tensorflow: `TensorContractionThreadPool.h' file not found` when using `--copt=-march=native`

When trying to run

$ ./configure
........
$ bazel build --copt=-march=native -c opt //tensorflow/tools/pip_package:build_pip_package --verbose_failures

it fails with the ./third_party/eigen3/unsupported/Eigen/CXX11/FixedPoint:42:10: fatal error: 'src/Tensor/TensorContractionThreadPool.h' file not found error.

Similar problem was seen in #4680, #580,

I am on Mac OS X Sierra 10.12.2 with no CUDA and cuDNN installed. I am using virtual environment on Python 2.7

Here is the checked commit and bazel version

$ git rev-parse HEAD
ac28ae043df4bc6f112f964f6df22845b8a05390
$ bazel version
Build label: 0.4.3-homebrew
Build target: bazel-out/local-opt/bin/src/main/java/com/google/devtools/build/lib/bazel/BazelServer_deploy.jar
Build time: Thu Dec 22 15:20:15 2016 (1482420015)
Build timestamp: 1482420015
Build timestamp as int: 1482420015

This works fine:

$ git checkout remotes/origin/r0.12
$ ./configure # With defaults
.........
$ bazel build --copt=-march=native -c opt //tensorflow/tools/pip_package:build_pip_package --verbose_failures
# This finishes correctly

Here is the full terminal log when bazel is run on the master branch:

$ git checkout master
$ ./configure # With defaults
.........
$ bazel build --copt=-march=native -c opt //tensorflow/tools/pip_package:build_pip_package --verbose_failures
INFO: Found 1 target...
ERROR: /Users/zafar/GitHub/tensorflow/tensorflow/core/kernels/BUILD:856:1: C++ compilation of rule '//tensorflow/core/kernels:gather_functor' failed: cc_wrapper.sh failed: error executing command
  (cd /private/var/tmp/_bazel_zafar/c40dcca6773e4515fd11c724e0ebae51/execroot/tensorflow && \
  exec env - \
    PATH=/Users/zafar/.virtualenvs/tf-dev-env/bin:/Users/zafar/.rbenv/shims:/Users/zafar/.node/bin:/Users/zafar/bin:/Users/zafar/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/MacGPG2/bin:/Library/TeX/texbin \
    TMPDIR=/var/folders/yx/nf9nvmpn4_79r7nbzkn8cz8h0000gn/T/ \
  external/local_config_cc/cc_wrapper.sh -U_FORTIFY_SOURCE '-D_FORTIFY_SOURCE=1' -fstack-protector -Wall -Wthread-safety -Wself-assign -fcolor-diagnostics -fno-omit-frame-pointer -g0 -O2 -DNDEBUG -ffunction-sections -fdata-sections '-march=native' '-std=c++0x' -MD -MF bazel-out/local-opt/bin/tensorflow/core/kernels/_objs/gather_functor/tensorflow/core/kernels/gather_functor.pic.d '-frandom-seed=bazel-out/local-opt/bin/tensorflow/core/kernels/_objs/gather_functor/tensorflow/core/kernels/gather_functor.pic.o' -fPIC -DEIGEN_MPL2_ONLY -iquote . -iquote bazel-out/local-opt/genfiles -iquote external/bazel_tools -iquote bazel-out/local-opt/genfiles/external/bazel_tools -iquote external/eigen_archive -iquote bazel-out/local-opt/genfiles/external/eigen_archive -iquote external/local_config_sycl -iquote bazel-out/local-opt/genfiles/external/local_config_sycl -isystem external/bazel_tools/tools/cpp/gcc3 -isystem external/eigen_archive -isystem bazel-out/local-opt/genfiles/external/eigen_archive -DEIGEN_AVOID_STL_ARRAY -Iexternal/gemmlowp -Wno-sign-compare -fno-exceptions -Wno-builtin-macro-redefined '-D__DATE__="redacted"' '-D__TIMESTAMP__="redacted"' '-D__TIME__="redacted"' -c tensorflow/core/kernels/gather_functor.cc -o bazel-out/local-opt/bin/tensorflow/core/kernels/_objs/gather_functor/tensorflow/core/kernels/gather_functor.pic.o): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1.
In file included from tensorflow/core/kernels/gather_functor.cc:50:
In file included from ./tensorflow/core/kernels/gather_functor.h:22:
In file included from ./tensorflow/core/framework/type_traits.h:22:
In file included from ./tensorflow/core/framework/numeric_types.h:25:
./third_party/eigen3/unsupported/Eigen/CXX11/FixedPoint:42:10: fatal error: 'src/Tensor/TensorContractionThreadPool.h' file not found
#include "src/Tensor/TensorContractionThreadPool.h"
         ^
1 error generated.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 34.692s, Critical Path: 25.26s