Caffe: make: *** [.build_release/lib/libcaffe.so.1.0.0] Error 1

[Needrom]

Issue summary

failed to make -j

output of terminal:

LD -o .build_release/lib/libcaffe.so.1.0.0
clang: warning: argument unused during compilation: '-pthread'
Undefined symbols for architecture x86_64:
  "caffe::DecodeDatumToCVMat(caffe::Datum const&, bool)", referenced from:
      caffe::DataTransformer<float>::Transform(caffe::Datum const&, caffe::Blob<float>*) in data_transformer.o
      caffe::DataTransformer<float>::InferBlobShape(caffe::Datum const&) in data_transformer.o
      caffe::DataTransformer<double>::Transform(caffe::Datum const&, caffe::Blob<double>*) in data_transformer.o
      caffe::DataTransformer<double>::InferBlobShape(caffe::Datum const&) in data_transformer.o
  "caffe::DecodeDatumToCVMatNative(caffe::Datum const&)", referenced from:
      caffe::DataTransformer<float>::Transform(caffe::Datum const&, caffe::Blob<float>*) in data_transformer.o
      caffe::DataTransformer<float>::InferBlobShape(caffe::Datum const&) in data_transformer.o
      caffe::DataTransformer<double>::Transform(caffe::Datum const&, caffe::Blob<double>*) in data_transformer.o
      caffe::DataTransformer<double>::InferBlobShape(caffe::Datum const&) in data_transformer.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [.build_release/lib/libcaffe.so.1.0.0] Error 1

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 := 1
# 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 := /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 through *_61 lines for compatibility.
# For CUDA < 8.0, comment the *_60 and *_61 lines for compatibility.
CUDA_ARCH := -gencode arch=compute_20,code=sm_20 \
        -gencode arch=compute_20,code=sm_21 \
        -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 := /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)/anaconda
# 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

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

Your system configuration

Operating system: Mac os
Compiler:
CUDA version (if applicable): 7.5
CUDNN version (if applicable):
BLAS:
Python or MATLAB version (for pycaffe and matcaffe respectively): python 2.7

[SherlockZh]

My operating system is OSX 10.11.6 and I have exactly the same error.

[SherlockZh]

my output

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_conv_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_lcn_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_lrn_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_pooling_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_relu_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_sigmoid_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_softmax_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn_tanh_layer.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(parallel.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .build_release/lib/libcaffe.a(cudnn.o) has no symbols
Undefined symbols for architecture x86_64:
  "cv::String::deallocate()", referenced from:
      caffe::WindowDataLayer<float>::load_batch(caffe::Batch<float>*) in window_data_layer.o
      caffe::WindowDataLayer<double>::load_batch(caffe::Batch<double>*) in window_data_layer.o
      caffe::ReadImageToCVMat(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int, bool) in io.o
      caffe::ReadImageToDatum(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int, int, bool, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, caffe::Datum*) in io.o
  "cv::String::allocate(unsigned long)", referenced from:
      caffe::WindowDataLayer<float>::load_batch(caffe::Batch<float>*) in window_data_layer.o
      caffe::WindowDataLayer<double>::load_batch(caffe::Batch<double>*) in window_data_layer.o
      caffe::ReadImageToCVMat(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int, bool) in io.o
      caffe::ReadImageToDatum(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int, int, bool, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, caffe::Datum*) in io.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [.build_release/lib/libcaffe.so.1.0.0] Error 1
make: *** Waiting for unfinished jobs....

[Needrom]

I had fix this problem . if you change the config without mkae clean and remake all of this .it will still have that problem .So you should "make clean" and the "make -j" after modify you Makefile.config

[yanxiangyi]

It's not even a solution...TAT

[yanxiangyi]

Encounter the same problem but remake does't work...

[tomzhang666]

I also have this problem, does anyone fix it ?

[shingsoso]

same problem ...

[guohaoyu110]

anyone ?

[Suraj59]

AR -o .build_release/lib/libcaffe.a
LD -o .build_release/lib/libcaffe.so.1.0.0
/usr/bin/ld: cannot find -l -llmdb
collect2: error: ld returned 1 exit status
Makefile:575: recipe for target '.build_release/lib/libcaffe.so.1.0.0' failed
make: * [.build_release/lib/libcaffe.so.1.0.0] Error 1

[hanikh]

the same error. any solution?

[Suraj59]

Hey i found the Solution, it worked for me
run
dpkg -L libhdf5-dev | grep so
should output:
/usr/lib/x86_64-linux-gnu/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5hl_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5.so

Make sure the path /usr/lib/x86_64-linux-gnu (which contains libhdf5.so and libhdf5_hl.so) is in Makefile.config's LIBRARY_DIRS

[XiangyiCheng]

hey I ran
dpkg -L libhdf5-dev | grep so
it output:
/usr/lib/x86_64-linux-gnu/libhdf5_serial.so
/usr/lib/x86_64-linux-gnu/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_fortran.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5hl_fortran.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.so

anyone knows how to fix that?

[HHIR]

@XiangyiCheng I have same with you, did you fix it?

[sehyun03]

Well in my case, reinstalling protobuf worked.
My original protobuf installed by "apt-get install protobuf-dev" or pip caused this make: * [.build_release/lib/libcaffe.so.1.0.0] Error 1 error.

1. I removed all of the protobuf and its related directories.(except for something related to tensorflow or matlab)
2. I reinstalled protobuf following C++ Installation Instructions on https://github.com/google/protobuf.
3. problem solved(at least passed "make runtest")

[chqfeiyang]

it might be the using of opencv. try closing it.

[huige555551]

the same error. any solution?

[SergeTryhub]

After trying several things this is the way mine worked, rather than running make all in the caffe directory their website suggests doing the following:
mkdir build
cd build
cmake ..
make all
make install
make runtest
Website: http://caffe.berkeleyvision.org/installation.html#compilation

[me6ran]

Caffe is the mose silliest python module I have ever seen. it has been two days I spent my time to install this STUPID module, facing numerous issue, errors you name it. I just got sick of it. removing it and DONE.
So disappointing.

[xye43]

@XiangyiCheng @Hosseinhashemiir

if you have:
dpkg -L libhdf5-dev | grep so
it output:
/usr/lib/x86_64-linux-gnu/libhdf5_serial.so
/usr/lib/x86_64-linux-gnu/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5_serialhl_fortran.so
/usr/lib/x86_64-linux-gnu/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_fortran.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5hl_fortran.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/libhdf5_serial_fortran.so

simply add /usr/lib/x86_64-linux-gnu/hdf5/serial/ to Makefile.config's LIBRARY_DIRS

too late though...

[gmt710]

AR -o .build_release/lib/libcaffe.a
LD -o .build_release/lib/libcaffe.so.1.0.0
/usr/bin/ld: cannot find -l -llmdb
collect2: error: ld returned 1 exit status
Makefile:575: recipe for target '.build_release/lib/libcaffe.so.1.0.0' failed
make: * [.build_release/lib/libcaffe.so.1.0.0] Error 1

@Suraj59 hello.

I met the same problem with you and tried several ways. But the error also occures.Have you solved this ? Would you mind giving me some suggestions? I will be very grateful to you.

[zaloogarcia]

any solutions?

[newwhitecheng]

Although it's closed. I'll still write down my case and solution in case others encountered the same.

So you encounter the error make: *** [.build_release/lib/libcaffe.so.1.0.0] Error 1

This error message is too broad. It may caused by many reasons, thus, each people's answers are different. To solve this, you need to look the whole error message. Take my case as example, my error is

/usr/bin/x86_64-linux-gnu-ld: cannot find -lcudnn collect2: error: ld returned 1 exit status Makefile:572: recipe for target '.build_release/lib/libcaffe.so.1.0.0' failed make: *** [.build_release/lib/libcaffe.so.1.0.0] Error 1

The main reason is actually come from "cannot find -lcudnn." I tried two things.

1. redownload cudnn, untar and copy to CUDA toolkit by the following command

$ tar -xzvf cudnn-9.0-linux-x64-v7.tgz
$ sudo cp cuda/include/cudnn.h /usr/local/cuda/include
$ sudo cp cuda/lib64/libcudnn* /usr/local/cuda/lib64
$ sudo chmod a+r /usr/local/cuda/include/cudnn.h /usr/local/cuda/lib64/libcudnn*

1. Make sure the Makefile.config point to the correct CUDA_DIR
   CUDA_DIR := /usr/local/cuda

[Chappie74]

After trying several things this is the way mine worked, rather than running make all in the caffe directory their website suggests doing the following:
mkdir build
cd build
cmake ..
make all
make install
make runtest
Website: http://caffe.berkeleyvision.org/installation.html#compilation

worked

[irsyadtc]

I tried until cmake .. and still getting error.
I'm guessing missing pthread_create and Atlas are the causes. The output:

-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- 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: 1.65.1
-- Found the following Boost libraries:
-- system
-- thread
-- filesystem
-- chrono
-- date_time
-- atomic
-- Found GFlags: /usr/include
-- Found gflags (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libgflags.so)
-- Found Glog: /usr/include
-- Found glog (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libglog.so)
-- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so;-lpthread (found version "3.0.0")
-- Found PROTOBUF Compiler: /usr/bin/protoc
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/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 "1.10.0.1") found components: HL
-- Found LMDB: /usr/include
-- Found lmdb (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/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: 10.1
-- Found cuDNN: ver. 7.6.0 found (include: /usr/include, library: /usr/lib/x86_64-linux-gnu/libcudnn.so)
-- Added CUDA NVCC flags for: sm_52
-- OpenCV found (/usr/share/OpenCV)
CMake Error at /usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find Atlas (missing: Atlas_CLAPACK_INCLUDE_DIR
Atlas_CBLAS_LIBRARY Atlas_BLAS_LIBRARY Atlas_LAPACK_LIBRARY)
Call Stack (most recent call first):
/usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
cmake/Modules/FindAtlas.cmake:43 (find_package_handle_standard_args)
cmake/Dependencies.cmake:88 (find_package)
CMakeLists.txt:58 (include)

-- Configuring incomplete, errors occurred!
See also "/home/carem/caffe/build/CMakeFiles/CMakeOutput.log".
See also "/home/carem/caffe/build/CMakeFiles/CMakeError.log".

help please