Caffe Build issue using make method, (Protobuf, Libprotobuf issues)

[pkho...@terpmail.umd.edu]

Hi,

I have been trying to install caffe Today for hours but I am getting nowhere apparently, I used make method and after correcting many issues, now I am facing the error below which seems to be many other's issue as well, I tried many combinations but none has been successful, I tried with gcc 4.8, protobuf 2 and 3 but still getting the same error after many layers being compiled. I am using Anaconda3 so I removed protobuf and libprotobuf from conda so that there is going to be no confusion. I am hoping that someone know what else I can try so that i can finally get it to work. I appreciate the responses in advance.

 

Thanks.

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

.build_release/tools/caffe.o: In function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >* google::MakeCheckOpString<cudaError, cudaError>(cudaError const&, cudaError const&, char const*)':
caffe.cpp:(.text._ZN6google17MakeCheckOpStringI9cudaErrorS1_EEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc[_ZN6google17MakeCheckOpStringI9cudaErrorS1_EEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc]+0x40): undefined reference to `google::base::CheckOpMessageBuilder::NewString[abi:cxx11]()'
.build_release/tools/caffe.o: In function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >* google::MakeCheckOpString<unsigned long, int>(unsigned long const&, int const&, char const*)':
caffe.cpp:(.text._ZN6google17MakeCheckOpStringImiEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImiEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKT_RKT0_PKc]+0x40): undefined reference to `google::base::CheckOpMessageBuilder::NewString[abi:cxx11]()'
.build_release/tools/caffe.o: In function `main':
caffe.cpp:(.text.startup+0x38): undefined reference to `google::SetVersionString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
caffe.cpp:(.text.startup+0x62): undefined reference to `google::SetUsageMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
.build_release/tools/caffe.o: In function `_GLOBAL__sub_I_caffe.cpp':
caffe.cpp:(.text.startup+0x48e): 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> >*)'
caffe.cpp:(.text.startup+0x553): 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> >*)'
caffe.cpp:(.text.startup+0x611): 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> >*)'
caffe.cpp:(.text.startup+0x6cf): 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> >*)'
caffe.cpp:(.text.startup+0x7bc): 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> >*)'
.build_release/tools/caffe.o:caffe.cpp:(.text.startup+0x87a): more undefined references 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> >*)' follow
collect2: error: ld returned 1 exit status

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

Also before getting this error during compiling layers, I keep getting warnings about boost, glog, google such as below but I am not sure if they are relevant to the error

/anaconda3/envs/py27/include/google/protobuf/arena_impl.h(54): warning: integer conversion resulted in a change of sign

anaconda3/envs/py27/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp(75): warning: variable "tmp" was set but never used

anaconda3/envs/py27/include/glog/logging.h(362): warning: using-declaration ignored -- it refers to the current namespace

below is my Makefile.config:

## Refer to http://caffe.berkeleyvision.org/installation.html
# Contributions simplifying and improving our build system are welcome!

# cuDNN acceleration switch (uncomment to build with cuDNN).
USE_CUDNN := 1

# CPU-only switch (uncomment to build without GPU support).
# CPU_ONLY := 1

# uncomment to disable IO dependencies and corresponding data layers
# USE_OPENCV := 0
# USE_LEVELDB := 0
# USE_LMDB := 0

# uncomment to allow MDB_NOLOCK when reading LMDB files (only if necessary)
#    You should not set this flag if you will be reading LMDBs with any
#    possibility of simultaneous read and write
# ALLOW_LMDB_NOLOCK := 1

# Uncomment if you're using OpenCV 3
OPENCV_VERSION := 3

# To customize your choice of compiler, uncomment and set the following.
# N.B. the default for Linux is g++ and the default for OSX is clang++
# CUSTOM_CXX := g++

# CUDA directory contains bin/ and lib/ directories that we need.
CUDA_DIR := /opt/common/cuda/cuda-8.0.44
# On Ubuntu 14.04, if cuda tools are installed via
# "sudo apt-get install nvidia-cuda-toolkit" then use this instead:
# CUDA_DIR := /usr

# CUDA architecture setting: going with all of them.
# For CUDA < 6.0, comment the *_50 through *_61 lines for compatibility.
# For CUDA < 8.0, comment the *_60 and *_61 lines for compatibility.
# For CUDA >= 9.0, comment the *_20 and *_21 lines for compatibility.
CUDA_ARCH := -gencode arch=compute_30,code=sm_30 \
        -gencode arch=compute_35,code=sm_35 \
        -gencode arch=compute_50,code=sm_50 \
        -gencode arch=compute_52,code=sm_52
#        -gencode arch=compute_60,code=sm_60 \
#        -gencode arch=compute_61,code=sm_61 \
#        -gencode arch=compute_61,code=compute_61

# BLAS choice:
# atlas for ATLAS (default)
# mkl for MKL
# open for OpenBlas
BLAS := atlas
# Custom (MKL/ATLAS/OpenBLAS) include and lib directories.
# Leave commented to accept the defaults for your choice of BLAS
# (which should work)!
# BLAS_INCLUDE := /path/to/your/blas
# BLAS_LIB := /path/to/your/blas

# Homebrew puts openblas in a directory that is not on the standard search path
# BLAS_INCLUDE := $(shell brew --prefix openblas)/include
# BLAS_LIB := $(shell brew --prefix openblas)/lib

# This is required only if you will compile the matlab interface.
# MATLAB directory should contain the mex binary in /bin.
# MATLAB_DIR := /usr/local
MATLAB_DIR := /opt/common/matlab-r2015a

# NOTE: this is required only if you will compile the python interface.
# We need to be able to find Python.h and numpy/arrayobject.h.
# PYTHON_INCLUDE := /usr/include/python2.7 \
        /usr/lib/python2.7/dist-packages/numpy/core/include
# Anaconda Python distribution is quite popular. Include path:
# Verify anaconda location, sometimes it's in root.
ANACONDA_HOME := /scratch0/anaconda3/envs/py27
PYTHON_INCLUDE := $(ANACONDA_HOME)/include \
          $(ANACONDA_HOME)/include/python2.7 \
          $(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include

# Uncomment to use Python 3 (default is Python 2)
# PYTHON_LIBRARIES := boost_python3 python3.5m
# PYTHON_INCLUDE := /usr/include/python3.5m \
#                 /usr/lib/python3.5/dist-packages/numpy/core/include

# We need to be able to find libpythonX.X.so or .dylib.
# PYTHON_LIB := /usr/lib
PYTHON_LIB := $(ANACONDA_HOME)/lib

# Homebrew installs numpy in a non standard path (keg only)
# PYTHON_INCLUDE += $(dir $(shell python -c 'import numpy.core; print(numpy.core.__file__)'))/include
# PYTHON_LIB += $(shell brew --prefix numpy)/lib

# Uncomment to support layers written in Python (will link against Python libs)
WITH_PYTHON_LAYER := 1

# Whatever else you find you need goes here.
INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include
LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib

# If Homebrew is installed at a non standard location (for example your home directory) and you use it for general dependencies
# INCLUDE_DIRS += $(shell brew --prefix)/include
# LIBRARY_DIRS += $(shell brew --prefix)/lib

# NCCL acceleration switch (uncomment to build with NCCL)
# https://github.com/NVIDIA/nccl (last tested version: v1.2.3-1+cuda8.0)
# USE_NCCL := 1

# Uncomment to use `pkg-config` to specify OpenCV library paths.
# (Usually not necessary -- OpenCV libraries are normally installed in one of the above $LIBRARY_DIRS.)
# USE_PKG_CONFIG := 1

# N.B. both build and distribute dirs are cleared on `make clean`
BUILD_DIR := build
DISTRIBUTE_DIR := distribute

# Uncomment for debugging. Does not work on OSX due to https://github.com/BVLC/caffe/issues/171
# DEBUG := 1

# The ID of the GPU that 'make runtest' will use to run unit tests.
TEST_GPUID := 0


LINKFLAGS := -Wl,-rpath,$(ANACONDA_HOME)/lib

# enable pretty build (comment to see full commands)
Q ?= @

[Nicolas Rosa]

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