Compiling on Mac fails with message "use of undeclared identifier 'CLOCK_REALTIME'"

Question

Compiling on Mac fails with message "use of undeclared identifier 'CLOCK_REALTIME'"

drhalftone opened this issue 9 years ago · comments

In file included from ../nabo/kdtree_cpu.cpp:42:
In file included from /usr/local/include/boost/format.hpp:38:
In file included from /usr/local/include/boost/format/internals.hpp:20:
In file included from /usr/local/include/boost/optional.hpp:15:
/usr/local/include/boost/optional/optional.hpp:1276:3: warning: unused typedef 'boost_static_assert_typedef_1276' [-Wunused-local-typedef]
BOOST_STATIC_ASSERT_MSG(sizeof(CharType) == 0, "If you want to output boost::optional, include header <boost/optional/optional_io.hpp>");
^
/usr/local/include/boost/static_assert.hpp:36:48: note: expanded from macro 'BOOST_STATIC_ASSERT_MSG'

define BOOST_STATIC_ASSERT_MSG( B, Msg ) BOOST_STATIC_ASSERT( B )

/usr/local/include/boost/static_assert.hpp:170:16: note: expanded from macro 'BOOST_STATIC_ASSERT'
BOOST_JOIN(boost_static_assert_typedef_, LINE) BOOST_STATIC_ASSERT_UNUSED_ATTRIBUTE
^
/usr/local/include/boost/config/suffix.hpp:544:28: note: expanded from macro 'BOOST_JOIN'

define BOOST_JOIN( X, Y ) BOOST_DO_JOIN( X, Y )

/usr/local/include/boost/config/suffix.hpp:545:31: note: expanded from macro 'BOOST_DO_JOIN'

define BOOST_DO_JOIN( X, Y ) BOOST_DO_JOIN2(X,Y)

/usr/local/include/boost/config/suffix.hpp:546:32: note: expanded from macro 'BOOST_DO_JOIN2'

define BOOST_DO_JOIN2( X, Y ) X##Y

:123:1: note: expanded from here
boost_static_assert_typedef_1276
^
4 warnings generated.
[ 31%] Building CXX object CMakeFiles/nabo.dir/nabo/kdtree_opencl.cpp.o
Linking CXX static library libnabo.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnabo.a(kdtree_opencl.cpp.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnabo.a(kdtree_opencl.cpp.o) has no symbols
[ 31%] Built target nabo
Scanning dependencies of target trivial
[ 37%] Building CXX object examples/CMakeFiles/trivial.dir/trivial.cpp.o
Linking CXX executable trivial
[ 37%] Built target trivial
Scanning dependencies of target usage
[ 43%] Building CXX object examples/CMakeFiles/usage.dir/usage.cpp.o
Linking CXX executable usage
[ 43%] Built target usage
Scanning dependencies of target knnbench
[ 50%] Building CXX object tests/CMakeFiles/knnbench.dir/knnbench.cpp.o
../../tests/knnbench.cpp:69:18: error: use of undeclared identifier 'CLOCK_REALTIME'
clock_gettime(CLOCK_REALTIME, &ts);
^
1 error generated.
make[2]: *** [tests/CMakeFiles/knnbench.dir/knnbench.cpp.o] Error 1
make[1]: *** [tests/CMakeFiles/knnbench.dir/all] Error 2
make: *** [all] Error 2

Simon Lynen · Answer 1 · Wed Jan 13 2016 06:26:44 GMT+0800 (China Standard Time)

Can you give #46 a try please?

Dr. Daniel L. Lau · Answer 2 · Wed Jan 13 2016 08:23:27 GMT+0800 (China Standard Time)

I’m not entirely clear how to do this, but here is what I did. I used SourceTree to download a fresh copy of your repository (HEAD -> fix/clock_realtime_include origin/fix/clock_realtime_include).

I then ran the following commands in terminal:

SRC_DIR=pwd
BUILD_DIR=${SRC_DIR}/build
mkdir -p ${BUILD_DIR} && cd ${BUILD_DIR}
cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ${SRC_DIR}

And then got the errors described in the attached log files.

Simon Lynen · Answer 3 · Wed Jan 13 2016 09:07:55 GMT+0800 (China Standard Time)

@drhalftone so you still get the same error message?

Simon Lynen · Answer 4 · Wed Jan 13 2016 09:10:11 GMT+0800 (China Standard Time)

@drhalftone actually just saw that there is one more fix to patch. Can you update the branch fix/clock_realtime_include and try again?

Dr. Daniel L. Lau · Answer 5 · Wed Jan 13 2016 09:16:59 GMT+0800 (China Standard Time)

yes same error

On Jan 12, 2016, at 8:10 PM, Simon Lynen notifications@github.com wrote:

@drhalftone https://github.com/drhalftone actually just saw that there is one more fix to patch. Can you update the branch fix/clock_realtime_include and try again?

—
Reply to this email directly or view it on GitHub #45 (comment).

Dr. Daniel L. Lau · Answer 6 · Wed Jan 13 2016 09:19:27 GMT+0800 (China Standard Time)

Something worth noting is that Mac OS X’s native compilers no longer support OpenMP. Should this matter? Here is a snippet from the error log:

Performing C++ SOURCE FILE Test OpenMP_FLAG_DETECTED failed with the following output:
Change Dir: /Users/dllau/Libraries/libnabo/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_85263/fast"
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/cmTC_85263.dir/build.make CMakeFiles/cmTC_85263.dir/build
Building CXX object CMakeFiles/cmTC_85263.dir/src.cxx.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DOpenMP_FLAG_DETECTED -mp -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -o CMakeFiles/cmTC_85263.dir/src.cxx.o -c /Users/dllau/Libraries/libnabo/build/CMakeFiles/CMakeTmp/src.cxx
clang: error: unknown argument: '-mp'
make[1]: *** [CMakeFiles/cmTC_85263.dir/src.cxx.o] Error 1
make: *** [cmTC_85263/fast] Error 2

Source file was:

#include <omp.h>
int main() {
#ifdef _OPENMP
return 0;
#else
breaks_on_purpose
#endif
}

On Jan 12, 2016, at 8:16 PM, Daniel L. Lau lauconsulting@windstream.net wrote:

yes same error

<CMakeError.log>
<CMakeOutput.log>

On Jan 12, 2016, at 8:10 PM, Simon Lynen <notifications@github.com mailto:notifications@github.com> wrote:

@drhalftone https://github.com/drhalftone actually just saw that there is one more fix to patch. Can you update the branch fix/clock_realtime_include and try again?

—
Reply to this email directly or view it on GitHub #45 (comment).

Simon Lynen · Answer 7 · Wed Jan 13 2016 09:40:17 GMT+0800 (China Standard Time)

@drhalftone I am not sure which version of the code you are on. The lines you have in the error output don't match with what I see on the master branch. Also we have handling for OSX in the codebase since a while. Which branch are you using?

Simon Lynen · Answer 8 · Wed Jan 13 2016 09:41:49 GMT+0800 (China Standard Time)

@drhalftone the same is the case for open-mp handling. This also is done separately for osx.

Simon Lynen · Answer 9 · Wed Jan 13 2016 09:43:34 GMT+0800 (China Standard Time)

@drhalftone also I can see a verified build of the repository from master on OSX here: http://129.132.38.183:8080/job/libnabo/37/

Dr. Daniel L. Lau · Answer 10 · Wed Jan 13 2016 22:39:45 GMT+0800 (China Standard Time)

I followed the instructions on the libnabo github page. Here is the terminal commands that I used to delete the copy I had been working with, and cloning the github respository and then running the cmake commands that are listed on the github page:

DrHalftone:Libraries dllau$ rm -r libnabo/
override r--r--r-- dllau/pulse for libnabo//.git/objects/01/48b8a237be7eb2e3901e23eb66dda6c64656a9? y
override r--r--r-- dllau/pulse for libnabo//.git/objects/1b/e693929522a8272ea00b42cdefc38849318863? y
override r--r--r-- dllau/pulse for libnabo//.git/objects/39/a0c33c2522d201156a77125034349842d877a7? y
override r--r--r-- dllau/pulse for libnabo//.git/objects/e9/9e4fa8a134b6b5bd470512fad19df1b1049ba6? y
override r--r--r-- dllau/pulse for libnabo//.git/objects/pack/pack-4cc30b1bf628b5c4b222618a952c7caf182bd662.idx? y
override r--r--r-- dllau/pulse for libnabo//.git/objects/pack/pack-4cc30b1bf628b5c4b222618a952c7caf182bd662.pack? y
DrHalftone:Libraries dllau$ ls
libpointmatcher
DrHalftone:Libraries dllau$ git clone git://github.com/ethz-asl/libnabo.git
Cloning into 'libnabo'...
remote: Counting objects: 1612, done.
remote: Total 1612 (delta 0), reused 0 (delta 0), pack-reused 1611
Receiving objects: 100% (1612/1612), 1.40 MiB | 922.00 KiB/s, done.
Resolving deltas: 100% (948/948), done.
Checking connectivity... done.
DrHalftone:Libraries dllau$ cd libnabo/
DrHalftone:libnabo dllau$ ls
CHANGELOG.rst cmake_uninstall.cmake.in libnaboConfigVersion.cmake.in
CMakeLists.txt debian nabo
Doxyfile.in examples package.xml
README.md experimental python
UseDoxygen.cmake libnaboConfig.cmake.in tests
DrHalftone:libnabo dllau$ SRC_DIR=pwd
DrHalftone:libnabo dllau$ BUILD_DIR=${SRC_DIR}/build
DrHalftone:libnabo dllau$ mkdir -p ${BUILD_DIR} && cd ${BUILD_DIR}
DrHalftone:build dllau$ cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ${SRC_DIR}
-- The C compiler identification is AppleClang 7.0.2.7000181
-- The CXX compiler identification is AppleClang 7.0.2.7000181
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Doxygen: /usr/local/bin/doxygen (found version "1.8.10")
-- Found DOXYFILE_IN: /Users/dllau/Libraries/libnabo/Doxyfile.in
-- Found LATEX: /Library/TeX/texbin/latex
CMake Warning (dev) at UseDoxygen.cmake:112 (get_target_property):
Policy CMP0045 is not set: Error on non-existent target in
get_target_property. Run "cmake --help-policy CMP0045" for policy details.
Use the cmake_policy command to set the policy and suppress this warning.

get_target_property() called with non-existent target "doc".
Call Stack (most recent call first):
CMakeLists.txt:40 (include)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Boost version: 1.59.0
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
OpenCL disabled, not looking for it
ANN found, enabling it in benchmarks
FLANN found, enabling it in benchmarks
-- Looking for _POSIX_TIMERS
-- Looking for _POSIX_TIMERS - found
CMake Error at tests/CMakeLists.txt:95 (message):
Compiling a test executable failed.
Call Stack (most recent call first):
tests/CMakeLists.txt:105 (try_compile_cloud_types)

-- Configuring incomplete, errors occurred!
See also "/Users/dllau/Libraries/libnabo/build/CMakeFiles/CMakeOutput.log".
See also "/Users/dllau/Libraries/libnabo/build/CMakeFiles/CMakeError.log".
DrHalftone:build dllau$

On Jan 12, 2016, at 8:40 PM, Simon Lynen notifications@github.com wrote:

@drhalftone https://github.com/drhalftone I am not sure which version of the code you are on. The lines you have in the error output don't match with what I see on the master branch. Also we have handling for OSX in the codebase since a while. Which branch are you using?

—
Reply to this email directly or view it on GitHub #45 (comment).

Simon Lynen · Answer 11 · Wed Jan 13 2016 23:51:02 GMT+0800 (China Standard Time)

@drhalftone ok, I think you are missing a few dependencies. You will need to make sure you have eigen and boost installed.

i.e. in case you use homebrew:

brew install eigen
brew install boost

Dr. Daniel L. Lau · Answer 12 · Thu Jan 14 2016 00:14:50 GMT+0800 (China Standard Time)

DrHalftone:build dllau$ brew install eigen
Warning: eigen-3.2.6 already installed
DrHalftone:build dllau$ brew install boost
Warning: boost-1.59.0 already installed

On Jan 13, 2016, at 10:51 AM, Simon Lynen notifications@github.com wrote:

@drhalftone https://github.com/drhalftone ok, I think you are missing a few dependencies. You will need to make sure you have eigen and boost installed.

i.e. in case you use homebrew:

brew install eigen
brew install boost
—
Reply to this email directly or view it on GitHub #45 (comment).

Simon Lynen · Answer 13 · Thu Jan 14 2016 00:27:11 GMT+0800 (China Standard Time)

I see. Ok it seems the compilation of one of the verification targets fails. Can you post the contents of

"/Users/dllau/Libraries/libnabo/build/CMakeFiles/CMakeOutput.log".
"/Users/dllau/Libraries/libnabo/build/CMakeFiles/CMakeError.log".

Here?

Dr. Daniel L. Lau · Answer 14 · Thu Jan 14 2016 00:32:03 GMT+0800 (China Standard Time)

Archive.zip

Simon Lynen · Answer 15 · Thu Jan 14 2016 00:56:08 GMT+0800 (China Standard Time)

ok, there seems to be some issue with the way the open-mp detection breaks on your machine. I suggest commenting this line here: https://github.com/ethz-asl/libnabo/blob/master/CMakeLists.txt#L52

Dr. Daniel L. Lau · Answer 16 · Thu Jan 14 2016 02:14:32 GMT+0800 (China Standard Time)

DrHalftone:libnabo dllau$ rm -r build
DrHalftone:libnabo dllau$ SRC_DIR=pwd
DrHalftone:libnabo dllau$ BUILD_DIR=${SRC_DIR}/build
DrHalftone:libnabo dllau$ mkdir -p ${BUILD_DIR} && cd ${BUILD_DIR}
DrHalftone:build dllau$ cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ${SRC_DIR}
CMake Warning (dev) at UseDoxygen.cmake:112 (get_target_property):
Policy CMP0045 is not set: Error on non-existent target in
get_target_property. Run "cmake --help-policy CMP0045" for policy details.
Use the cmake_policy command to set the policy and suppress this warning.

get_target_property() called with non-existent target "doc".
Call Stack (most recent call first):
CMakeLists.txt:40 (include)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Boost version: 1.59.0
OpenCL disabled, not looking for it
ANN found, enabling it in benchmarks
FLANN found, enabling it in benchmarks
CMake Error at tests/CMakeLists.txt:95 (message):
Compiling a test executable failed.
Call Stack (most recent call first):
tests/CMakeLists.txt:105 (try_compile_cloud_types)

-- Configuring incomplete, errors occurred!
See also "/Users/dllau/Libraries/libnabo/CMakeFiles/CMakeOutput.log".
DrHalftone:build dllau$

openmp

find_package(OpenMP)

if (OPENMP_FOUND)
add_definitions(-fopenmp -DHAVE_OPENMP)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
if (CMAKE_COMPILER_IS_GNUCC)
set(EXTRA_LIBS ${EXTRA_LIBS} gomp)
endif(CMAKE_COMPILER_IS_GNUCC)
endif(OPENMP_FOUND)

On Jan 13, 2016, at 11:56 AM, Simon Lynen notifications@github.com wrote:

ok, there seems to be some issue with the way the open-mp detection breaks on your machine. I suggest commenting this line here: https://github.com/ethz-asl/libnabo/blob/master/CMakeLists.txt#L52 https://github.com/ethz-asl/libnabo/blob/master/CMakeLists.txt#L52
—
Reply to this email directly or view it on GitHub #45 (comment).

Simon Lynen · Answer 17 · Thu Jan 14 2016 03:09:38 GMT+0800 (China Standard Time)

@drhalftone since I cannot reproduce the problem here and in the interest of time I suggest you disable the compile time tests in:
https://github.com/ethz-asl/libnabo/blob/master/tests/CMakeLists.txt#L105-L113 by deleting the lines. These are meant for developers which change libnabo and don't impact the runtime of the library.