Windows missing unistd.h and getopt.h to build

[maxrohleder]

Build Setup:

• running bazel 3.1.0 on powershell (msys2 in path for bash) (powershell is recommended here)
• cuda 10.1 with cudNN 7.6 files copied into the respective folders (bin, lib, include)
• Visual Studio 2019 Professional (Compiler Version 19.26.28806)

I confirmed here that these fit together.

Preparations:

This repository includes the tensorflow/custom-op code with the two example ops replaced with the pyronn-layers following the steps described here. Additionally the fixes to the problems described in #1 and #2 were fixed. These changes are minimal and should not affect the build.

Running configure.sh creates this .bazelrc for me:

build:cuda --define=using_cuda=true --define=using_cuda_nvcc=true
build:cuda --crosstool_top=@local_config_cuda//crosstool:toolchain
build --spawn_strategy=standalone
build --strategy=Genrule=standalone
build -c opt
build --copt=/experimental:preprocessor
build --host_copt=/experimental:preprocessor
build --action_env TF_HEADER_DIR="C:/Users/z0045kxy/Miniconda3/envs/tftest2/lib/site-packages/tensorflow/include"
build --action_env TF_SHARED_LIBRARY_DIR="C:/Users/z0045kxy/Miniconda3/envs/tftest2/lib/site-packages/tensorflow/python"
build --action_env TF_SHARED_LIBRARY_NAME="_pywrap_tensorflow_internal.lib"
build --action_env TF_NEED_CUDA="1"
build --action_env TF_CUDA_VERSION="10.1"
build --action_env TF_CUDNN_VERSION="7"
build --action_env CUDNN_INSTALL_PATH="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1"
build --action_env CUDA_TOOLKIT_PATH="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1"
build --config=cuda
test --config=cuda

The error:

As this looks fine, I run bazel build build_pip_pkg --verbose_failures, which failes with this error:

(tftest2) PS C:\Users\z0045kxy\Documents\win-pyronn> bazel build build_pip_pkg --verbose_failures
WARNING: Ignoring JAVA_HOME, because it must point to a JDK, not a JRE.
Starting local Bazel server and connecting to it...
INFO: Analyzed target //:build_pip_pkg (21 packages loaded, 105 targets configured).
INFO: Found 1 target...
INFO: Deleting stale sandbox base C:/users/z0045kxy/_bazel_z0045kxy/tc4sfiy3/sandbox
ERROR: C:/users/z0045kxy/documents/win-pyronn/pyronn_layers/BUILD:32:1: C++ compilation of rule '//pyronn_layers:pyronn_layers_ops_gpu' failed (Exit 2): python.exe failed: error executing command
  cd C:/users/z0045kxy/_bazel_z0045kxy/tc4sfiy3/execroot/__main__
  SET CUDA_TOOLKIT_PATH=C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1
    SET CUDNN_INSTALL_PATH=C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1
    SET INCLUDE=C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\VC\Tools\MSVC\14.26.28801\ATLMFC\include;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\VC\Tools\MSVC\14.26.28801\include;C:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\ucrt;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\um;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt;C:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt
    SET LIB=C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\VC\Tools\MSVC\14.26.28801\ATLMFC\lib\x64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\VC\Tools\MSVC\14.26.28801\lib\x64;C:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\lib\um\x64;C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\ucrt\x64;C:\Program Files (x86)\Windows Kits\10\lib\10.0.19041.0\um\x64;
    SET PATH=C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\\Extensions\Microsoft\IntelliCode\CLI;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\VC\Tools\MSVC\14.26.28801\bin\HostX64\x64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\VC\VCPackages;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\CommonExtensions\Microsoft\TestWindow;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\CommonExtensions\Microsoft\TeamFoundation\Team Explorer;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\MSBuild\Current\bin\Roslyn;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Team Tools\Performance Tools\x64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Team Tools\Performance Tools;C:\Program Files (x86)\Microsoft Visual Studio\Shared\Common\VSPerfCollectionTools\vs2019\\x64;C:\Program Files (x86)\Microsoft Visual Studio\Shared\Common\VSPerfCollectionTools\vs2019\;C:\Program Files (x86)\Microsoft SDKs\Windows\v10.0A\bin\NETFX 4.8 Tools\x64\;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\CommonExtensions\Microsoft\FSharp\;C:\Program Files (x86)\Windows Kits\10\bin\10.0.19041.0\x64;C:\Program Files (x86)\Windows Kits\10\bin\x64;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\\MSBuild\Current\Bin;C:\WINDOWS\Microsoft.NET\Framework64\v4.0.30319;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\Tools\;;C:\WINDOWS\system32;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\CommonExtensions\Microsoft\CMake\Ninja;C:\Program Files (x86)\Microsoft Visual Studio\2019\Professional\Common7\IDE\VC\Linux\bin\ConnectionManagerExe
    SET PWD=/proc/self/cwd
    SET RUNFILES_MANIFEST_ONLY=1
    SET TEMP=C:\Users\z0045kxy\AppData\Local\Temp
    SET TF_CUDA_VERSION=10.1
    SET TF_CUDNN_VERSION=7
    SET TF_HEADER_DIR=C:/Users/z0045kxy/Miniconda3/envs/tftest2/lib/site-packages/tensorflow/include
    SET TF_NEED_CUDA=1
    SET TF_SHARED_LIBRARY_DIR=C:/Users/z0045kxy/Miniconda3/envs/tftest2/lib/site-packages/tensorflow/python
    SET TF_SHARED_LIBRARY_NAME=_pywrap_tensorflow_internal.lib
    SET TMP=C:\Users\z0045kxy\AppData\Local\Temp
  C:/Users/z0045kxy/Miniconda3/envs/tftest2/python.exe -B external/local_config_cuda/crosstool/windows/msvc_wrapper_for_nvcc.py /nologo /DCOMPILER_MSVC /DNOMINMAX /D_WIN32_WINNT=0x0600 /D_CRT_SECURE_NO_DEPRECATE /D_CRT_SECURE_NO_WARNINGS /D_SILENCE_STDEXT_HASH_DEPRECATION_WARNINGS /bigobj /Zm500 /J /Gy /GF /EHsc /wd4351 /wd4291 /wd4250 /wd4996 /I. /Ibazel-out/x64_windows-opt/bin /Iexternal/local_config_tf /Ibazel-out/x64_windows-opt/bin/external/local_config_tf /Iexternal/local_config_cuda /Ibazel-out/x64_windows-opt/bin/external/local_config_cuda /Ibazel-out/x64_windows-opt/bin/external/local_config_cuda/cuda/_virtual_includes/cuda_headers_virtual /Iexternal/local_config_tf/include /Ibazel-out/x64_windows-opt/bin/external/local_config_tf/include /Iexternal/local_config_cuda/cuda /Ibazel-out/x64_windows-opt/bin/external/local_config_cuda/cuda /Iexternal/local_config_cuda/cuda/cuda/include /Ibazel-out/x64_windows-opt/bin/external/local_config_cuda/cuda/cuda/include /showIncludes /MD /O2 /DNDEBUG /experimental:preprocessor /D__CLANG_SUPPORT_DYN_ANNOTATION__ /DEIGEN_MPL2_ONLY /DEIGEN_MAX_ALIGN_BYTES=64 /DEIGEN_HAS_TYPE_TRAITS=0 /DTF_USE_SNAPPY /showIncludes /MD /O2 /DNDEBUG /w -DWIN32_LEAN_AND_MEAN -DNOGDI /d2ReducedOptimizeHugeFunctions /arch:AVX /std:c++14 -DTENSORFLOW_MONOLITHIC_BUILD /DPLATFORM_WINDOWS /DEIGEN_HAS_C99_MATH /DTENSORFLOW_USE_EIGEN_THREADPOOL /DEIGEN_AVOID_STL_ARRAY /Iexternal/gemmlowp /wd4018 /wd4577 /DNOGDI /UTF_COMPILE_LIBRARY -DTENSORFLOW_USE_NVCC=1 -DGOOGLE_CUDA=1 -x cuda -nvcc_options=relaxed-constexpr -nvcc_options=ftz=true /Fobazel-out/x64_windows-opt/bin/pyronn_layers/_objs/pyronn_layers_ops_gpu/cone_projector_3D_CudaKernel_hardware_interp.cu.o /c pyronn_layers/cc/kernels/cone_projector_3D_CudaKernel_hardware_interp.cu.cc
Execution platform: @local_config_platform//:host
cl : Command line warning D9035 : option 'experimental:preprocessor' has been deprecated and will be removed in a future release
cl : Command line warning D9036 : use 'Zc:preprocessor' instead of 'experimental:preprocessor'
bazel-out/x64_windows-opt/bin/external/local_config_tf/include\unsupported/Eigen/CXX11/Tensor(74): fatal error C1083: Cannot open include file: 'unistd.h': No such file or directory
Target //:build_pip_pkg failed to build
INFO: Elapsed time: 33.424s, Critical Path: 26.77s
INFO: 0 processes.
FAILED: Build did NOT complete successfully

Possible origin:

The build process fails while compiling the file from the time_two example /time_two_kernels.cu.o . From the error Cannot open include file: 'unistd.h , I recon that these are not included in the windows C++ standard libraries. A little bit of stackoverflow digging confirms this (see this thread). If I follow the advice from the thread and add a 'dummy' unistd.h in one of the include folders, a similar error occurs for getopt.h.

[maxrohleder]

I tryied adding the two header files from here and here to the root folder of the project, as . is listed as an include directory:

/I. 
/Ibazel-out/x64_windows-opt/bin 
/Iexternal/local_config_tf /Ibazel-out/x64_windows-opt/bin/external/local_config_tf 
/Iexternal/local_config_cuda /Ibazel-out/x64_windows-opt/bin/external/local_config_cuda 
/Ibazel-out/x64_windows-opt/bin/external/local_config_cuda/cuda/_virtual_includes/cuda_headers_virtual 
/Iexternal/local_config_tf/include 
/Ibazel-out/x64_windows-opt/bin/external/local_config_tf/include 
/Iexternal/local_config_cuda/cuda /Ibazel-out/x64_windows-opt/bin/external/local_config_cuda/cuda /Iexternal/local_config_cuda/cuda/cuda/include 
/Ibazel-out/x64_windows-opt/bin/external/local_config_cuda/cuda/cuda/include

I had to remove all typedefs and the defines for rand.

When this is done, the compilation is successful, but bazel throws this error:

ERROR: C:/users/z0045kxy/documents/win-pyronn/pyronn_layers/BUILD:32:1: undeclared inclusion(s) in rule '//pyronn_layers:pyronn_layers_ops_gpu':
this rule is missing dependency declarations for the following files included by 'pyronn_layers/cc/kernels/cone_backprojector_3D_CudaKernel.cu.cc':
  'unistd.h'
  'getopt.h'

Anyone knows how to adapt the BUILD file to allow this? Or is the approach generally set up to fail?

[maxrohleder]

FIX:

Editing this file: bazel-out/x64_windows-opt/bin/external/local_config_tf/include\unsupported/Eigen/CXX11/Tensor(74) is no use, as it gets created again on every build.

Instead, modify the source of the tensorflow library you are building against. For me, this is at:
C:\Users\z0045kxy\Miniconda3\envs\tftest2\Lib\site-packages\tensorflow\include\unsupported\Eigen\CXX11\Tensor

Open this file and remove #include <unistd.h> from line l. 74

After that, run

bazel clean --expunge
bazel build --enable_runfiles build_pip_pkg --verbose_failures

to start a clean rebuild.