tensorflow build fails with "missing dependency" error - tensorflow

Question

I'm completely new to bazel and tensorflow so the solution to this may be obvious to someone with some experience. My bazel build of tensorflow fails with a "missing dependency" error message. Here is the relevant sequence of build commands and output:
(tf-gpu)kss#linux-9c32:~/projects> git clone --recurse-submodules https://github.com/tensorflow/tensorflow tensorflow-nogpu
Cloning into 'tensorflow-nogpu'...
remote: Counting objects: 16735, done.
remote: Compressing objects: 100% (152/152), done.
remote: Total 16735 (delta 73), reused 0 (delta 0), pack-reused 16583
Receiving objects: 100% (16735/16735), 25.25 MiB | 911.00 KiB/s, done.
Resolving deltas: 100% (10889/10889), done.
Checking connectivity... done.
Submodule 'google/protobuf' (https://github.com/google/protobuf.git) registered for path 'google/protobuf'
Cloning into 'google/protobuf'...
remote: Counting objects: 30266, done.
remote: Compressing objects: 100% (113/113), done.
remote: Total 30266 (delta 57), reused 0 (delta 0), pack-reused 30151
Receiving objects: 100% (30266/30266), 28.90 MiB | 1.98 MiB/s, done.
Resolving deltas: 100% (20225/20225), done.
Checking connectivity... done.
Submodule path 'google/protobuf': checked out '0906f5d18a2548024b511eadcbb4cfc0ca56cd67'
(tf-gpu)kss#linux-9c32:~/projects> cd tensorflow-nogpu/
(tf-gpu)kss#linux-9c32:~/projects/tensorflow-nogpu> ./configure
Please specify the location of python. [Default is /home/kss/.venv/tf-gpu/bin/python]:
Do you wish to build TensorFlow with GPU support? [y/N]
No GPU support will be enabled for TensorFlow
Configuration finished
(tf-gpu)kss#linux-9c32:~/projects/tensorflow-nogpu> bazel build -c opt //tensorflow/tools/pip_package:build_pip_package
Sending SIGTERM to previous Bazel server (pid=8491)... done.
....
INFO: Found 1 target...
ERROR: /home/kss/.cache/bazel/_bazel_kss/b97e0e942a10977a6b42467ea6712cbf/external/re2/BUILD:9:1: undeclared inclusion(s) in rule '#re2//:re2':
this rule is missing dependency declarations for the following files included by 'external/re2/re2/perl_groups.cc':
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/stddef.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/stdarg.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/stdint.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/x86intrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/ia32intrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/mmintrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/xmmintrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/mm_malloc.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/emmintrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/immintrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/fxsrintrin.h'
'/usr/lib64/gcc/x86_64-suse-linux/4.8/include/adxintrin.h'.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
Use --verbose_failures to see the command lines of failed build steps.
INFO: Elapsed time: 144.661s, Critical Path: 1.18s
(tf-gpu)kss#linux-9c32:~/projects/tensorflow-nogpu>
The version of bazel I'm using is release 0.1.4, I'm running on openSUSE 13.2. I confirmed that the header files do exist which is probably expected:
(tf-gpu)kss#linux-9c32:~/projects/tensorflow-nogpu> ll /usr/lib64/gcc/x86_64-suse-linux/4.8/include/stddef.h
-rw-r--r-- 1 root root 13619 Oct 6 2014 /usr/lib64/gcc/x86_64-suse-linux/4.8/include/stddef.h
Note for anyone who finds this question:
Use Damien's answer below except that you have to use --crosstool_top rather than --crosstool. Also if you are building for GPU acceleration you will also need to modify the CROSSTOOL file in the tensorflow repo like:
(tf-gpu)kss#linux-9c32:~/projects/tensorflow-gpu> git diff third_party/gpus/crosstool/CROSSTOOL | cat
diff --git a/third_party/gpus/crosstool/CROSSTOOL b/third_party/gpus/crosstool/CROSSTOOL
index dfde7cd..b63f950 100644
--- a/third_party/gpus/crosstool/CROSSTOOL
+++ b/third_party/gpus/crosstool/CROSSTOOL
## -56,6 +56,7 ## toolchain {
cxx_builtin_include_directory: "/usr/lib/gcc/"
cxx_builtin_include_directory: "/usr/local/include"
cxx_builtin_include_directory: "/usr/include"
+ cxx_builtin_include_directory: "/usr/lib64/gcc"
tool_path { name: "gcov" path: "/usr/bin/gcov" }
# C(++) compiles invoke the compiler (as that is the one knowing where

Answer 1

You should tweak the C++ compiler.
To do so, here's the best way to proceed:
edit the file tools/cpp/CROSSTOOL (https://github.com/bazelbuild/bazel/blob/master/tools/cpp/CROSSTOOL) from your package path directory (should be in ~/.bazel/base_workspace, can be found with bazel info package_path) to add a line cxx_builtin_include_directory: /usr/lib64/gcc around line 100 (see https://github.com/bazelbuild/bazel/blob/master/tools/cpp/CROSSTOOL#L101).
Then echo "build --crosstool=//tools/cpp:toolchain" >>~/.bazelrc and then retries to build.
Sorry for the mess, we are working on making C++ toolchain work better out of the box.

Answer 2

Bazel complaints of system header files because compiler uses -MD (as opposed to -MMD) flag when generating dependences. While using -MD is reasonable for an environment that changes often, listing dependency on system header files causes the 'missing dependency declarations' errors.
What helped me was converting the '-MD' flag into '-MMD' flag in the compiler wrapper files third_party/gpus/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc.tpl just before 'subprocess.call([CPU_COMPILER]...)':
cpu_compiler_flags = ['-MMD' if flag == '-MD' else flag for flag in cpu_compiler_flags]
and third_party/sycl/crosstool/computecpp.tpl, similar place:
computecpp_device_compiler_flags = ['-MMD' if flag == '-MD' else flag for flag in computecpp_device_compiler_flags]