tensorflow: Undeclared inclusions and missing dependencies in building

The following commands were run on a Fedora 23 64 bits on Tensorflow master, but I get similar results on the 0.8 branch.

Using Bazel 0.2.1 on a laptop without graphics card:

$ bazel build -c opt --verbose_failures //tensorflow/tools/pip_package:build_pip_package
INFO: Found 1 target...
ERROR: /home/david/.cache/bazel/_bazel_david/47d00ffdd2fc0515138a34f138cebd63/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/util/rune.cc':
  '/lib/gcc/x86_64-redhat-linux/5.3.1/include/stdarg.h'
  '/lib/gcc/x86_64-redhat-linux/5.3.1/include/stddef.h'
  '/lib/gcc/x86_64-redhat-linux/5.3.1/include/stdint.h'.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 1.394s, Critical Path: 0.34s

On a machine with Cuda 7.5 and cudnn 5 installed, GCC 4.9 built locally (but I get the same results with system’s GCC 5.3.1):

With bazel 0.1.1:

$ bazel build -c opt --config=cuda --spawn_strategy=standalone //tensorflow/tools/pip_package:build_pip_package
Warning: ignoring LD_PRELOAD in environment.
ERROR: /home/david/gits/tensorflow/WORKSPACE:16:6: First argument of load() is a path, not a label. It should start with a single slash if it is an absolute path..
ERROR: /home/david/gits/tensorflow/WORKSPACE:20:6: First argument of load() is a path, not a label. It should start with a single slash if it is an absolute path..
ERROR: WORKSPACE file could not be parsed.
ERROR: no such package 'external': Package 'external' contains errors.
INFO: Elapsed time: 0.065s

With Bazel 0.2.1:

bazel build -c opt --config=cuda --spawn_strategy=standalone //tensorflow/tools/pip_package:build_pip_package
Warning: ignoring LD_PRELOAD in environment.
Sending SIGTERM to previous Bazel server (pid=19634)... done.
.....
INFO: Found 1 target...
ERROR: /home/david/.cache/bazel/_bazel_david/47d00ffdd2fc0515138a34f138cebd63/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':
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stddef.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stdarg.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stdint.h'
  '/home/david/.local/include/c++/4.9.3/ctime'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++config.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/os_defines.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/cpu_defines.h'
  '/home/david/.local/include/c++/4.9.3/vector'
  '/home/david/.local/include/c++/4.9.3/bits/stl_algobase.h'
  '/home/david/.local/include/c++/4.9.3/bits/functexcept.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/cpp_type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/numeric_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_pair.h'
  '/home/david/.local/include/c++/4.9.3/bits/move.h'
  '/home/david/.local/include/c++/4.9.3/bits/concept_check.h'
  '/home/david/.local/include/c++/4.9.3/type_traits'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_types.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_funcs.h'
  '/home/david/.local/include/c++/4.9.3/debug/debug.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator.h'
  '/home/david/.local/include/c++/4.9.3/bits/ptr_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/predefined_ops.h'
  '/home/david/.local/include/c++/4.9.3/bits/allocator.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++allocator.h'
  '/home/david/.local/include/c++/4.9.3/ext/new_allocator.h'
  '/home/david/.local/include/c++/4.9.3/new'
  '/home/david/.local/include/c++/4.9.3/exception'
  '/home/david/.local/include/c++/4.9.3/bits/atomic_lockfree_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_ptr.h'
  '/home/david/.local/include/c++/4.9.3/bits/nested_exception.h'
  '/home/david/.local/include/c++/4.9.3/bits/memoryfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_construct.h'
  '/home/david/.local/include/c++/4.9.3/ext/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_uninitialized.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_vector.h'
  '/home/david/.local/include/c++/4.9.3/initializer_list'
  '/home/david/.local/include/c++/4.9.3/bits/stl_bvector.h'
  '/home/david/.local/include/c++/4.9.3/bits/functional_hash.h'
  '/home/david/.local/include/c++/4.9.3/bits/hash_bytes.h'
  '/home/david/.local/include/c++/4.9.3/bits/range_access.h'
  '/home/david/.local/include/c++/4.9.3/bits/vector.tcc'
  '/home/david/.local/include/c++/4.9.3/string'
  '/home/david/.local/include/c++/4.9.3/bits/stringfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/char_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/postypes.h'
  '/home/david/.local/include/c++/4.9.3/cwchar'
  '/home/david/.local/include/c++/4.9.3/cstdint'
  '/home/david/.local/include/c++/4.9.3/bits/localefwd.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++locale.h'
  '/home/david/.local/include/c++/4.9.3/clocale'
  '/home/david/.local/include/c++/4.9.3/iosfwd'
  '/home/david/.local/include/c++/4.9.3/cctype'
  '/home/david/.local/include/c++/4.9.3/bits/ostream_insert.h'
  '/home/david/.local/include/c++/4.9.3/bits/cxxabi_forced.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_function.h'
  '/home/david/.local/include/c++/4.9.3/backward/binders.h'
  '/home/david/.local/include/c++/4.9.3/bits/basic_string.h'
  '/home/david/.local/include/c++/4.9.3/ext/atomicity.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/gthr.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/gthr-default.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/atomic_word.h'
  '/home/david/.local/include/c++/4.9.3/ext/string_conversions.h'
  '/home/david/.local/include/c++/4.9.3/cstdlib'
  '/home/david/.local/include/c++/4.9.3/cstdio'
  '/home/david/.local/include/c++/4.9.3/cerrno'
  '/home/david/.local/include/c++/4.9.3/bits/basic_string.tcc'
  '/home/david/.local/include/c++/4.9.3/algorithm'
  '/home/david/.local/include/c++/4.9.3/utility'
  '/home/david/.local/include/c++/4.9.3/bits/stl_relops.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_algo.h'
  '/home/david/.local/include/c++/4.9.3/bits/algorithmfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_heap.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_tempbuf.h'
  '/home/david/.local/include/c++/4.9.3/random'
  '/home/david/.local/include/c++/4.9.3/cmath'
  '/home/david/.local/include/c++/4.9.3/limits'
  '/home/david/.local/include/c++/4.9.3/bits/random.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/opt_random.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/x86intrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/ia32intrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/mmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/xmmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/mm_malloc.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/emmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/pmmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/tmmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/ammintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/smmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/popcntintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/wmmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/immintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/avxintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/avx2intrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/avx512fintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/avx512erintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/avx512pfintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/avx512cdintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/shaintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/lzcntintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/bmiintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/bmi2intrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/fmaintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/f16cintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/rtmintrin.h'
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  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/mm3dnow.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/prfchwintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/fma4intrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/xopintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/lwpintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/tbmintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/rdseedintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/fxsrintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/xsaveintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/xsaveoptintrin.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/adxintrin.h'
  '/home/david/.local/include/c++/4.9.3/bits/random.tcc'
  '/home/david/.local/include/c++/4.9.3/numeric'
  '/home/david/.local/include/c++/4.9.3/bits/stl_numeric.h'
  '/home/david/.local/include/c++/4.9.3/map'
  '/home/david/.local/include/c++/4.9.3/bits/stl_tree.h'
  '/home/david/.local/include/c++/4.9.3/ext/aligned_buffer.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_map.h'
  '/home/david/.local/include/c++/4.9.3/tuple'
  '/home/david/.local/include/c++/4.9.3/array'
  '/home/david/.local/include/c++/4.9.3/stdexcept'
  '/home/david/.local/include/c++/4.9.3/bits/uses_allocator.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_multimap.h'
  '/home/david/.local/include/c++/4.9.3/stack'
  '/home/david/.local/include/c++/4.9.3/deque'
  '/home/david/.local/include/c++/4.9.3/bits/stl_deque.h'
  '/home/david/.local/include/c++/4.9.3/bits/deque.tcc'
  '/home/david/.local/include/c++/4.9.3/bits/stl_stack.h'
  '/home/david/.local/include/c++/4.9.3/ostream'
  '/home/david/.local/include/c++/4.9.3/ios'
  '/home/david/.local/include/c++/4.9.3/bits/ios_base.h'
  '/home/david/.local/include/c++/4.9.3/bits/locale_classes.h'
  '/home/david/.local/include/c++/4.9.3/bits/locale_classes.tcc'
  '/home/david/.local/include/c++/4.9.3/streambuf'
  '/home/david/.local/include/c++/4.9.3/bits/streambuf.tcc'
  '/home/david/.local/include/c++/4.9.3/bits/basic_ios.h'
  '/home/david/.local/include/c++/4.9.3/bits/locale_facets.h'
  '/home/david/.local/include/c++/4.9.3/cwctype'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/ctype_base.h'
  '/home/david/.local/include/c++/4.9.3/bits/streambuf_iterator.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/ctype_inline.h'
  '/home/david/.local/include/c++/4.9.3/bits/locale_facets.tcc'
  '/home/david/.local/include/c++/4.9.3/bits/basic_ios.tcc'
  '/home/david/.local/include/c++/4.9.3/bits/ostream.tcc'
  '/home/david/.local/include/c++/4.9.3/set'
  '/home/david/.local/include/c++/4.9.3/bits/stl_set.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_multiset.h'
  '/home/david/.local/include/c++/4.9.3/tr1/unordered_set'
  '/home/david/.local/include/c++/4.9.3/tr1/type_traits'
  '/home/david/.local/include/c++/4.9.3/tr1/functional_hash.h'
  '/home/david/.local/include/c++/4.9.3/tr1/hashtable.h'
  '/home/david/.local/include/c++/4.9.3/tr1/hashtable_policy.h'
  '/home/david/.local/include/c++/4.9.3/tr1/unordered_set.h'
  '/home/david/.local/include/c++/4.9.3/sstream'
  '/home/david/.local/include/c++/4.9.3/istream'
  '/home/david/.local/include/c++/4.9.3/bits/istream.tcc'
  '/home/david/.local/include/c++/4.9.3/bits/sstream.tcc'.
Target //tensorflow/tools/pip_package:build_pip_package failed to build
Use --verbose_failures to see the command lines of failed build steps.

bazel build -c opt --config=cuda //tensorflow/cc:tutorials_example_trainer
Warning: ignoring LD_PRELOAD in environment.
INFO: Found 1 target...
ERROR: /home/david/.cache/bazel/_bazel_david/47d00ffdd2fc0515138a34f138cebd63/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/util/valgrind.cc':
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stddef.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stdarg.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stdint.h'
  '/home/david/.local/include/c++/4.9.3/ctime'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++config.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/os_defines.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/cpu_defines.h'
  '/home/david/.local/include/c++/4.9.3/vector'
  '/home/david/.local/include/c++/4.9.3/bits/stl_algobase.h'
  '/home/david/.local/include/c++/4.9.3/bits/functexcept.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/cpp_type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/numeric_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_pair.h'
  '/home/david/.local/include/c++/4.9.3/bits/move.h'
  '/home/david/.local/include/c++/4.9.3/bits/concept_check.h'
  '/home/david/.local/include/c++/4.9.3/type_traits'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_types.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_funcs.h'
  '/home/david/.local/include/c++/4.9.3/debug/debug.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator.h'
  '/home/david/.local/include/c++/4.9.3/bits/ptr_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/predefined_ops.h'
  '/home/david/.local/include/c++/4.9.3/bits/allocator.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++allocator.h'
  '/home/david/.local/include/c++/4.9.3/ext/new_allocator.h'
  '/home/david/.local/include/c++/4.9.3/new'
  '/home/david/.local/include/c++/4.9.3/exception'
  '/home/david/.local/include/c++/4.9.3/bits/atomic_lockfree_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_ptr.h'
  '/home/david/.local/include/c++/4.9.3/bits/nested_exception.h'
  '/home/david/.local/include/c++/4.9.3/bits/memoryfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_construct.h'
  '/home/david/.local/include/c++/4.9.3/ext/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_uninitialized.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_vector.h'
  '/home/david/.local/include/c++/4.9.3/initializer_list'
  '/home/david/.local/include/c++/4.9.3/bits/stl_bvector.h'
  '/home/david/.local/include/c++/4.9.3/bits/functional_hash.h'
  '/home/david/.local/include/c++/4.9.3/bits/hash_bytes.h'
  '/home/david/.local/include/c++/4.9.3/bits/range_access.h'
  '/home/david/.local/include/c++/4.9.3/bits/vector.tcc'
  '/home/david/.local/include/c++/4.9.3/string'
  '/home/david/.local/include/c++/4.9.3/bits/stringfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/char_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/postypes.h'
  '/home/david/.local/include/c++/4.9.3/cwchar'
  '/home/david/.local/include/c++/4.9.3/cstdint'
  '/home/david/.local/include/c++/4.9.3/bits/localefwd.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++locale.h'
  '/home/david/.local/include/c++/4.9.3/clocale'
  '/home/david/.local/include/c++/4.9.3/iosfwd'
  '/home/david/.local/include/c++/4.9.3/cctype'
  '/home/david/.local/include/c++/4.9.3/bits/ostream_insert.h'
  '/home/david/.local/include/c++/4.9.3/bits/cxxabi_forced.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_function.h'
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  '/home/david/.local/include/c++/4.9.3/bits/sstream.tcc'.
Target //tensorflow/cc:tutorials_example_trainer failed to build
Use --verbose_failures to see the command lines of failed build steps.
INFO: Elapsed time: 2.889s, Critical Path: 2.49s

With Bazel 0.1.5:

bazel build -c opt --config=cuda --verbose_failures //tensorflow/cc:tutorials_example_trainer
Warning: ignoring LD_PRELOAD in environment.
INFO: Found 1 target...
ERROR: /home/david/gits/tensorflow/google/protobuf/BUILD:64:1: undeclared inclusion(s) in rule '//google/protobuf:protobuf':
this rule is missing dependency declarations for the following files included by 'google/protobuf/src/google/protobuf/io/strtod.cc':
  '/home/david/.local/include/c++/4.9.3/cstdio'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++config.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/os_defines.h'
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  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stddef.h'
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  '/home/david/.local/include/c++/4.9.3/bits/functexcept.h'
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  '/home/david/.local/include/c++/4.9.3/bits/atomic_lockfree_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_ptr.h'
  '/home/david/.local/include/c++/4.9.3/bits/nested_exception.h'
  '/home/david/.local/include/c++/4.9.3/bits/localefwd.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++locale.h'
  '/home/david/.local/include/c++/4.9.3/clocale'
  '/home/david/.local/include/c++/4.9.3/iosfwd'
  '/home/david/.local/include/c++/4.9.3/cctype'
  '/home/david/.local/include/c++/4.9.3/bits/ostream_insert.h'
  '/home/david/.local/include/c++/4.9.3/bits/cxxabi_forced.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_function.h'
  '/home/david/.local/include/c++/4.9.3/backward/binders.h'
  '/home/david/.local/include/c++/4.9.3/bits/range_access.h'
  '/home/david/.local/include/c++/4.9.3/bits/basic_string.h'
  '/home/david/.local/include/c++/4.9.3/ext/atomicity.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/gthr.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/gthr-default.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/atomic_word.h'
  '/home/david/.local/include/c++/4.9.3/initializer_list'
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  '/home/david/.local/include/c++/4.9.3/cstdlib'
  '/home/david/.local/include/c++/4.9.3/cerrno'
  '/home/david/.local/include/c++/4.9.3/bits/functional_hash.h'
  '/home/david/.local/include/c++/4.9.3/bits/hash_bytes.h'
  '/home/david/.local/include/c++/4.9.3/bits/basic_string.tcc'
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  '/home/david/.local/include/c++/4.9.3/utility'
  '/home/david/.local/include/c++/4.9.3/bits/stl_relops.h'.
Target //tensorflow/cc:tutorials_example_trainer failed to build
INFO: Elapsed time: 2.634s, Critical Path: 2.21s

$ bazel build -c opt --config=cuda --verbose_failures --spawn_strategy=standalone //tensorflow/cc:tutorials_example_trainer
Warning: ignoring LD_PRELOAD in environment.
INFO: Found 1 target...
ERROR: /home/david/gits/tensorflow/google/protobuf/BUILD:64:1: undeclared inclusion(s) in rule '//google/protobuf:protobuf':
this rule is missing dependency declarations for the following files included by 'google/protobuf/src/google/protobuf/stubs/substitute.cc':
  '/home/david/.local/include/c++/4.9.3/string'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++config.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/os_defines.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/cpu_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/stringfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/memoryfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/char_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_algobase.h'
  '/home/david/.local/include/c++/4.9.3/bits/functexcept.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/cpp_type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/numeric_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_pair.h'
  '/home/david/.local/include/c++/4.9.3/bits/move.h'
  '/home/david/.local/include/c++/4.9.3/bits/concept_check.h'
  '/home/david/.local/include/c++/4.9.3/type_traits'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_types.h'
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  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include-fixed/syslimits.h'
  '/home/david/.local/include/c++/4.9.3/utility'
  '/home/david/.local/include/c++/4.9.3/bits/stl_relops.h'
  '/home/david/.local/include/c++/4.9.3/vector'
  '/home/david/.local/include/c++/4.9.3/bits/stl_construct.h'
  '/home/david/.local/include/c++/4.9.3/ext/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_uninitialized.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_vector.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_bvector.h'
  '/home/david/.local/include/c++/4.9.3/bits/vector.tcc'
  '/home/david/.local/include/c++/4.9.3/limits'
  '/home/david/.local/include/c++/4.9.3/unordered_map'
  '/home/david/.local/include/c++/4.9.3/tuple'
  '/home/david/.local/include/c++/4.9.3/array'
  '/home/david/.local/include/c++/4.9.3/stdexcept'
  '/home/david/.local/include/c++/4.9.3/bits/uses_allocator.h'
  '/home/david/.local/include/c++/4.9.3/ext/aligned_buffer.h'
  '/home/david/.local/include/c++/4.9.3/bits/hashtable.h'
  '/home/david/.local/include/c++/4.9.3/bits/hashtable_policy.h'
  '/home/david/.local/include/c++/4.9.3/bits/unordered_map.h'
  '/home/david/.local/include/c++/4.9.3/unordered_set'
  '/home/david/.local/include/c++/4.9.3/bits/unordered_set.h'.
Target //tensorflow/cc:tutorials_example_trainer failed to build
ERROR: /home/david/gits/tensorflow/tensorflow/cc/BUILD:28:1 undeclared inclusion(s) in rule '//google/protobuf:protobuf':
this rule is missing dependency declarations for the following files included by 'google/protobuf/src/google/protobuf/stubs/substitute.cc':
  '/home/david/.local/include/c++/4.9.3/string'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++config.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/os_defines.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/cpu_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/stringfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/memoryfwd.h'
  '/home/david/.local/include/c++/4.9.3/bits/char_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_algobase.h'
  '/home/david/.local/include/c++/4.9.3/bits/functexcept.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/cpp_type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/type_traits.h'
  '/home/david/.local/include/c++/4.9.3/ext/numeric_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_pair.h'
  '/home/david/.local/include/c++/4.9.3/bits/move.h'
  '/home/david/.local/include/c++/4.9.3/bits/concept_check.h'
  '/home/david/.local/include/c++/4.9.3/type_traits'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_types.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator_base_funcs.h'
  '/home/david/.local/include/c++/4.9.3/debug/debug.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_iterator.h'
  '/home/david/.local/include/c++/4.9.3/bits/ptr_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/predefined_ops.h'
  '/home/david/.local/include/c++/4.9.3/bits/postypes.h'
  '/home/david/.local/include/c++/4.9.3/cwchar'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stdarg.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stddef.h'
  '/home/david/.local/include/c++/4.9.3/cstdint'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include/stdint.h'
  '/home/david/.local/include/c++/4.9.3/bits/allocator.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++allocator.h'
  '/home/david/.local/include/c++/4.9.3/ext/new_allocator.h'
  '/home/david/.local/include/c++/4.9.3/new'
  '/home/david/.local/include/c++/4.9.3/exception'
  '/home/david/.local/include/c++/4.9.3/bits/atomic_lockfree_defines.h'
  '/home/david/.local/include/c++/4.9.3/bits/exception_ptr.h'
  '/home/david/.local/include/c++/4.9.3/bits/nested_exception.h'
  '/home/david/.local/include/c++/4.9.3/bits/localefwd.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/c++locale.h'
  '/home/david/.local/include/c++/4.9.3/clocale'
  '/home/david/.local/include/c++/4.9.3/iosfwd'
  '/home/david/.local/include/c++/4.9.3/cctype'
  '/home/david/.local/include/c++/4.9.3/bits/ostream_insert.h'
  '/home/david/.local/include/c++/4.9.3/bits/cxxabi_forced.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_function.h'
  '/home/david/.local/include/c++/4.9.3/backward/binders.h'
  '/home/david/.local/include/c++/4.9.3/bits/range_access.h'
  '/home/david/.local/include/c++/4.9.3/bits/basic_string.h'
  '/home/david/.local/include/c++/4.9.3/ext/atomicity.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/gthr.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/gthr-default.h'
  '/home/david/.local/include/c++/4.9.3/x86_64-unknown-linux-gnu/bits/atomic_word.h'
  '/home/david/.local/include/c++/4.9.3/initializer_list'
  '/home/david/.local/include/c++/4.9.3/ext/string_conversions.h'
  '/home/david/.local/include/c++/4.9.3/cstdlib'
  '/home/david/.local/include/c++/4.9.3/cstdio'
  '/home/david/.local/include/c++/4.9.3/cerrno'
  '/home/david/.local/include/c++/4.9.3/bits/functional_hash.h'
  '/home/david/.local/include/c++/4.9.3/bits/hash_bytes.h'
  '/home/david/.local/include/c++/4.9.3/bits/basic_string.tcc'
  '/home/david/.local/include/c++/4.9.3/cstddef'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include-fixed/limits.h'
  '/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include-fixed/syslimits.h'
  '/home/david/.local/include/c++/4.9.3/utility'
  '/home/david/.local/include/c++/4.9.3/bits/stl_relops.h'
  '/home/david/.local/include/c++/4.9.3/vector'
  '/home/david/.local/include/c++/4.9.3/bits/stl_construct.h'
  '/home/david/.local/include/c++/4.9.3/ext/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/alloc_traits.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_uninitialized.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_vector.h'
  '/home/david/.local/include/c++/4.9.3/bits/stl_bvector.h'
  '/home/david/.local/include/c++/4.9.3/bits/vector.tcc'
  '/home/david/.local/include/c++/4.9.3/limits'
  '/home/david/.local/include/c++/4.9.3/unordered_map'
  '/home/david/.local/include/c++/4.9.3/tuple'
  '/home/david/.local/include/c++/4.9.3/array'
  '/home/david/.local/include/c++/4.9.3/stdexcept'
  '/home/david/.local/include/c++/4.9.3/bits/uses_allocator.h'
  '/home/david/.local/include/c++/4.9.3/ext/aligned_buffer.h'
  '/home/david/.local/include/c++/4.9.3/bits/hashtable.h'
  '/home/david/.local/include/c++/4.9.3/bits/hashtable_policy.h'
  '/home/david/.local/include/c++/4.9.3/bits/unordered_map.h'
  '/home/david/.local/include/c++/4.9.3/unordered_set'
  '/home/david/.local/include/c++/4.9.3/bits/unordered_set.h'.
INFO: Elapsed time: 0.999s, Critical Path: 0.80s

Bazel 2.2b fails when tensorflow tries to parse the version:

 bazel build -c opt --config=cuda --verbose_failures --spawn_strategy=standalone //tensorflow/cc:tutorials_example_trainer
Warning: ignoring LD_PRELOAD in environment.
Sending SIGTERM to previous Bazel server (pid=24216)... done.
......
ERROR: /home/david/gits/tensorflow/WORKSPACE:21:1: Traceback (most recent call last):
    File "/home/david/gits/tensorflow/WORKSPACE", line 21
        check_version("0.1.4")
    File "/home/david/gits/tensorflow/tensorflow/tensorflow.bzl", line 22, in check_version
        _parse_bazel_version(native.bazel_version)
    File "/home/david/gits/tensorflow/tensorflow/tensorflow.bzl", line 15, in _parse_bazel_version
        int(number)
invalid literal for int(): "2b".
ERROR: Error evaluating WORKSPACE file.
ERROR: no such package 'external': Package 'external' contains errors.
INFO: Elapsed time: 0.610s

Correcting that mistake I get a bulld error again:

 bazel build -c opt --config=cuda --spawn_strategy=standalone --verbose_failures //tensorflow/tools/pip_package:build_pip_package
Warning: ignoring LD_PRELOAD in environment.
ERROR: no such package 'external': Package 'external' contains errors.
INFO: Elapsed time: 0.084s

How can I get it to work? I am interested in building Tensorflow with vector instructions for my laptop and linking against the latest cudnn for my workstation.

About this issue

Original URL
State: closed
Created 8 years ago
Comments: 29 (14 by maintainers)

Most upvoted comments

Hi. This is my story of how I got TensorFlow to compile on my Fedora 23 machine. Maybe it will be useful for you:

How to compile TensorFlow from source on Fedora 23 with a custom compiler.

Compiling TensorFlow with GPU support is possible, but a bit tricky on Fedora 23 and up. The compilation requires a specific GCC version which is not available from Fedora repoisitories and specifying the compiler is more complicated than it should be.

Compiling GCC

For CUDA version 7.5, you need to obtain the source code for GCC version 4.9. You can obtain it from here.

Next, you need to install GCC compile-time dependencies:

sudo dnf install mpfr-devel gmp-devel libmpc-devel isl-devel

Now you have to configure the GCC build. For details, check out the GCC configuration page. I suggest installing into a custom prefix, such as /opt/gcc-4.9. I suggest enabling only C and C++ and skipping the rest of the GCC languages to save time and disk space. The options --with-as, --with-ld and --with-nm are required, because otherwise TensorFlow build will fail, complaining that those binaries cannot be found.

/configure --prefix=/opt/gcc-4.9 --disable-nls --enable-languages=c,c++ --with-ld=/bin/ld --with-nm=/bin/nm --with-as=/usr/bin/as

When this step is done, you can compile GCC with the following command:

make -j4

This assumes you want to use 4 processing cores. You can use more or less, or omit the -j option entirely.

Finally, run as root:

make install

Compiling bazel

Obtain the bazel source code. You need the current master branch, NOT any of the recent releases.

git clone https://github.com/bazelbuild/bazel.git

To compile bazel, you need to specify

export CC=/opt/gcc-4.9/bin/gcc
./compile

This will produce the bazel binary in path/to/bazel/output/bazel

Compiling TensorFlow

Obtain the TensorFlow source code

git clone --recurse-submodules https://github.com/tensorflow/tensorflow

Modify the file third_party/gpus/crosstool/CROSSTOOL: Find the toolchain entry where the toolchain_identifieris set to "local_linux". Only change entries here, the rest is irrelevant.

Replace the following lines:

cxx_builtin_include_directory: “/usr/lib/gcc/” cxx_builtin_include_directory: “/usr/local/include”

with the following lines: cxx_builtin_include_directory: “/opt/gcc-4.9/lib/gcc/” cxx_builtin_include_directory: “/opt/gcc-4.9/local/include” cxx_builtin_include_directory: “/opt/gcc-4.9/include”

Next, run the ./configure and set your options. Specify your self-compiled GCC (for me /opt/gcc-4.9/bin/gcc) as the compiler to be used by nvcc.

To compile the source, use the following command line:

path/to/bazel/output/bazel build -c opt --config=cuda --genrule_strategy=standalone --local_resources 4096,4.0,1.0 -j 4 //tensorflow/cc:tutorials_example_trainer

Explanations:

build: what bazel should do
-c opt: Don’t know, says so in the docu
–config=cuda: Compile with CUDA support. Don’t ask me why you have to specify that again, even though you did so in ./configure.
–genrule_strategy=standalone: This compiles in “standalone mode”. Don’t ask me what that is, but it’s required so that generated output files can find the libcudart.so that they are linked to (see issue #2053).
–local_resources 4096,4.0,1.0 -j 4: Use at most 4096M of memory, 4.0 CPU’s, 1.0 of I/O and 4 threads. This is required so that the compilation doesn’t crash due to out-of-memory (I have 8GB of physical memory and 4GB of swap). The 4096 is still a lie, because the compilation still used more - but at least it didn’t crash.
//tensorflow/cc:tutorials_example_trainer: What to build.

I sincerely hope that this guide will be obsolete very soon, and you can just get cracking without all these workarounds. But for now, this will probably be useful.

akors on Apr 27, 2016

@akors well spotted.

This is how the relevant section of CROSTOOL looks like, and the build finishes:

 56   # TODO(bazel-team): In theory, the path here ought to exactly match the path
 57   # used by gcc. That works because bazel currently doesn't track files at
 58   # absolute locations and has no remote execution, yet. However, this will need
 59   # to be fixed, maybe with auto-detection?
 60   cxx_builtin_include_directory: "/home/david/.local/gcc-4.9/lib/gcc"
 61   cxx_builtin_include_directory: "/home/david/.local/gcc-4.9/include"
 62   cxx_builtin_include_directory: "/home/david/.local/gcc-4.9/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include"
 63   cxx_builtin_include_directory: "/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include"
 64   cxx_builtin_include_directory: "/home/david/.local/include/"
 65   cxx_builtin_include_directory: "/home/david/.local/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/include-fixed/"
 66   cxx_builtin_include_directory: "/usr/include"
 67   tool_path { name: "gcov" path: "/usr/bin/gcov" }

Dapid on Apr 28, 2016

For the four first issues:

A known issue, and not an easy answer. I know that we have a inflight fix for resource detection on OS X, I will gather more info tomorrow.
–genrule_strategy=standalone should be in tensorflow’s bazel.rc until all the hermeticity issue in TF build are resolved. I think Bazel’s one with custom c++ toolchain should be solved prior (see bazelbuild/bazel#1019).
(last 2 issues): TF’s cuda crosstool should do autoconfiguration just like we do for the main c++

Explanations extended: Explanations:

build: what bazel should do

-c opt: build using optimization C++ flags
–config=cuda: select cuda configuration, which is different from detecting the cuda environment which could be done inside bazel now.
–genrule_strategy=standalone: deactivate namespace sandbox because some tools are outside of mounted paths, this can also be fixed remote repositories (bazelbuild/bazel#1019 for bazel).
–local_resources 4096,4.0,1.0: unecessary, -j 4 is sufficient
-j 4: 4 simultaneous jobs maximum. We should improve resources detection and estimation to better compute than number.
//tensorflow/cc:tutorials_example_trainer: What to build.

damienmg on Apr 27, 2016