Caffe: getting undefined reference to `std::__throw_out_of_range_fmt(char const*, ...) on this branch only!

Created on 22 Jan 2017 · 3Comments · Source: weiliu89/caffe

Issue summary

I have Caffe built on my Ubuntu 14.04.5 and I am using it right now for my projects. I copied my makefile which I used to compile and build caffe(master branch) to the caffe-ssd directory and initiated the building procedure, but when I tried to build this branch I faced:

...
NVCC src/caffe/solvers/sgd_solver.cu
NVCC src/caffe/solvers/adam_solver.cu
NVCC src/caffe/solvers/adadelta_solver.cu
NVCC src/caffe/solvers/rmsprop_solver.cu
NVCC src/caffe/layers/detection_output_layer.cu
/usr/include/boost/property_tree/detail/json_parser_read.hpp: In constructor ‘boost::property_tree::json_parser::json_grammar<Ptree>::definition<Scanner>::definition(const boost::property_tree::json_parser::json_grammar<Ptree>&)’:
/usr/include/boost/property_tree/detail/json_parser_read.hpp:257:264: error: ‘type name’ declared as function returning an array
                 escape
                                                                                                                                                                                                                                                                        ^
/usr/include/boost/property_tree/detail/json_parser_read.hpp:257:264: error: ‘type name’ declared as function returning an array
make: *** [.build_release/cuda/src/caffe/layers/detection_output_layer.o] Error 1

Which as it was explained here was solved by installing gcc 5 .
I changed my Makefile.config to use the new gcc compiler like this :

# 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 := /usr/bin/g++-5

This went on until it gave me this error :

...
NVCC src/caffe/layers/normalize_layer.cu
NVCC src/caffe/layers/tanh_layer.cu
NVCC src/caffe/layers/slice_layer.cu
NVCC src/caffe/layers/cudnn_softmax_layer.cu
NVCC src/caffe/layers/im2col_layer.cu
NVCC src/caffe/layers/smooth_L1_loss_layer.cu
AR -o .build_release/lib/libcaffe.a
LD -o .build_release/lib/libcaffe.so.1.0.0-rc3
CXX tools/compute_image_mean.cpp
CXX/LD -o .build_release/tools/compute_image_mean.bin
.build_release/lib/libcaffe.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
collect2: error: ld returned 1 exit status
make: *** [.build_release/tools/compute_image_mean.bin] Error 1
hossein@hossein-pc:/media/hossein/tmpstore/caffe-ssd$

Steps to reproduce

Simply trying to build this branch gives this error!

Your system configuration

Operating system: ubuntu 14.04.5
Compiler:gcc-4.8 and gcc-5
CUDA version (if applicable): 8
CUDNN version (if applicable): 5.1
BLAS: OpenBLAS 0.2.20.dev
Python or MATLAB version (for pycaffe and matcaffe respectively): python 2.7

This is the makefile by the way:

## 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 := /usr/bin/g++-5

# CUDA directory contains bin/ and lib/ directories that we need.
CUDA_DIR := /usr/local/cuda
# 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 lines for compatibility.
CUDA_ARCH := -gencode arch=compute_52,code=sm_52

# BLAS choice:
# atlas for ATLAS (default)
# mkl for MKL
# open for OpenBlas
BLAS := open
# 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 := /Applications/MATLAB_R2012b.app

# 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 := $(HOME)/anaconda2
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

# 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

# Fix for cv::imread and cv::imdecode errors
#LIBRARIES += glog gflags protobuf leveldb snappy lmdb boost_system hdf5_hl hdf5 m opencv_core opencv_highgui opencv_imgproc opencv_imgcodecs
LIBRARIES += glog gflags protobuf leveldb snappy \
  lmdb boost_system hdf5_hl hdf5 m \
  opencv_core opencv_highgui opencv_imgproc opencv_imgcodecs


# 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

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

Source

Coderx7

Most helpful comment

OK Here is how you solve this issue, for me it was because of the anadonda2 having libstdc++.so.6 , and I had to have libstdc++.so.6.0.22 available in /usr/lib/x86_64-linux-gnu/ (which I had) .
I had to rename all instances of libstdc++.so.6 to something like libstdc++.so.6_ , and then update the linker library path by :
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
and it was solved!
for more information click here