Problem with building PyTorch from source on Linux
❓ Problem with building PyTorch from source

Hello everyone,

I have problem with building PyTorch from source. I followed the official build instructions. I use Anaconda Python 3.7.1 (version 2018.12, build py37_0). I installed all neccessary dependencies using conda and issued  python setup.py install command to build it. It builds all files successfully but then it fails at the installation step saying: 

build/temp.linux-x86_64-3.7/torch/csrc/stub.o: file not recognized: file format not recognized


I tried building with gcc/g++ versions 5,6,7 but it did not help.  Can you help me resolve this problem?

Build output in terminal

This is the output of python setup.py install with the error I am getting:

[manjaro-pc pytorch]# python setup.py install
Building wheel torch-1.1.0a0+44809fd
-- Building version 1.1.0a0+44809fd
[0/1] Install the project...
-- Install configuration: "Release"
running install
running build
running build_py
copying torch/version.py -&gt; build/lib.linux-x86_64-3.7/torch
copying caffe2/proto/caffe2_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
copying caffe2/proto/caffe2_legacy_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
copying caffe2/proto/predictor_consts_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
copying caffe2/proto/metanet_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
copying caffe2/proto/torch_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
copying caffe2/proto/prof_dag_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
copying caffe2/proto/hsm_pb2.py -&gt; build/lib.linux-x86_64-3.7/caffe2/proto
running build_ext
-- Building with NumPy bindings
-- Not using cuDNN
-- Not using MIOpen
-- Not using CUDA
-- Not using MKLDNN
-- Not using NCCL
-- Building without distributed package

Copying extension caffe2.python.caffe2_pybind11_state
Copying caffe2.python.caffe2_pybind11_state from torch/lib/python3.7/site-packages/caffe2/python/caffe2_pybind11_state.cpython-37m-x86_64-linux-gnu.so to /home/manjaro/Downloads/pytorch/build/lib.linux-x86_64-3.7/caffe2/python/caffe2_pybind11_state.cpython-37m-x86_64-linux-gnu.so
building 'torch._C' extension
gcc -pthread -B /opt/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda/include/python3.7m -c torch/csrc/stub.cpp -o build/temp.linux-x86_64-3.7/torch/csrc/stub.o -std=c++11 -Wall -Wextra -Wno-strict-overflow -Wno-unused-parameter -Wno-missing-field-initializers -Wno-write-strings -Wno-unknown-pragmas -Wno-deprecated-declarations -fno-strict-aliasing -Wno-missing-braces
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
g++ -pthread -shared -B /opt/anaconda/compiler_compat -L/opt/anaconda/lib -Wl,-rpath=/opt/anaconda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/torch/csrc/stub.o -L/home/manjaro/Downloads/pytorch/torch/lib -lshm -ltorch_python -o build/lib.linux-x86_64-3.7/torch/_C.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN/lib
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/torch/csrc/stub.o: unable to initialize decompress status for section .debug_info
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/torch/csrc/stub.o: unable to initialize decompress status for section .debug_info
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/torch/csrc/stub.o: unable to initialize decompress status for section .debug_info
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/torch/csrc/stub.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.7/torch/csrc/stub.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1


From this output, I assume the error was caused by this line:

g++ -pthread -shared -B /opt/anaconda/compiler_compat -L/opt/anaconda/lib -Wl,-rpath=/opt/anaconda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/torch/csrc/stub.o -L/home/manjaro/Downloads/pytorch/torch/lib -lshm -ltorch_python -o build/lib.linux-x86_64-3.7/torch/_C.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN/lib


My environment

PyTorch version: 1.0
Is debug build: N/A
CUDA used to build PyTorch: 10

OS: Manjaro Linux
GCC version: (GCC) 6.4.1 20171002
CMake version: version 3.12.2

Python version: 3.7
Is CUDA available: N/A
CUDA runtime version: 10.0.130
GPU models and configuration: GPU 0: GeForce GTX 650
Nvidia driver version: 415.27
cuDNN version: Probably one of the following:
/usr/lib/libcudnn.so.7.4.1
/usr/lib/libcudnn_static_v7.a

Versions of relevant libraries:
[pip] Could not collect
[conda] blas                      1.0                         mkl  
[conda] magma-cuda100             2.4.0                         1    pytorch
[conda] mkl                       2019.1                      144  
[conda] mkl-include               2019.1                      144  
[conda] mkl-service               1.1.2            py37he904b0f_5  
[conda] mkl_fft                   1.0.6            py37hd81dba3_0  
[conda] mkl_random                1.0.2            py37hd81dba3_0  
[conda] mkldnn                    0.16.1                        0    mingfeima


My CMake configuration printed before building PyTorch


Building wheel torch-1.1.0a0+44809fd
-- Building version 1.1.0a0+44809fd
['cmake',
 '/home/manjaro/Downloads/pytorch',
 '-GNinja',
 '-DBLAS=MKL',
 '-DBUILDING_WITH_TORCH_LIBS=ON',
 '-DBUILD_BINARY=False',
 '-DBUILD_CAFFE2_OPS=False',
 '-DBUILD_PYTHON=True',
 '-DBUILD_SHARED_LIBS=ON',
 '-DBUILD_TEST=False',
 '-DBUILD_TORCH=ON',
 '-DCAFFE2_STATIC_LINK_CUDA=False',
 '-DCMAKE_BUILD_TYPE=Release',
 '-DCMAKE_CXX_FLAGS= ',
 '-DCMAKE_C_FLAGS= ',
 '-DCMAKE_EXE_LINKER_FLAGS=',
 '-DCMAKE_INSTALL_PREFIX=/home/manjaro/Downloads/pytorch/torch',
 '-DCMAKE_PREFIX_PATH=/opt/anaconda/bin/../',
 '-DCMAKE_SHARED_LINKER_FLAGS=',
 '-DINSTALL_TEST=False',
 '-DNCCL_EXTERNAL=False',
 '-DNUMPY_INCLUDE_DIR=/opt/anaconda/lib/python3.7/site-packages/numpy/core/include',
 '-DONNX_NAMESPACE=onnx_torch',
 '-DPYTHON_EXECUTABLE=/opt/anaconda/bin/python',
 '-DPYTHON_INCLUDE_DIR=/opt/anaconda/include/python3.7m',
 '-DPYTHON_LIBRARY=/opt/anaconda/lib/libpython3.7m.so.1.0',
 '-DTHD_SO_VERSION=1',
 '-DTORCH_BUILD_VERSION=1.1.0a0+44809fd',
 '-DUSE_CUDA=False',
 '-DUSE_DISTRIBUTED=False',
 '-DUSE_FBGEMM=False',
 '-DUSE_FFMPEG=False',
 '-DUSE_LEVELDB=False',
 '-DUSE_LMDB=False',
 '-DUSE_MKLDNN=False',
 '-DUSE_NNPACK=False',
 '-DUSE_NUMPY=True',
 '-DUSE_OPENCV=False',
 '-DUSE_QNNPACK=False',
 '-DUSE_ROCM=False',
 '-DUSE_SYSTEM_EIGEN_INSTALL=OFF',
 '-DUSE_SYSTEM_NCCL=False',
 '-DUSE_TENSORRT=False']
{'BLAS': 'MKL',
 'BUILD_CAFFE2_OPS': '0',
 'BUILD_TEST': '0',
 'CMAKE_PREFIX_PATH': '/opt/anaconda/bin/../',
 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus',
 'HG': '/usr/bin/hg',
 'HOME': '/root',
 'LANG': 'en_US.UTF-8',
 'LC_ADDRESS': 'sk_SK.UTF-8',
 'LC_IDENTIFICATION': 'sk_SK.UTF-8',
 'LC_MEASUREMENT': 'sk_SK.UTF-8',
 'LC_MONETARY': 'sk_SK.UTF-8',
 'LC_NAME': 'sk_SK.UTF-8',
 'LC_NUMERIC': 'sk_SK.UTF-8',
 'LC_PAPER': 'sk_SK.UTF-8',
 'LC_TELEPHONE': 'sk_SK.UTF-8',
 'LC_TIME': 'sk_SK.UTF-8',
 'LD_LIBRARY_PATH': ':/usr/local/lib64:/usr/local/lib:/opt/cuda/lib64',
 'LOGNAME': 'manjaro',
 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:',
 'MAIL': '/var/spool/mail/manjaro',
 'MAX_JOBS': '4',
 'MOZ_PLUGIN_PATH': '/usr/lib/mozilla/plugins',
 'NO_CAFFE2_OPS': '1',
 'NO_CUDA': '1',
 'NO_CUDNN': '1',
 'NO_DISTRIBUTED': '1',
 'NO_FBGEMM': '1',
 'NO_MIOPEN': '1',
 'NO_MKLDNN': '1',
 'NO_NNPACK': '1',
 'NO_QNNPACK': '1',
 'NO_TEST': '1',
 'OLDPWD': '/home/manjaro/Downloads',
 'PATH': '/opt/anaconda/bin:/opt/anaconda/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/opt/cuda/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/usr/local/bin:/opt/cuda/bin:/usr/local/bin:/opt/cuda/bin',
 'PWD': '/home/manjaro/Downloads/pytorch',
 'PYTHONPATH': ':/usr/local/lib/python3.7/site-packages/:/usr/local/lib/python3.7/site-packages/',
 'QT_LINUX_ACCESSIBILITY_ALWAYS_ON': '1',
 'SHELL': '/bin/bash',
 'SHLVL': '2',
 'SSH_CLIENT': '62.197.243.30 45360 44444',
 'SSH_CONNECTION': '62.197.243.30 45360 192.168.1.147 44444',
 'SSH_TTY': '/dev/pts/4',
 'TERM': 'xterm-256color',
 'TORCH_CUDA_ARCH_LIST': '3.0',
 'USER': 'manjaro',
 'USE_CUDA': '0',
 'USE_CUDNN': '0',
 'USE_DISTRIBUTED': '0',
 'USE_FBGEMM': '0',
 'USE_MIOPEN': '0',
 'USE_MKLDNN': '0',
 'USE_NNPACK': '0',
 'USE_QNNPACK': '0',
 'XDG_DATA_DIRS': '/home/manjaro/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share',
 'XDG_RUNTIME_DIR': '/run/user/1000',
 'XDG_SESSION_ID': 'c8',
 'YAOURT_COLORS': 'nb=1:pkg=1:ver=1;32:lver=1;45:installed=1;42:grp=1;34:od=1;41;5:votes=1;44:dsc=0:other=1;35',
 '_': '/opt/anaconda/bin/python'}
-- The CXX compiler identification is GNU 5.4.1
-- The C compiler identification is GNU 5.4.1
-- 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
-- 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
-- Performing Test COMPILER_WORKS
-- Performing Test COMPILER_WORKS - Success
-- Performing Test SUPPORT_GLIBCXX_USE_C99
-- Performing Test SUPPORT_GLIBCXX_USE_C99 - Success
-- Performing Test CAFFE2_EXCEPTION_PTR_SUPPORTED
-- Performing Test CAFFE2_EXCEPTION_PTR_SUPPORTED - Success
-- std::exception_ptr is supported.
-- Performing Test CAFFE2_IS_NUMA_AVAILABLE
-- Performing Test CAFFE2_IS_NUMA_AVAILABLE - Success
-- NUMA is available
-- Performing Test CAFFE2_NEED_TO_TURN_OFF_DEPRECATION_WARNING
-- Performing Test CAFFE2_NEED_TO_TURN_OFF_DEPRECATION_WARNING - Success
-- Performing Test CAFFE2_COMPILER_SUPPORTS_AVX2_EXTENSIONS
-- Performing Test CAFFE2_COMPILER_SUPPORTS_AVX2_EXTENSIONS - Success
-- Current compiler supports avx2 extension. Will build perfkernels.
-- Performing Test CAFFE2_COMPILER_SUPPORTS_AVX512_EXTENSIONS
-- Performing Test CAFFE2_COMPILER_SUPPORTS_AVX512_EXTENSIONS - Success
-- Current compiler supports avx512f extension. Will build fbgemm.
-- Performing Test COMPILER_SUPPORTS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_SUPPORTS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_SUPPORTS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_SUPPORTS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_SUPPORTS_RDYNAMIC
-- Performing Test COMPILER_SUPPORTS_RDYNAMIC - Success
-- Building using own protobuf under third_party per request.
-- Use custom protobuf build.
-- 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  
-- Caffe2 protobuf include directory: $&lt;BUILD_INTERFACE:/home/manjaro/Downloads/pytorch/third_party/protobuf/src&gt;$&lt;INSTALL_INTERFACE:include&gt;
-- Trying to find preferred BLAS backend of choice: MKL
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of void*
-- Check size of void* - done
-- Checking for [mkl_intel_lp64 - mkl_gnu_thread - mkl_core - gomp - pthread - m - dl]
--   Library mkl_intel_lp64: /opt/anaconda/lib/libmkl_intel_lp64.so
--   Library mkl_gnu_thread: /opt/anaconda/lib/libmkl_gnu_thread.so
--   Library mkl_core: /opt/anaconda/lib/libmkl_core.so
-- Found OpenMP_C: -fopenmp (found version "4.0") 
-- Found OpenMP_CXX: -fopenmp (found version "4.0") 
-- Found OpenMP: TRUE (found version "4.0")  
--   Library gomp: -fopenmp
--   Library pthread: /usr/lib/libpthread.so
--   Library m: /usr/lib/libm.so
--   Library dl: /usr/lib/libdl.so
-- Looking for cblas_sgemm
-- Looking for cblas_sgemm - found
-- MKL library found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Caffe2: Found gflags with new-style gflags target.
-- Caffe2: Cannot find glog automatically. Using legacy find.
-- Found glog: /usr/include  
-- Caffe2: Found glog (include: /usr/include, library: /usr/lib/libglog.so)
-- Found Numa: /usr/include  
-- Found Numa  (include: /usr/include, library: /usr/lib/libnuma.so)
-- Downloading PSimd to /home/manjaro/Downloads/pytorch/build/confu-srcs/psimd (define PSIMD_SOURCE_DIR to avoid it)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/manjaro/Downloads/pytorch/build/confu-deps/psimd-download
[1/9] Creating directories for 'psimd'
[2/9] Performing download step (git clone) for 'psimd'
Cloning into 'psimd'...
Already on 'master'
Your branch is up to date with 'origin/master'.
[3/9] No patch step for 'psimd'
[4/9] Performing update step for 'psimd'
Current branch master is up to date.
[5/9] No configure step for 'psimd'
[6/9] No build step for 'psimd'
[7/9] No install step for 'psimd'
[8/9] No test step for 'psimd'
[9/9] Completed 'psimd'
-- Using third party subdirectory Eigen.
Python 3.7.1
-- Found PythonInterp: /opt/anaconda/bin/python (found suitable version "3.7.1", minimum required is "2.7") 
-- Found PythonLibs: /opt/anaconda/lib/libpython3.7m.so.1.0 (found suitable version "3.7.1", minimum required is "2.7") 
-- Found PythonInterp: /opt/anaconda/bin/python (found version "3.7.1") 
-- Found PythonLibs: /opt/anaconda/lib/libpython3.7m.so.1.0
-- System pybind11 found
-- pybind11 include dirs: /usr/include;/opt/anaconda/include/python3.7m
CMake Warning at cmake/Dependencies.cmake:805 (message):
  Not using CUDA, so disabling NCCL.  Suppress this warning with
  -DUSE_NCCL=OFF.
Call Stack (most recent call first):
  CMakeLists.txt:219 (include)


CMake Warning at cmake/Dependencies.cmake:950 (message):
  Metal is only used in ios builds.
Call Stack (most recent call first):
  CMakeLists.txt:219 (include)


-- 
-- ******** Summary ********
--   CMake version         : 3.12.2
--   CMake command         : /opt/anaconda/bin/cmake
--   System                : Linux
--   C++ compiler          : /usr/bin/c++
--   C++ compiler version  : 5.4.1
--   CXX flags             :   -fvisibility-inlines-hidden -Wnon-virtual-dtor
--   Build type            : Release
--   Compile definitions   : TH_BLAS_MKL
--   CMAKE_PREFIX_PATH     : /opt/anaconda/bin/../
--   CMAKE_INSTALL_PREFIX  : /home/manjaro/Downloads/pytorch/torch
--   CMAKE_MODULE_PATH     : /home/manjaro/Downloads/pytorch/cmake/Modules;/usr/share/cmake/pybind11
-- 
--   ONNX version          : 1.4.1
--   ONNX NAMESPACE        : onnx_torch
--   ONNX_BUILD_TESTS      : OFF
--   ONNX_BUILD_BENCHMARKS : OFF
--   ONNX_USE_LITE_PROTO   : OFF
--   ONNXIFI_DUMMY_BACKEND : OFF
-- 
--   Protobuf compiler     : 
--   Protobuf includes     : 
--   Protobuf libraries    : 
--   BUILD_ONNX_PYTHON     : OFF
-- Found gcc &gt;=5 and CUDA &lt;= 7.5, adding workaround C++ flags
-- Could not find CUDA with FP16 support, compiling without torch.CudaHalfTensor
-- Removing -DNDEBUG from compile flags
-- Found OpenMP_C: -fopenmp (found version "4.0") 
-- Found OpenMP_CXX: -fopenmp (found version "4.0") 
-- Compiling with OpenMP support
-- MAGMA not found. Compiling without MAGMA support
-- Could not find hardware support for NEON on this machine.
-- No OMAP3 processor on this machine.
-- No OMAP4 processor on this machine.
-- Looking for cpuid.h
-- Looking for cpuid.h - found
-- Performing Test HAVE_GCC_GET_CPUID
-- Performing Test HAVE_GCC_GET_CPUID - Success
-- Performing Test NO_GCC_EBX_FPIC_BUG
-- Performing Test NO_GCC_EBX_FPIC_BUG - Success
-- Performing Test C_HAS_AVX_1
-- Performing Test C_HAS_AVX_1 - Failed
-- Performing Test C_HAS_AVX_2
-- Performing Test C_HAS_AVX_2 - Success
-- Performing Test C_HAS_AVX2_1
-- Performing Test C_HAS_AVX2_1 - Failed
-- Performing Test C_HAS_AVX2_2
-- Performing Test C_HAS_AVX2_2 - Success
-- Performing Test CXX_HAS_AVX_1
-- Performing Test CXX_HAS_AVX_1 - Failed
-- Performing Test CXX_HAS_AVX_2
-- Performing Test CXX_HAS_AVX_2 - Success
-- Performing Test CXX_HAS_AVX2_1
-- Performing Test CXX_HAS_AVX2_1 - Failed
-- Performing Test CXX_HAS_AVX2_2
-- Performing Test CXX_HAS_AVX2_2 - Success
-- AVX compiler support found
-- AVX2 compiler support found
-- Performing Test HAS_C11_ATOMICS
-- Performing Test HAS_C11_ATOMICS - Failed
-- Performing Test HAS_MSC_ATOMICS
-- Performing Test HAS_MSC_ATOMICS - Failed
-- Performing Test HAS_GCC_ATOMICS
-- Performing Test HAS_GCC_ATOMICS - Success
-- Atomics: using GCC intrinsics
-- Performing Test BLAS_F2C_DOUBLE_WORKS
-- Performing Test BLAS_F2C_DOUBLE_WORKS - Failed
-- Performing Test BLAS_F2C_FLOAT_WORKS
-- Performing Test BLAS_F2C_FLOAT_WORKS - Success
-- Performing Test BLAS_USE_CBLAS_DOT
-- Performing Test BLAS_USE_CBLAS_DOT - Success
-- Found a library with BLAS API (mkl).
-- Found a library with LAPACK API (mkl).
disabling CUDA because NOT USE_CUDA is set
-- CuDNN not found. Compiling without CuDNN support
disabling ROCM because NOT USE_ROCM is set
-- MIOpen not found. Compiling without MIOpen support
disabling MKLDNN because USE_MKLDNN is not set
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for mmap
-- Looking for mmap - found
-- Looking for shm_open
-- Looking for shm_open - found
-- Looking for shm_unlink
-- Looking for shm_unlink - found
-- Looking for malloc_usable_size
-- Looking for malloc_usable_size - found
-- Performing Test C_HAS_THREAD
-- Performing Test C_HAS_THREAD - Success
-- GCC 5.4.1: Adding gcc and gcc_s libs to link line
-- NUMA paths:
-- /usr/include
-- /usr/lib/libnuma.so
disabling CUDA because USE_CUDA is set false
-- Check size of long double
-- Check size of long double - done
-- Performing Test COMPILER_SUPPORTS_LONG_DOUBLE
-- Performing Test COMPILER_SUPPORTS_LONG_DOUBLE - Success
-- Performing Test COMPILER_SUPPORTS_FLOAT128
-- Performing Test COMPILER_SUPPORTS_FLOAT128 - Success
-- Performing Test COMPILER_SUPPORTS_SSE2
-- Performing Test COMPILER_SUPPORTS_SSE2 - Success
-- Performing Test COMPILER_SUPPORTS_SSE4
-- Performing Test COMPILER_SUPPORTS_SSE4 - Success
-- Performing Test COMPILER_SUPPORTS_AVX
-- Performing Test COMPILER_SUPPORTS_AVX - Success
-- Performing Test COMPILER_SUPPORTS_FMA4
-- Performing Test COMPILER_SUPPORTS_FMA4 - Success
-- Performing Test COMPILER_SUPPORTS_AVX2
-- Performing Test COMPILER_SUPPORTS_AVX2 - Success
-- Performing Test COMPILER_SUPPORTS_SVE
-- Performing Test COMPILER_SUPPORTS_SVE - Failed
-- Performing Test COMPILER_SUPPORTS_AVX512F
-- Performing Test COMPILER_SUPPORTS_AVX512F - Failed
-- Found OpenMP_C: -fopenmp (found version "4.0") 
-- Found OpenMP_CXX: -fopenmp (found version "4.0") 
-- Performing Test COMPILER_SUPPORTS_OPENMP
-- Performing Test COMPILER_SUPPORTS_OPENMP - Success
-- Performing Test COMPILER_SUPPORTS_WEAK_ALIASES
-- Performing Test COMPILER_SUPPORTS_WEAK_ALIASES - Success
-- Performing Test COMPILER_SUPPORTS_BUILTIN_MATH
-- Performing Test COMPILER_SUPPORTS_BUILTIN_MATH - Success
-- Configuring build for SLEEF-v3.2
   Target system: Linux-4.14.94-1-MANJARO
   Target processor: x86_64
   Host system: Linux-4.14.94-1-MANJARO
   Host processor: x86_64
   Detected C compiler: GNU @ /usr/bin/cc
-- Using option `-Wall -Wno-unused -Wno-attributes -Wno-unused-result -Wno-psabi -ffp-contract=off -fno-math-errno -fno-trapping-math` to compile libsleef
-- Building shared libs : OFF
-- MPFR : /opt/anaconda/lib/libmpfr.so
-- MPFR header file in /opt/anaconda/include
-- GMP : /opt/anaconda/lib/libgmp.so
-- RUNNING_ON_TRAVIS : 0
-- COMPILER_SUPPORTS_OPENMP : 1
-- /usr/bin/c++ /home/manjaro/Downloads/pytorch/torch/abi-check.cpp -o /home/manjaro/Downloads/pytorch/build/abi-check
-- Determined _GLIBCXX_USE_CXX11_ABI=1
-- NCCL operators skipped due to no CUDA support
-- Excluding ideep operators as we are not using ideep
-- Excluding image processing operators due to no opencv
-- Excluding video processing operators due to no opencv
-- MPI operators skipped due to no MPI support
-- Include Observer library
-- Using lib/python3.7/site-packages as python relative installation path
CMake Warning at CMakeLists.txt:416 (message):
  Generated cmake files are only fully tested if one builds with system glog,
  gflags, and protobuf.  Other settings may generate files that are not well
  tested.


-- 
-- ******** Summary ********
-- General:
--   CMake version         : 3.12.2
--   CMake command         : /opt/anaconda/bin/cmake
--   System                : Linux
--   C++ compiler          : /usr/bin/c++
--   C++ compiler version  : 5.4.1
--   BLAS                  : MKL
--   CXX flags             :   -fvisibility-inlines-hidden -D_FORCE_INLINES -D_MWAITXINTRIN_H_INCLUDED -D__STRICT_ANSI__ -fopenmp -O2 -fPIC -Wno-narrowing -Wall -Wextra -Wno-missing-field-initializers -Wno-type-limits -Wno-array-bounds -Wno-unknown-pragmas -Wno-sign-compare -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-unused-result -Wno-strict-overflow -Wno-strict-aliasing -Wno-error=deprecated-declarations -Wno-error=pedantic -Wno-error=redundant-decls -Wno-error=old-style-cast -Wno-unused-but-set-variable -Wno-maybe-uninitialized
--   Build type            : Release
--   Compile definitions   : TH_BLAS_MKL;ONNX_NAMESPACE=onnx_torch;USE_GCC_ATOMICS=1;HAVE_MMAP=1;_FILE_OFFSET_BITS=64;HAVE_SHM_OPEN=1;HAVE_SHM_UNLINK=1;HAVE_MALLOC_USABLE_SIZE=1
--   CMAKE_PREFIX_PATH     : /opt/anaconda/bin/../
--   CMAKE_INSTALL_PREFIX  : /home/manjaro/Downloads/pytorch/torch
-- 
--   TORCH_VERSION         : 1.1.0
--   CAFFE2_VERSION        : 1.1.0
--   BUILD_ATEN_MOBILE     : OFF
--   BUILD_ATEN_ONLY       : OFF
--   BUILD_BINARY          : False
--   BUILD_CUSTOM_PROTOBUF : ON
--     Link local protobuf : ON
--   BUILD_DOCS            : OFF
--   BUILD_PYTHON          : True
--     Python version      : 3.7.1
--     Python executable   : /opt/anaconda/bin/python
--     Pythonlibs version  : 3.7.1
--     Python library      : /opt/anaconda/lib/libpython3.7m.so.1.0
--     Python includes     : /opt/anaconda/include/python3.7m
--     Python site-packages: lib/python3.7/site-packages
--   BUILD_CAFFE2_OPS      : False
--   BUILD_SHARED_LIBS     : ON
--   BUILD_TEST            : False
--   USE_ASAN              : OFF
--   USE_CUDA              : False
--   USE_ROCM              : False
--   USE_EIGEN_FOR_BLAS    : 
--   USE_FBGEMM            : OFF
--   USE_FFMPEG            : False
--   USE_GFLAGS            : ON
--   USE_GLOG              : ON
--   USE_LEVELDB           : False
--   USE_LITE_PROTO        : OFF
--   USE_LMDB              : False
--   USE_METAL             : OFF
--   USE_MKL               : ON
--   USE_MKLDNN            : OFF
--   USE_NCCL              : OFF
--   USE_NNPACK            : False
--   USE_NUMPY             : ON
--   USE_OBSERVERS         : ON
--   USE_OPENCL            : OFF
--   USE_OPENCV            : False
--   USE_OPENMP            : OFF
--   USE_PROF              : OFF
--   USE_QNNPACK           : False
--   USE_REDIS             : OFF
--   USE_ROCKSDB           : OFF
--   USE_ZMQ               : OFF
--   USE_DISTRIBUTED       : False
--   Public Dependencies  : Threads::Threads;caffe2::mkl;glog::glog
--   Private Dependencies : cpuinfo;/usr/lib/libnuma.so;fp16;onnxifi_loader;rt;gcc_s;gcc;dl
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    NCCL_EXTERNAL
    THD_SO_VERSION


Problem solved. 

I found what was wrong and I fixed it. The whole problem lies in the fact that Anaconda distribution comes with its own ld linker that is located in /opt/anaconda/compiler_compat/ and it overshadows system ld residing at /usr/bin.

To fix my error I ran python setup.py clean and then I temporarily renamed Anaconda's ld linker to ld-old to make it invisible during PyTorch installation.
