'src/symbolize.cc' || echo './'`src/symbolize.cc

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-symbolize.lo -MD -MP -MF src/.deps/libglog_la-symbolize.Tpo -c src/symbolize.cc  -fPIC -DPIC -o src/.libs/libglog_la-symbolize.o

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-symbolize.lo -MD -MP -MF src/.deps/libglog_la-symbolize.Tpo -c src/symbolize.cc -o src/libglog_la-symbolize.o >/dev/null 2>&1

mv -f src/.deps/libglog_la-symbolize.Tpo src/.deps/libglog_la-symbolize.Plo

/bin/bash ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src  -I./src     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2 -MT src/libglog_la-signalhandler.lo -MD -MP -MF src/.deps/libglog_la-signalhandler.Tpo -c -o src/libglog_la-signalhandler.lo `test -f 'src/signalhandler.cc' || echo './'`src/signalhandler.cc

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-signalhandler.lo -MD -MP -MF src/.deps/libglog_la-signalhandler.Tpo -c src/signalhandler.cc  -fPIC -DPIC -o src/.libs/libglog_la-signalhandler.o

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -DNDEBUG -g -O2 -MT src/libglog_la-signalhandler.lo -MD -MP -MF src/.deps/libglog_la-signalhandler.Tpo -c src/signalhandler.cc -o src/libglog_la-signalhandler.o >/dev/null 2>&1

mv -f src/.deps/libglog_la-signalhandler.Tpo src/.deps/libglog_la-signalhandler.Plo

/bin/bash ./libtool  --tag=CXX   --mode=link g++    -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -DNDEBUG -g -O2    -o libglog.la -rpath /usr/local/lib  src/libglog_la-logging.lo src/libglog_la-raw_logging.lo src/libglog_la-vlog_is_on.lo src/libglog_la-utilities.lo src/libglog_la-demangle.lo src/libglog_la-symbolize.lo src/libglog_la-signalhandler.lo   -lgflags  -lpthread 

libtool: link: rm -fr  .libs/libglog.a .libs/libglog.la .libs/libglog.lai .libs/libglog.so .libs/libglog.so.0 .libs/libglog.so.0.0.0

libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o  src/.libs/libglog_la-logging.o src/.libs/libglog_la-raw_logging.o src/.libs/libglog_la-vlog_is_on.o src/.libs/libglog_la-utilities.o src/.libs/libglog_la-demangle.o src/.libs/libglog_la-symbolize.o src/.libs/libglog_la-signalhandler.o   -lgflags -lpthread -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o  -g -O2   -Wl,-soname -Wl,libglog.so.0 -o .libs/libglog.so.0.0.0

libtool: link: (cd ".libs" && rm -f "libglog.so.0" && ln -s "libglog.so.0.0.0" "libglog.so.0")

libtool: link: (cd ".libs" && rm -f "libglog.so" && ln -s "libglog.so.0.0.0" "libglog.so")

libtool: link: ar cru .libs/libglog.a  src/libglog_la-logging.o src/libglog_la-raw_logging.o src/libglog_la-vlog_is_on.o src/libglog_la-utilities.o src/libglog_la-demangle.o src/libglog_la-symbolize.o src/libglog_la-signalhandler.o

ar: `u' modifier ignored since `D' is the default (see `U')

libtool: link: ranlib .libs/libglog.a

libtool: link: ( cd ".libs" && rm -f "libglog.la" && ln -s "../libglog.la" "libglog.la" )

g++ -DHAVE_CONFIG_H -I. -I./src  -I./src  -pthread     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -g -O2 -MT src/logging_unittest-logging_unittest.o -MD -MP -MF src/.deps/logging_unittest-logging_unittest.Tpo -c -o src/logging_unittest-logging_unittest.o `test -f 'src/logging_unittest.cc' || echo './'`src/logging_unittest.cc

In file included from src/utilities.h:82:0,

                 from src/logging_unittest.cc:33:

src/logging_unittest.cc: In function ‘void TestLogging(bool)’:

src/glog/logging.h:917:30: warning: typedef ‘INVALID_REQUESTED_LOG_SEVERITY’ locally defined but not used [-Wunused-local-typedefs]

                              INVALID_REQUESTED_LOG_SEVERITY);           \

                              ^

src/glog/logging.h:912:73: note: in definition of macro ‘GOOGLE_GLOG_COMPILE_ASSERT’

 pedef google::glog_internal_namespace_::CompileAssert<(bool(expr))> msg[bool(ex

                                                                     ^

src/logging_unittest.cc:254:5: note: in expansion of macro ‘LOG_EVERY_N’

     LOG_EVERY_N(ERROR, 4) << "Log every 4, iteration " << COUNTER << endl;

     ^

mv -f src/.deps/logging_unittest-logging_unittest.Tpo src/.deps/logging_unittest-logging_unittest.Po

/bin/bash ./libtool  --tag=CXX   --mode=link g++ -pthread     -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare  -DNO_FRAME_POINTER  -g -O2 -pthread  -o logging_unittest  src/logging_unittest-logging_unittest.o  libglog.la  -lgflags    -lgflags -lpthread 

libtool: link: g++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -DNO_FRAME_POINTER -g -O2 -pthread -o .libs/logging_unittest src/logging_unittest-logging_unittest.o  ./.libs/libglog.so -lgflags -lpthread -pthread

src/logging_unittest-logging_unittest.o: In function `__static_initialization_and_destruction_0':

/home/bassel/basselTMP/glog-0.3.4/src/googletest.h:93: undefined reference to `google::FlagRegisterer::FlagRegisterer<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(char const*, char const*, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)'

/home/bassel/basselTMP/glog-0.3.4/src/googletest.h:94: undefined reference to `google::FlagRegisterer::FlagRegisterer<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(char const*, char const*, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)'

/home/bassel/basselTMP/glog-0.3.4/src/googletest.h:96: undefined reference to `google::FlagRegisterer::FlagRegisterer<bool>(char const*, char const*, char const*, bool*, bool*)'

/home/bassel/basselTMP/glog-0.3.4/src/googletest.h:100: undefined reference to `google::FlagRegisterer::FlagRegisterer<int>(char const*, char const*, char const*, int*, int*)'

collect2: error: ld returned 1 exit status

Makefile:1090: recipe for target 'logging_unittest' failed

make: *** [logging_unittest] Error 1

On Tuesday, March 21, 

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[Dennis Mungai]

Hello Bassel,

Clean up your sources, download caffe again and repeat the build, as above.

I want to see what point a fresh build on your host fails on.

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[Bassel Safwat]

Doing this I could locate my issue! you made my day today :D

The issue I had is I was using anaconda for my environment, so in the makefile.config I used this one:

#PYTHON_LIB := /usr/lib

PYTHON_LIB := $(ANACONDA_HOME)/lib

so changing it back to

PYTHON_LIB := /usr/lib

#PYTHON_LIB := $(ANACONDA_HOME)/lib

solved the issue!

Note: I first ran into an issue:

/usr/bin/ld: cannot find -lhdf5_hl

/usr/bin/ld: cannot find -lhdf5

but following this solution, adding the following lines fixed the issue and 'make all' succeeds now

INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial
LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/aarch64-linux-gnu/hdf5/serial

anyway I am still wondering whynot using the python lib  as the anaconda lib path ?

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