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matcaffe error #72

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KeeganRen opened this issue Mar 23, 2016 · 3 comments
Open

matcaffe error #72

KeeganRen opened this issue Mar 23, 2016 · 3 comments

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@KeeganRen
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ren@keegan  /home/ren/Code/RCNN/Caffe/caffe-0.999   make matcaffe  00:37:21
/usr/local/MATLAB/R2014a/bin/mex matlab/caffe/matcaffe.cpp build/lib/libcaffe.a
CXXFLAGS="$CXXFLAGS -pthread -fPIC -DNDEBUG -O2 -DUSE_MKL -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include -Ibuild/src -I./src -I./include -I/usr/local/cuda-7.0/include -I/opt/intel/composer_xe_2013_sp1.3.174/mkl/include -Wall"
CXXLIBS="$CXXLIBS -L/usr/lib -L/usr/local/lib -L/usr/lib -L/usr/local/cuda-7.0/lib64 -L/usr/local/cuda-7.0/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lcudart -lcublas -lcurand -lpthread -lglog -lprotobuf -lleveldb -lsnappy -lboost_system -lhdf5_hl -lhdf5 -lopencv_core -lopencv_highgui -lopencv_imgproc -lmkl_rt" -v -output matlab/caffe/caffe.mexa64
Verbose mode is on.
Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require the use of
-largeArrayDims and remove the -compatibleArrayDims option.
For more information:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
No MEX options file identified; looking for an implicit selection.
... Looking for compiler 'g++' ...
... Executing command 'which g++' ...Yes ('/usr/bin/g++').
... Executing command 'g++ -print-file-name=libstdc++.so' ...Yes ('/usr/lib/gcc/x86_64-linux-gnu/4.8/libstdc++.so').
Found installed compiler 'g++'.

Options file details

Compiler location: $GCC_DIR
Options file: /usr/local/MATLAB/R2014a/bin/glnxa64/mexopts/g++_glnxa64.xml
CMDLINE1 : /usr/bin/g++ -c -DMX_COMPAT_32   -D_GNU_SOURCE -DMATLAB_MEX_FILE  -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/simulink/include" -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -pthread -fPIC -DNDEBUG -O2 -DUSE_MKL -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include -Ibuild/src -I./src -I./include -I/usr/local/cuda-7.0/include -I/opt/intel/composer_xe_2013_sp1.3.174/mkl/include -Wall -O -DNDEBUG /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/matcaffe.cpp -o /tmp/mex_254501929137558_22314/matcaffe.o
CMDLINE2 : /usr/bin/g++ -pthread -Wl,--no-undefined  -shared -O -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" /tmp/mex_254501929137558_22314/matcaffe.o   -L/usr/lib -L/usr/local/lib -L/usr/lib -L/usr/local/cuda-7.0/lib64 -L/usr/local/cuda-7.0/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lcudart -lcublas -lcurand -lpthread -lglog -lprotobuf -lleveldb -lsnappy -lboost_system -lhdf5_hl -lhdf5 -lopencv_core -lopencv_highgui -lopencv_imgproc -lmkl_rt build/lib/libcaffe.a  -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -o /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.mexa64
CMDLINE3 : rm -f /tmp/mex_254501929137558_22314/matcaffe.o
CXX : /usr/bin/g++
DEFINES : -DMX_COMPAT_32   -D_GNU_SOURCE -DMATLAB_MEX_FILE 
MATLABMEX : -DMATLAB_MEX_FILE 
CXXFLAGS : -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -pthread -fPIC -DNDEBUG -O2 -DUSE_MKL -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include -Ibuild/src -I./src -I./include -I/usr/local/cuda-7.0/include -I/opt/intel/composer_xe_2013_sp1.3.174/mkl/include -Wall
INCLUDE : -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/simulink/include"
CXXOPTIMFLAGS : -O -DNDEBUG
CXXDEBUGFLAGS : -g
LDXX : /usr/bin/g++
LDFLAGS : -pthread -Wl,--no-undefined 
LDTYPE : -shared
LINKEXPORT : -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map"
LINKLIBS : build/lib/libcaffe.a  -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++
LDOPTIMFLAGS : -O
LDDEBUGFLAGS : -g
OBJEXT : .o
LDEXT : .mexa64
GCC : /usr/bin/g++
CPPLIB_DIR : /usr/lib/gcc/x86_64-linux-gnu/4.8/libstdc++.so
MATLABROOT : /usr/local/MATLAB/R2014a
ARCH : glnxa64
SRC : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/matcaffe.cpp
OBJ : /tmp/mex_254501929137558_22314/matcaffe.o
OBJS : /tmp/mex_254501929137558_22314/matcaffe.o 
SRCROOT : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/matcaffe
DEF : /tmp/mex_254501929137558_22314/caffe.def
EXP : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.exp
LIB : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.lib
EXE : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.mexa64
ILK : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.ilk
MANIFEST : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.mexa64.manifest
TEMPNAME : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe
EXEDIR : /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/
EXENAME : caffe
CXXLIBS :  -L/usr/lib -L/usr/local/lib -L/usr/lib -L/usr/local/cuda-7.0/lib64 -L/usr/local/cuda-7.0/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lcudart -lcublas -lcurand -lpthread -lglog -lprotobuf -lleveldb -lsnappy -lboost_system -lhdf5_hl -lhdf5 -lopencv_core -lopencv_highgui -lopencv_imgproc -lmkl_rt
OPTIM : -O -DNDEBUG
LINKOPTIM : -O

Building with 'g++'.
Warning: You are using gcc version '4.8.5'. The version of gcc is not supported. The version currently supported with MEX is '4.7.x'. For a list of currently supported compilers see: http://www.mathworks.com/support/compilers/current_release.
Warning: You are using gcc version '4.8.5-2ubuntu1~14.04.1)'. The version of gcc is not supported. The version currently supported with MEX is '4.7.x'. For a list of currently supported compilers see: http://www.mathworks.com/support/compilers/current_release.
/usr/bin/g++ -c -DMX_COMPAT_32 -D_GNU_SOURCE -DMATLAB_MEX_FILE -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/simulink/include" -ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -pthread -fPIC -DNDEBUG -O2 -DUSE_MKL -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include -Ibuild/src -I./src -I./include -I/usr/local/cuda-7.0/include -I/opt/intel/composer_xe_2013_sp1.3.174/mkl/include -Wall -O -DNDEBUG /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/matcaffe.cpp -o /tmp/mex_254501929137558_22314/matcaffe.o
/home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/matcaffe.cpp: In function ‘mxArray* do_get_weights()’:
/home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/matcaffe.cpp:188:50: warning: narrowing conversion of ‘(& layer_blobs)->std::vector<_Tp, _Alloc>::sizeboost::shared_ptr<caffe::Blob, std::allocatorboost::shared_ptr<caffe::Blob > >()’ from ‘std::vectorboost::shared_ptr<caffe::Blob, std::allocatorboost::shared_ptr<caffe::Blob > >::size_type {aka long unsigned int}’ to ‘const mwSize {aka const int}’ inside { } is ill-formed in C++11 [-Wnarrowing]
const mwSize dims[2] = {layer_blobs.size(), 1};
^

/usr/bin/g++ -pthread -Wl,--no-undefined -shared -O -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" /tmp/mex_254501929137558_22314/matcaffe.o -L/usr/lib -L/usr/local/lib -L/usr/lib -L/usr/local/cuda-7.0/lib64 -L/usr/local/cuda-7.0/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib -L/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64 -lcudart -lcublas -lcurand -lpthread -lglog -lprotobuf -lleveldb -lsnappy -lboost_system -lhdf5_hl -lhdf5 -lopencv_core -lopencv_highgui -lopencv_imgproc -lmkl_rt build/lib/libcaffe.a -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -o /home/ren/Code/RCNN/Caffe/caffe-0.999/matlab/caffe/caffe.mexa64
build/lib/libcaffe.a(common.o): In function caffe::Caffe::Caffe()': common.cpp:(.text+0x99): undefined reference tocublasCreate_v2'
common.cpp:(.text+0xeb): undefined reference to curandCreateGenerator' common.cpp:(.text+0x14d): undefined reference tocurandSetPseudoRandomGeneratorSeed'
build/lib/libcaffe.a(common.o): In function caffe::Caffe::~Caffe()': common.cpp:(.text+0x354): undefined reference tocublasDestroy_v2'
common.cpp:(.text+0x376): undefined reference to curandDestroyGenerator' build/lib/libcaffe.a(common.o): In functioncaffe::Caffe::SetDevice(int)':
common.cpp:(.text+0xcf0): undefined reference to cublasDestroy_v2' common.cpp:(.text+0xd1e): undefined reference tocurandDestroyGenerator'
common.cpp:(.text+0xd5e): undefined reference to cublasCreate_v2' common.cpp:(.text+0xd8c): undefined reference tocurandCreateGenerator'
common.cpp:(.text+0xdc0): undefined reference to curandSetPseudoRandomGeneratorSeed' build/lib/libcaffe.a(common.o): In functioncaffe::Caffe::set_random_seed(unsigned int)':
common.cpp:(.text+0x158f): undefined reference to curandDestroyGenerator' common.cpp:(.text+0x15bd): undefined reference tocurandCreateGenerator'
common.cpp:(.text+0x15ec): undefined reference to curandSetPseudoRandomGeneratorSeed' build/lib/libcaffe.a(net.o): In functioncaffe::Net::ToProto(caffe::NetParameter_, bool)':
net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x34): undefined reference to google::protobuf::internal::kEmptyString' net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x84): undefined reference togoogle::protobuf::internal::StringTypeHandlerBase::New()'
net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x1ea): undefined reference to google::protobuf::internal::StringTypeHandlerBase::New()' net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x2aa): undefined reference togoogle::protobuf::internal::StringTypeHandlerBase::New()'
net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x399): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x3b9): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x3de): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' net.cpp:(.text._ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIfE7ToProtoEPNS_12NetParameterEb]+0x3f3): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
build/lib/libcaffe.a(net.o): In function caffe::Net<double>::ToProto(caffe::NetParameter_, bool)': net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x34): undefined reference to google::protobuf::internal::kEmptyString'
net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x84): undefined reference togoogle::protobuf::internal::StringTypeHandlerBase::New()' net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x1ea): undefined reference to google::protobuf::internal::StringTypeHandlerBase::New()'
net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x2aa): undefined reference togoogle::protobuf::internal::StringTypeHandlerBase::New()' net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x399): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x3b9): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x3de): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
net.cpp:(.text._ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb[_ZN5caffe3NetIdE7ToProtoEPNS_12NetParameterEb]+0x3f3): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' build/lib/libcaffe.a(net.o): In function caffe::Net::Forward(std::string const&, float*)':
net.cpp:(.text._ZN5caffe3NetIfE7ForwardERKSsPf[_ZN5caffe3NetIfE7ForwardERKSsPf]+0x45): undefined reference togoogle::protobuf::MessageLite::ParseFromString(std::string const&)' net.cpp:(.text._ZN5caffe3NetIfE7ForwardERKSsPf[_ZN5caffe3NetIfE7ForwardERKSsPf]+0x189): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
net.cpp:(.text._ZN5caffe3NetIfE7ForwardERKSsPf[ZN5caffe3NetIfE7ForwardERKSsPf]+0x1b5): undefined reference togoogle::protobuf::MessageLite::SerializeToString(std::string_) const' build/lib/libcaffe.a(net.o): In function caffe::Net::Forward(std::string const&, double)':
net.cpp:(.text._ZN5caffe3NetIdE7ForwardERKSsPd[_ZN5caffe3NetIdE7ForwardERKSsPd]+0x45): undefined reference to google::protobuf::MessageLite::ParseFromString(std::string const&)' net.cpp:(.text._ZN5caffe3NetIdE7ForwardERKSsPd[_ZN5caffe3NetIdE7ForwardERKSsPd]+0x189): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
net.cpp:(.text._ZN5caffe3NetIdE7ForwardERKSsPd[ZN5caffe3NetIdE7ForwardERKSsPd]+0x1b5): undefined reference to google::protobuf::MessageLite::SerializeToString(std::string*) const' build/lib/libcaffe.a(layer_factory.o): In functioncaffe::Layer::ToProto(caffe::LayerParameter, bool)':
layer_factory.cpp:(.text.ZN5caffe5LayerIfE7ToProtoEPNS_14LayerParameterEb[ZN5caffe5LayerIfE7ToProtoEPNS_14LayerParameterEb]+0x149): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' build/lib/libcaffe.a(layer_factory.o): In functioncaffe::Layer::ToProto(caffe::LayerParameter, bool)':
layer_factory.cpp:(.text.ZN5caffe5LayerIdE7ToProtoEPNS_14LayerParameterEb[ZN5caffe5LayerIdE7ToProtoEPNS_14LayerParameterEb]+0x149): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' build/lib/libcaffe.a(insert_splits.o): In functioncaffe::ConfigureSplitLayer(std::string const&, std::string const&, int, int, caffe::LayerParameter)':
insert_splits.cpp:(.text+0x8b7): undefined reference to google::protobuf::internal::StringTypeHandlerBase::New()' insert_splits.cpp:(.text+0x8fe): undefined reference togoogle::protobuf::internal::kEmptyString'
insert_splits.cpp:(.text+0x96c): undefined reference to google::protobuf::internal::StringTypeHandlerBase::New()' insert_splits.cpp:(.text+0x9e9): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
insert_splits.cpp:(.text+0xa4f): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' build/lib/libcaffe.a(insert_splits.o): In functioncaffe::InsertSplits(caffe::NetParameter const&, caffe::NetParameter)':
insert_splits.cpp:(.text+0x2017): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' insert_splits.cpp:(.text+0x2118): undefined reference togoogle::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)'
insert_splits.cpp:(.text+0x214f): undefined reference to google::protobuf::internal::RepeatedPtrFieldBase::Reserve(int)' build/lib/libcaffe.a(upgrade_proto.o): In functioncaffe::UpgradeLayerParameter(caffe::LayerParameter const&, caffe::LayerParameter*)':
upgrade_proto.cpp:(.text+0x380): undefined reference to google::protobuf::internal::StringTypeHandlerBase::New()' upgrade_proto.cpp:(.text+0x400): undefined reference togoogle::protobuf::internal::StringTypeHandlerBase::New()'
upgrade
make: *** [matlab/caffe/caffe.mexa64] Error 255
@ghost
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ghost commented Apr 13, 2017

had you solved this problem? I have the same bug. Can you help me ?

@jinyu121
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Some blog says that the version of protobuf causes this issue, for your version is too new. Please try a older protobuf venison, such as 2.5.0.
I haven't try it yet.

@unicoe
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unicoe commented Sep 16, 2017

@jinyu121 It‘s useless。

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@jinyu121 @KeeganRen @unicoe