Undefined reference to boost::filesystem when running make test

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Denis Yakovenko

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Dec 12, 2016, 3:11:34 AM12/12/16
to Caffe Users
I'm trying to build Caffe with Cuda 8.0, CuDNN and OpenCV 3.1 on my Ubuntu 16.04 machine.

I've followed the official guide and now I can successfully run
sudo make all
in Caffe root directory.

However, when I run
sudo make test
I get the error below:

.............................................
CXX src/caffe/test/test_accuracy_layer.cpp
CXX src/caffe/test/test_util_blas.cpp
CXX src/caffe/test/test_filter_layer.cpp
CXX src/caffe/test/test_layer_factory.cpp
CXX src/caffe/test/test_net.cpp
NVCC src/caffe/test/test_im2col_kernel.cu
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
CXX src/gtest/gtest-all.cpp
CXX/LD -o .build_release/test/test_all.testbin src/caffe/test/test_caffe_main.cpp
.build_release/src/caffe/test/test_gradient_based_solver.o: In function `caffe::MakeTempDir(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)':
test_gradient_based_solver.cpp:(.text._ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x56): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_gradient_based_solver.cpp:(.text._ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x8a): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_gradient_based_solver.cpp:(.text._ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x124): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_gradient_based_solver.cpp:(.text._ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5caffe11MakeTempDirEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x15a): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_hdf5_output_layer.o: In function `caffe::MakeTempFilename(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)':
test_hdf5_output_layer.cpp:(.text._ZN5caffe16MakeTempFilenameEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN5caffe16MakeTempFilenameEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x1d4): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
.build_release/src/caffe/test/test_db.o: In function `caffe::DBTest<caffe::TypeLevelDB>::SetUp()':
test_db.cpp:(.text._ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv[_ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv]+0x7f): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_db.cpp:(.text._ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv[_ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv]+0xaf): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_db.cpp:(.text._ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv[_ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv]+0x163): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_db.cpp:(.text._ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv[_ZN5caffe6DBTestINS_11TypeLevelDBEE5SetUpEv]+0x19d): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_db.o: In function `caffe::DBTest<caffe::TypeLMDB>::SetUp()':
test_db.cpp:(.text._ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv[_ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv]+0x7f): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_db.cpp:(.text._ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv[_ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv]+0xaf): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_db.cpp:(.text._ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv[_ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv]+0x163): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_db.cpp:(.text._ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv[_ZN5caffe6DBTestINS_8TypeLMDBEE5SetUpEv]+0x19d): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_upgrade_proto.o: In function `caffe::NetUpgradeTest_TestUpgradeV1LayerType_Test::TestBody()':
test_upgrade_proto.cpp:(.text+0x2a21): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_upgrade_proto.cpp:(.text+0x2a5b): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_upgrade_proto.cpp:(.text+0x2b04): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_upgrade_proto.cpp:(.text+0x2b43): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_layer_factory.o: In function `caffe::LayerFactoryTest_TestCreateLayer_Test<caffe::CPUDevice<float> >::TestBody()':
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv]+0x4d9): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv]+0x513): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv]+0x5c4): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIfEEE8TestBodyEv]+0x603): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_layer_factory.o: In function `caffe::LayerFactoryTest_TestCreateLayer_Test<caffe::CPUDevice<double> >::TestBody()':
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv]+0x4c1): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv]+0x4fb): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv]+0x5a4): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9CPUDeviceIdEEE8TestBodyEv]+0x5e3): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_layer_factory.o: In function `caffe::LayerFactoryTest_TestCreateLayer_Test<caffe::GPUDevice<float> >::TestBody()':
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv]+0x4d9): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv]+0x513): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv]+0x5c4): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIfEEE8TestBodyEv]+0x603): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
.build_release/src/caffe/test/test_layer_factory.o: In function `caffe::LayerFactoryTest_TestCreateLayer_Test<caffe::GPUDevice<double> >::TestBody()':
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv]+0x4c1): undefined reference to `boost::filesystem::detail::temp_directory_path(boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv]+0x4fb): undefined reference to `boost::filesystem::path::operator/=(boost::filesystem::path const&)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv]+0x5a4): undefined reference to `boost::filesystem::detail::unique_path(boost::filesystem::path const&, boost::system::error_code*)'
test_layer_factory.cpp:(.text._ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv[_ZN5caffe37LayerFactoryTest_TestCreateLayer_TestINS_9GPUDeviceIdEEE8TestBodyEv]+0x5e3): undefined reference to `boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)'
collect2: error: ld returned 1 exit status
Makefile:599: recipe for target '.build_release/test/test_all.testbin' failed
make: *** [.build_release/test/test_all.testbin] Error 1

My process of building Caffe is the following (assuming I'm in a root Caffe folder):
sudo make clean
mkdir build
cd build
sudo cmake ..
cd ..
sudo make all
sudo make test
 My Boost version is 1.58 and I've installed it using
sudo apt-get install libboost-all-dev

and when I run the cmake script, it seems like the system finds the needed versions. Below is the output of "cmake .." command:

-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   system
--   thread
--   filesystem
--   chrono
--   date_time
--   atomic
-- Found GFlags: /usr/local/include  
-- Found gflags  (include: /usr/local/include, library: /usr/local/lib/libgflags.a)
-- Found Glog: /usr/local/include  
-- Found glog    (include: /usr/local/include, library: /usr/local/lib/libglog.so)
-- Found Protobuf: /usr/local/lib/libprotobuf.so  
-- Found PROTOBUF Compiler: /usr/local/bin/protoc
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5_hl.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.16") 
-- Found LMDB: /usr/local/include  
-- Found lmdb    (include: /usr/local/include, library: /usr/local/lib/liblmdb.so)
-- Found LevelDB: /usr/include  
-- Found LevelDB (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libleveldb.so)
-- Found Snappy: /usr/include  
-- Found Snappy  (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libsnappy.so)
-- CUDA detected: 8.0
-- Found cuDNN: ver. 5.1.5 found (include: /usr/local/cuda/include, library: /usr/local/cuda/lib64/libcudnn.so)
-- Added CUDA NVCC flags for: sm_30
-- OpenCV found (/usr/local/share/OpenCV)
-- Found Atlas: /usr/include  
-- Found Atlas (include: /usr/include, library: /usr/lib/libatlas.so)
-- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.12", minimum required is "2.7") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found suitable version "2.7.12", minimum required is "2.7") 
-- Found NumPy: /usr/local/lib/python2.7/dist-packages/numpy/core/include (found suitable version "1.11.2", minimum required is "1.7.1") 
-- NumPy ver. 1.11.2 found (include: /usr/local/lib/python2.7/dist-packages/numpy/core/include)
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   python
-- Could NOT find Doxygen (missing:  DOXYGEN_EXECUTABLE) 
-- Found Git: /usr/bin/git (found version "2.7.4") 
-- 
-- ******************* Caffe Configuration Summary *******************
-- General:
--   Version           :   1.0.0-rc3
--   Git               :   rc3-303-g5a201dd-dirty
--   System            :   Linux
--   C++ compiler      :   /usr/bin/c++
--   Release CXX flags :   -O3 -DNDEBUG -fPIC -Wall -Wno-sign-compare -Wno-uninitialized
--   Debug CXX flags   :   -g -fPIC -Wall -Wno-sign-compare -Wno-uninitialized
--   Build type        :   Release
-- 
--   BUILD_SHARED_LIBS :   ON
--   BUILD_python      :   ON
--   BUILD_matlab      :   OFF
--   BUILD_docs        :   ON
--   CPU_ONLY          :   OFF
--   USE_OPENCV        :   ON
--   USE_LEVELDB       :   ON
--   USE_LMDB          :   ON
--   ALLOW_LMDB_NOLOCK :   OFF
-- 
-- Dependencies:
--   BLAS              :   Yes (Atlas)
--   Boost             :   Yes (ver. 1.58)
--   glog              :   Yes
--   gflags            :   Yes
--   protobuf          :   Yes (ver. 3.1.0)
--   lmdb              :   Yes (ver. 0.9.70)
--   LevelDB           :   Yes (ver. 1.18)
--   Snappy            :   Yes (ver. 1.1.3)
--   OpenCV            :   Yes (ver. 3.1.0)
--   CUDA              :   Yes (ver. 8.0)
-- 
-- NVIDIA CUDA:
--   Target GPU(s)     :   Auto
--   GPU arch(s)       :   sm_30
--   cuDNN             :   Yes (ver. 5.1.5)
-- 
-- Python:
--   Interpreter       :   /usr/bin/python2.7 (ver. 2.7.12)
--   Libraries         :   /usr/lib/x86_64-linux-gnu/libpython2.7.so (ver 2.7.12)
--   NumPy             :   /usr/local/lib/python2.7/dist-packages/numpy/core/include (ver 1.11.2)
-- 
-- Documentaion:
--   Doxygen           :   No
--   config_file       :   
-- 
-- Install:
--   Install path      :   /home/denis/code/caffe/build/install
-- 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/denis/code/caffe/build

To add more information, here's the gist of my Makefile and the gist of my Makefile.config.

I use Anaconda2 with Python 2.7 and I've created the virtual environment using conda (which I called deep-learning), so when I run the python command in my terminal and check the OpenCV version, I get the following output:

(deep-learning) ➜  caffe git:(master) ✗ python
Python 2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import cv2
>>> print cv2.__version__
3.1.0
Could you please help me to resolve my issue with boost and build the Caffe normally?
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