[Openmp-dev] cmake 3.7.0-rc1 breaks stage2 bootstrap in openmp on 10.11 with Xcode 8

[Jack Howarth via Openmp-dev]

On Sat, Oct 8, 2016 at 2:22 PM, Jack Howarth
<howarth.mailing.lists at gmail.com> wrote:
> On Sat, Oct 8, 2016 at 2:08 PM, Jack Howarth
> <howarth.mailing.lists at gmail.com> wrote:
>> On Sat, Oct 8, 2016 at 1:33 PM, Jack Howarth
>> <howarth.mailing.lists at gmail.com> wrote:
>>> The new cmake 3.7.0-rc1 release produces a stage2 bootstrap failure in
>>> openmp project build on OS X 10.11 under Xcode 8....
>>>
>>> In file included from
>>> /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/kmp_alloc.c:16:
>>> In file included from
>>> /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/kmp.h:98:
>>> /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/kmp_lock.h:26:10:
>>> fatal error: 'atomic' file not found
>>> #include <atomic>
>>>          ^
>>>
>>
>> Appending -v to see the header search paths emitted from the compiler
>> shows the following....
>>
>> compiling without -sysroot (which is the behavior for cmake 3.6.2 and
>> earlier)....
>>
>> clang -cc1 version 4.0.0 based upon LLVM 4.0.0 default target
>> x86_64-apple-darwin15.6.0
>> ignoring nonexistent directory
>> "/sw/src/fink.build/llvm40-4.0.0-1/build/stage1/bin/../include/c++/v1"
>> ignoring nonexistent directory "/usr/local/include"
>> #include "..." search starts here:
>> #include <...> search starts here:
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/projects/openmp/runtime/src
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/i18n
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/include/45
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/thirdparty/ittnotify
>>  /sw/include
>>  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage1/bin/../lib/clang/4.0.0/include
>>  /usr/include
>>  /System/Library/Frameworks (framework directory)
>>  /Library/Frameworks (framework directory)
>> End of search list.
>>
>> compiling with -isysroot
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk
>> as cmake 3.7.0-rc1 does...
>>
>> lang -cc1 version 4.0.0 based upon LLVM 4.0.0 default target
>> x86_64-apple-darwin15.6.0
>> ignoring nonexistent directory
>> "/sw/src/fink.build/llvm40-4.0.0-1/build/stage1/bin/../include/c++/v1"
>> ignoring nonexistent directory
>> "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1"
>> ignoring nonexistent directory
>> "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/local/include"
>> ignoring nonexistent directory
>> "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/Library/Frameworks"
>> #include "..." search starts here:
>> #include <...> search starts here:
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/projects/openmp/runtime/src
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/i18n
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/include/45
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/thirdparty/ittnotify
>>  /sw/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage1/bin/../lib/clang/4.0.0/include
>>  /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include
>>  /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks
>> (framework directory)
>> End of search list.
>>
>> compiling with -isysroot / instead....
>>
>> clang -cc1 version 4.0.0 based upon LLVM 4.0.0 default target
>> x86_64-apple-darwin15.6.0
>> ignoring nonexistent directory
>> "/sw/src/fink.build/llvm40-4.0.0-1/build/stage1/bin/../include/c++/v1"
>> ignoring nonexistent directory "/usr/local/include"
>> #include "..." search starts here:
>> #include <...> search starts here:
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/projects/openmp/runtime/src
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/include
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/i18n
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/include/45
>>  /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/thirdparty/ittnotify
>>  /sw/include
>>  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1
>>  /sw/src/fink.build/llvm40-4.0.0-1/build/stage1/bin/../lib/clang/4.0.0/include
>>  /usr/include
>>  /System/Library/Frameworks (framework directory)
>>  /Library/Frameworks (framework directory)
>> End of search list.
>>
>> So for both no usage of -sysroot or '-sysroot /', the search path of
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1
>> is appended for the compiler but the case of  '-isysroot
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk',
>> the compiler attempts to use the non-existent search path of
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1.
>>
>
> This issue seems to be specific to the llvm.org clang compiler. Using....
>
> clang-4.0  -std=c++11  -x c++ --sysroot
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk
> test.c -v
>
> produces the bad search path of
>
> ignoring nonexistent directory
> "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1"
>
> whereas for the Apple clang 8.0 compiler, the same compilation
> produces the valid search path of...
>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
>

A workaround for this issue under cmake 3.7.0-rc1 is to pass
-DLIBOMP_CFLAGS="-cxx-isystem $libcxx_srcdir" to the stage2 and stage3
cmake options.

>
>
>>> This appears to be due to the new cmake 3.7.0-rc1 resulting in
>>> -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk
>>> being used in the compilation of openmp....
>>>
>>> cd /sw/src/fink.build/llvm40-4.0.0-1/build/stage2/projects/openmp/runtime/src
>>> && /sw/src/fink.build/llvm40-4.0.0-1/opt-bin/cc-st1-clang
>>> -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS
>>> -Domp_EXPORTS -I/sw/src/fink.build/llvm40-4.0.0-1/build/stage2/projects/openmp/runtime/src
>>> -I/sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src
>>> -I/sw/src/fink.build/llvm40-4.0.0-1/build/stage2/include
>>> -I/sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/include
>>> -I/sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/i18n
>>> -I/sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/include/45
>>> -I/sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/thirdparty/ittnotify
>>>  -Wall -W -Wno-unused-parameter -Wwrite-strings
>>> -Wmissing-field-initializers -pedantic -Wno-long-long
>>> -Wcovered-switch-default -Wdelete-non-virtual-dtor -Werror=date-time
>>> -O3 -DNDEBUG -arch x86_64 -arch i386 -isysroot
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk
>>> -fPIC   -D _GNU_SOURCE -D _REENTRANT -I/sw/include -std=c++11
>>> -fno-exceptions -Wno-sign-compare -Wno-unused-function
>>> -Wno-unused-local-typedef -Wno-unused-value -Wno-unused-variable
>>> -Wno-switch -Wno-covered-switch-default -Wno-deprecated-register
>>> -Wno-gnu-anonymous-struct -Wno-unknown-pragmas
>>> -Wno-missing-field-initializers -Wno-missing-braces -Wno-comment
>>> -Wno-self-assign -Wno-vla-extension -Wno-format-pedantic -x c++ -o
>>> CMakeFiles/omp.dir/kmp_alloc.c.o   -c
>>> /sw/src/fink.build/llvm40-4.0.0-1/llvm-4.0.0.src/projects/openmp/runtime/src/kmp_alloc.c
>>>
>>> The problem doesn't exist under cmake 3.6.2 because the openmp build
>>> doesn't append  -isysroot in that case.
>>>               Jack
>>> ps Note this seems to be related to using any SDK for -sysroot as
>>> substituting...
>>>
>>> -isysroot /Volumes/Xcode/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
>>>
>>> from the Xcode 7.3.1 release also fails but substituting...
>>>
>>> -isysroot /
>>>
>>> or omitting -sysroot entirely allows the compilation to succeed. So it
>>> seems that the openmp code doesn't like being compiled against SDKs
>>> rather than / on darwin.