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Compilation error for cpp tests on macOS with gcc and thread sanitizer #4331

Open
Tracked by #5153
StrikerRUS opened this issue May 29, 2021 · 6 comments
Open
Tracked by #5153

Compilation error for cpp tests on macOS with gcc and thread sanitizer #4331

StrikerRUS opened this issue May 29, 2021 · 6 comments
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bug help wanted

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@StrikerRUS
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/Users/runner/work/1/s/include/LightGBM/utils/common.h:57:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
   57 | #define _mm_malloc(a, b) malloc(a)
      |                          ^~~~~~
Full log 
2021-05-29T18:39:02.3137310Z -- The C compiler identification is GNU 10.2.0
2021-05-29T18:39:02.9219720Z -- The CXX compiler identification is GNU 10.2.0
2021-05-29T18:39:02.9595090Z -- Checking whether C compiler has -isysroot
2021-05-29T18:39:03.0275960Z -- Checking whether C compiler has -isysroot - yes
2021-05-29T18:39:03.0301610Z -- Checking whether C compiler supports OSX deployment target flag
2021-05-29T18:39:03.0757480Z -- Checking whether C compiler supports OSX deployment target flag - yes
2021-05-29T18:39:03.0885560Z -- Detecting C compiler ABI info
2021-05-29T18:39:04.1723340Z -- Detecting C compiler ABI info - done
2021-05-29T18:39:04.1880470Z -- Check for working C compiler: /usr/local/bin/gcc-10 - skipped
2021-05-29T18:39:04.1893690Z -- Detecting C compile features
2021-05-29T18:39:04.1911360Z -- Detecting C compile features - done
2021-05-29T18:39:04.1995340Z -- Checking whether CXX compiler has -isysroot
2021-05-29T18:39:04.2428190Z -- Checking whether CXX compiler has -isysroot - yes
2021-05-29T18:39:04.2430300Z -- Checking whether CXX compiler supports OSX deployment target flag
2021-05-29T18:39:04.2836060Z -- Checking whether CXX compiler supports OSX deployment target flag - yes
2021-05-29T18:39:04.2880870Z -- Detecting CXX compiler ABI info
2021-05-29T18:39:04.5925030Z -- Detecting CXX compiler ABI info - done
2021-05-29T18:39:04.6093710Z -- Check for working CXX compiler: /usr/local/bin/g++-10 - skipped
2021-05-29T18:39:04.6098040Z -- Detecting CXX compile features
2021-05-29T18:39:04.6106720Z -- Detecting CXX compile features - done
2021-05-29T18:39:04.6128590Z -- Sanitizers: thread
2021-05-29T18:39:04.6129980Z -- Sanitizers compile flags:  -fsanitize=thread
2021-05-29T18:39:04.6156710Z -- Performing Test MM_PREFETCH
2021-05-29T18:39:05.1854760Z -- Performing Test MM_PREFETCH - Failed
2021-05-29T18:39:05.1955100Z -- Performing Test MM_MALLOC
2021-05-29T18:39:05.5547250Z -- Performing Test MM_MALLOC - Failed
2021-05-29T18:39:05.6130890Z -- Could NOT find GTest (missing: GTest_DIR)
2021-05-29T18:39:05.6179760Z -- Did not find Google Test in the system root. Fetching Google Test now...
2021-05-29T18:39:08.1549630Z CMake Deprecation Warning at build/_deps/googletest-src/CMakeLists.txt:4 (cmake_minimum_required):
2021-05-29T18:39:08.1550850Z   Compatibility with CMake < 2.8.12 will be removed from a future version of
2021-05-29T18:39:08.1551500Z   CMake.
2021-05-29T18:39:08.1551740Z 
2021-05-29T18:39:08.1552300Z   Update the VERSION argument <min> value or use a ...<max> suffix to tell
2021-05-29T18:39:08.1552990Z   CMake that the project does not need compatibility with older versions.
2021-05-29T18:39:08.1553350Z 
2021-05-29T18:39:08.1553610Z 
2021-05-29T18:39:08.1631240Z CMake Deprecation Warning at build/_deps/googletest-src/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
2021-05-29T18:39:08.1632860Z   Compatibility with CMake < 2.8.12 will be removed from a future version of
2021-05-29T18:39:08.1633950Z   CMake.
2021-05-29T18:39:08.1634690Z 
2021-05-29T18:39:08.1635680Z   Update the VERSION argument <min> value or use a ...<max> suffix to tell
2021-05-29T18:39:08.1637480Z   CMake that the project does not need compatibility with older versions.
2021-05-29T18:39:08.1638340Z 
2021-05-29T18:39:08.1639670Z 
2021-05-29T18:39:08.1641320Z CMake Deprecation Warning at build/_deps/googletest-src/googletest/CMakeLists.txt:56 (cmake_minimum_required):
2021-05-29T18:39:08.1642580Z   Compatibility with CMake < 2.8.12 will be removed from a future version of
2021-05-29T18:39:08.1643570Z   CMake.
2021-05-29T18:39:08.1644280Z 
2021-05-29T18:39:08.1645310Z   Update the VERSION argument <min> value or use a ...<max> suffix to tell
2021-05-29T18:39:08.1646410Z   CMake that the project does not need compatibility with older versions.
2021-05-29T18:39:08.1646900Z 
2021-05-29T18:39:08.1647460Z 
2021-05-29T18:39:08.1901010Z -- Found PythonInterp: /Users/runner/runners/2.187.1/miniconda/bin/python (found version "3.8.5") 
2021-05-29T18:39:08.1970460Z -- Looking for pthread.h
2021-05-29T18:39:08.5137880Z -- Looking for pthread.h - not found
2021-05-29T18:39:08.5169550Z -- Could NOT find Threads (missing: Threads_FOUND) 
2021-05-29T18:39:08.5307370Z -- Could NOT find Threads (missing: Threads_FOUND) 
2021-05-29T18:39:08.5359810Z -- Configuring done
2021-05-29T18:39:08.7928170Z -- Generating done
2021-05-29T18:39:08.8303560Z -- Build files have been written to: /Users/runner/work/1/s/build
2021-05-29T18:39:08.9265520Z [  2%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
2021-05-29T18:39:15.6612650Z [  5%] Linking CXX static library ../../../lib/libgtest.a
2021-05-29T18:39:17.0241600Z [  5%] Built target gtest
2021-05-29T18:39:17.0793700Z [ 11%] Building CXX object CMakeFiles/testlightgbm.dir/tests/cpp_tests/test_common.cpp.o
2021-05-29T18:39:17.0910810Z [ 11%] Building CXX object CMakeFiles/testlightgbm.dir/tests/cpp_tests/test_chunked_array.cpp.o
2021-05-29T18:39:17.1030100Z [ 14%] Building CXX object CMakeFiles/testlightgbm.dir/tests/cpp_tests/test_main.cpp.o
2021-05-29T18:39:17.1183830Z [ 17%] Building CXX object CMakeFiles/testlightgbm.dir/src/boosting/boosting.cpp.o
2021-05-29T18:39:20.4011940Z [ 17%] Building CXX object CMakeFiles/testlightgbm.dir/src/boosting/gbdt.cpp.o
2021-05-29T18:39:20.4714620Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:20.4780450Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:20.4882380Z                  from /Users/runner/work/1/s/src/boosting/boosting.cpp:5:
2021-05-29T18:39:20.4985170Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:57:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:20.5069060Z    57 | #define _mm_malloc(a, b) malloc(a)
2021-05-29T18:39:20.5170460Z       |                          ^~~~~~
2021-05-29T18:39:20.5171480Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:20.5273200Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:20.5331850Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:20.5433840Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:20.5535920Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:20.5638900Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:20.5740780Z                  from /Users/runner/work/1/s/src/boosting/boosting.cpp:5:
2021-05-29T18:39:20.5843850Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:40:7: note: previous declaration of 'void* malloc(size_t)'
2021-05-29T18:39:20.5946190Z    40 | void *malloc(size_t __size) __result_use_check __alloc_size(1);
2021-05-29T18:39:20.6048020Z       |       ^~~~~~
2021-05-29T18:39:20.6150630Z In file included from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/xmmintrin.h:34,
2021-05-29T18:39:20.6253830Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/emmintrin.h:31,
2021-05-29T18:39:20.6356340Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/pmmintrin.h:31,
2021-05-29T18:39:20.6459010Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/x86_64-apple-darwin18/bits/opt_random.h:34,
2021-05-29T18:39:20.6561060Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/random:50,
2021-05-29T18:39:20.6663270Z                  from /Users/runner/work/1/s/include/LightGBM/utils/random.h:9,
2021-05-29T18:39:20.6765340Z                  from /Users/runner/work/1/s/include/LightGBM/feature_group.h:11,
2021-05-29T18:39:20.6867390Z                  from /Users/runner/work/1/s/include/LightGBM/dataset.h:9,
2021-05-29T18:39:20.6969560Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:9,
2021-05-29T18:39:20.7071520Z                  from /Users/runner/work/1/s/src/boosting/gbdt.h:9,
2021-05-29T18:39:20.7173540Z                  from /Users/runner/work/1/s/src/boosting/dart.hpp:16,
2021-05-29T18:39:20.7275930Z                  from /Users/runner/work/1/s/src/boosting/boosting.cpp:7:
2021-05-29T18:39:20.7378780Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: In function 'void* malloc(size_t)':
2021-05-29T18:39:20.7481820Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:39:7: error: '__align' was not declared in this scope
2021-05-29T18:39:20.7483520Z    39 |   if (__align & (__align - 1))
2021-05-29T18:39:20.7584650Z       |       ^~~~~~~
2021-05-29T18:39:20.7687220Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:54:9: error: '__align' was not declared in this scope
2021-05-29T18:39:20.7789180Z    54 |     if (__align < 2 * sizeof (void *))
2021-05-29T18:39:20.7845820Z       |         ^~~~~~~
2021-05-29T18:39:20.7948370Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:57:35: error: '__align' was not declared in this scope
2021-05-29T18:39:20.8002040Z    57 |   __malloc_ptr = malloc (__size + __align);
2021-05-29T18:39:20.8103600Z       |                                   ^~~~~~~
2021-05-29T18:39:20.8205230Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:20.8306970Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:20.8408740Z                  from /Users/runner/work/1/s/src/boosting/boosting.cpp:5:
2021-05-29T18:39:20.8511770Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: At global scope:
2021-05-29T18:39:20.8614520Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:58:21: error: 'void free(void*)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:20.8718330Z    58 | #define _mm_free(a) free(a)
2021-05-29T18:39:20.8820040Z       |                     ^~~~
2021-05-29T18:39:20.8922030Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:20.9024000Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:20.9125990Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:20.9218000Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:20.9309600Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:20.9411680Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:20.9513580Z                  from /Users/runner/work/1/s/src/boosting/boosting.cpp:5:
2021-05-29T18:39:20.9616980Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:42:7: note: previous declaration of 'void free(void*)'
2021-05-29T18:39:20.9718880Z    42 | void  free(void *);
2021-05-29T18:39:20.9733860Z       |       ^~~~
2021-05-29T18:39:22.0795870Z [ 20%] Building CXX object CMakeFiles/testlightgbm.dir/src/boosting/gbdt_model_text.cpp.o
2021-05-29T18:39:23.1624000Z [ 22%] Building CXX object CMakeFiles/testlightgbm.dir/src/boosting/gbdt_prediction.cpp.o
2021-05-29T18:39:23.4555490Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:23.4657560Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:23.4757780Z                  from /Users/runner/work/1/s/src/boosting/gbdt.h:8,
2021-05-29T18:39:23.4859620Z                  from /Users/runner/work/1/s/src/boosting/gbdt.cpp:5:
2021-05-29T18:39:23.4960630Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:57:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:23.5061370Z    57 | #define _mm_malloc(a, b) malloc(a)
2021-05-29T18:39:23.5162810Z       |                          ^~~~~~
2021-05-29T18:39:23.5263240Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:23.5365110Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:23.5465720Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:23.5567470Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:23.5667780Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:23.5768260Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:23.5869850Z                  from /Users/runner/work/1/s/src/boosting/gbdt.h:8,
2021-05-29T18:39:23.5969980Z                  from /Users/runner/work/1/s/src/boosting/gbdt.cpp:5:
2021-05-29T18:39:23.6071730Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:40:7: note: previous declaration of 'void* malloc(size_t)'
2021-05-29T18:39:23.6171920Z    40 | void *malloc(size_t __size) __result_use_check __alloc_size(1);
2021-05-29T18:39:23.6273360Z       |       ^~~~~~
2021-05-29T18:39:23.6275310Z In file included from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/xmmintrin.h:34,
2021-05-29T18:39:23.6377650Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/emmintrin.h:31,
2021-05-29T18:39:23.6480190Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/pmmintrin.h:31,
2021-05-29T18:39:23.6582900Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/x86_64-apple-darwin18/bits/opt_random.h:34,
2021-05-29T18:39:23.6684700Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/random:50,
2021-05-29T18:39:23.6786320Z                  from /Users/runner/work/1/s/include/LightGBM/utils/random.h:9,
2021-05-29T18:39:23.6888090Z                  from /Users/runner/work/1/s/include/LightGBM/feature_group.h:11,
2021-05-29T18:39:23.6989900Z                  from /Users/runner/work/1/s/include/LightGBM/dataset.h:9,
2021-05-29T18:39:23.7091890Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:9,
2021-05-29T18:39:23.7193720Z                  from /Users/runner/work/1/s/src/boosting/gbdt.h:9,
2021-05-29T18:39:23.7295350Z                  from /Users/runner/work/1/s/src/boosting/gbdt.cpp:5:
2021-05-29T18:39:23.7397850Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: In function 'void* malloc(size_t)':
2021-05-29T18:39:23.7500480Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:39:7: error: '__align' was not declared in this scope
2021-05-29T18:39:23.7603450Z    39 |   if (__align & (__align - 1))
2021-05-29T18:39:23.7704870Z       |       ^~~~~~~
2021-05-29T18:39:23.7807420Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:54:9: error: '__align' was not declared in this scope
2021-05-29T18:39:23.7909160Z    54 |     if (__align < 2 * sizeof (void *))
2021-05-29T18:39:23.8010870Z       |         ^~~~~~~
2021-05-29T18:39:23.8113410Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:57:35: error: '__align' was not declared in this scope
2021-05-29T18:39:23.8215370Z    57 |   __malloc_ptr = malloc (__size + __align);
2021-05-29T18:39:23.8317100Z       |                                   ^~~~~~~
2021-05-29T18:39:23.8418670Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:23.8520460Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:23.8622380Z                  from /Users/runner/work/1/s/src/boosting/gbdt.h:8,
2021-05-29T18:39:23.8724500Z                  from /Users/runner/work/1/s/src/boosting/gbdt.cpp:5:
2021-05-29T18:39:23.8827620Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: At global scope:
2021-05-29T18:39:23.8930100Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:58:21: error: 'void free(void*)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:23.9031970Z    58 | #define _mm_free(a) free(a)
2021-05-29T18:39:23.9133460Z       |                     ^~~~
2021-05-29T18:39:23.9235270Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:23.9337170Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:23.9438930Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:23.9540730Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:23.9642380Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:23.9744060Z                  from /Users/runner/work/1/s/include/LightGBM/boosting.h:8,
2021-05-29T18:39:23.9832800Z                  from /Users/runner/work/1/s/src/boosting/gbdt.h:8,
2021-05-29T18:39:23.9934390Z                  from /Users/runner/work/1/s/src/boosting/gbdt.cpp:5:
2021-05-29T18:39:24.0036960Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:42:7: note: previous declaration of 'void free(void*)'
2021-05-29T18:39:24.0139030Z    42 | void  free(void *);
2021-05-29T18:39:24.0240850Z       |       ^~~~
2021-05-29T18:39:24.4860710Z cc1plus: note: unrecognized command-line option '-Wno-unused-private-field' may have been intended to silence earlier diagnostics
2021-05-29T18:39:24.4961070Z make[3]: *** [CMakeFiles/testlightgbm.dir/src/boosting/boosting.cpp.o] Error 1
2021-05-29T18:39:24.5062950Z make[3]: *** Waiting for unfinished jobs....
2021-05-29T18:39:24.9223130Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:24.9261310Z                  from /Users/runner/work/1/s/src/boosting/gbdt_model_text.cpp:5:
2021-05-29T18:39:24.9364110Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:57:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:24.9419860Z    57 | #define _mm_malloc(a, b) malloc(a)
2021-05-29T18:39:24.9521600Z       |                          ^~~~~~
2021-05-29T18:39:24.9622460Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:24.9723660Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:24.9824640Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:24.9926210Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:25.0027730Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:25.0128220Z                  from /Users/runner/work/1/s/src/boosting/gbdt_model_text.cpp:5:
2021-05-29T18:39:25.0191840Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:40:7: note: previous declaration of 'void* malloc(size_t)'
2021-05-29T18:39:25.0294020Z    40 | void *malloc(size_t __size) __result_use_check __alloc_size(1);
2021-05-29T18:39:25.0295240Z       |       ^~~~~~
2021-05-29T18:39:25.0347810Z In file included from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/xmmintrin.h:34,
2021-05-29T18:39:25.0448640Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/emmintrin.h:31,
2021-05-29T18:39:25.0501160Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/pmmintrin.h:31,
2021-05-29T18:39:25.0603380Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/x86_64-apple-darwin18/bits/opt_random.h:34,
2021-05-29T18:39:25.0704830Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/random:50,
2021-05-29T18:39:25.0805590Z                  from /Users/runner/work/1/s/include/LightGBM/utils/random.h:9,
2021-05-29T18:39:25.0906940Z                  from /Users/runner/work/1/s/include/LightGBM/feature_group.h:11,
2021-05-29T18:39:25.0996460Z                  from /Users/runner/work/1/s/include/LightGBM/dataset.h:9,
2021-05-29T18:39:25.1083990Z                  from /Users/runner/work/1/s/include/LightGBM/metric.h:9,
2021-05-29T18:39:25.1162590Z                  from /Users/runner/work/1/s/src/boosting/gbdt_model_text.cpp:6:
2021-05-29T18:39:25.1263950Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: In function 'void* malloc(size_t)':
2021-05-29T18:39:25.1331630Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:39:7: error: '__align' was not declared in this scope
2021-05-29T18:39:25.1434620Z    39 |   if (__align & (__align - 1))
2021-05-29T18:39:25.1534770Z       |       ^~~~~~~
2021-05-29T18:39:25.1594640Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:54:9: error: '__align' was not declared in this scope
2021-05-29T18:39:25.1696840Z    54 |     if (__align < 2 * sizeof (void *))
2021-05-29T18:39:25.1752820Z       |         ^~~~~~~
2021-05-29T18:39:25.1855670Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:57:35: error: '__align' was not declared in this scope
2021-05-29T18:39:25.1928630Z    57 |   __malloc_ptr = malloc (__size + __align);
2021-05-29T18:39:25.2024280Z       |                                   ^~~~~~~
2021-05-29T18:39:25.2097610Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:25.2199400Z                  from /Users/runner/work/1/s/src/boosting/gbdt_model_text.cpp:5:
2021-05-29T18:39:25.2266490Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: At global scope:
2021-05-29T18:39:25.2362740Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:58:21: error: 'void free(void*)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:25.2464820Z    58 | #define _mm_free(a) free(a)
2021-05-29T18:39:25.2554190Z       |                     ^~~~
2021-05-29T18:39:25.2656200Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:25.2756890Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:25.2758600Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:25.2837050Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:25.2938860Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:25.3037580Z                  from /Users/runner/work/1/s/src/boosting/gbdt_model_text.cpp:5:
2021-05-29T18:39:25.3139050Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:42:7: note: previous declaration of 'void free(void*)'
2021-05-29T18:39:25.3240880Z    42 | void  free(void *);
2021-05-29T18:39:25.3342540Z       |       ^~~~
2021-05-29T18:39:25.7728410Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:25.7829000Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:8,
2021-05-29T18:39:25.7929690Z                  from /Users/runner/work/1/s/src/boosting/gbdt_prediction.cpp:5:
2021-05-29T18:39:25.8031970Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:57:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:25.8090540Z    57 | #define _mm_malloc(a, b) malloc(a)
2021-05-29T18:39:25.8192140Z       |                          ^~~~~~
2021-05-29T18:39:25.8230100Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:25.8332020Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:25.8434230Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:25.8536150Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:25.8637900Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:25.8705850Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:8,
2021-05-29T18:39:25.8802020Z                  from /Users/runner/work/1/s/src/boosting/gbdt_prediction.cpp:5:
2021-05-29T18:39:25.8872090Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:40:7: note: previous declaration of 'void* malloc(size_t)'
2021-05-29T18:39:25.8948990Z    40 | void *malloc(size_t __size) __result_use_check __alloc_size(1);
2021-05-29T18:39:25.9047330Z       |       ^~~~~~
2021-05-29T18:39:25.9150080Z In file included from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/xmmintrin.h:34,
2021-05-29T18:39:25.9252700Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/emmintrin.h:31,
2021-05-29T18:39:25.9334010Z                  from /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/pmmintrin.h:31,
2021-05-29T18:39:25.9436900Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/x86_64-apple-darwin18/bits/opt_random.h:34,
2021-05-29T18:39:25.9498370Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/random:50,
2021-05-29T18:39:25.9580640Z                  from /Users/runner/work/1/s/include/LightGBM/utils/random.h:9,
2021-05-29T18:39:25.9655240Z                  from /Users/runner/work/1/s/include/LightGBM/feature_group.h:11,
2021-05-29T18:39:25.9757020Z                  from /Users/runner/work/1/s/include/LightGBM/dataset.h:9,
2021-05-29T18:39:25.9856110Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:9,
2021-05-29T18:39:25.9970280Z                  from /Users/runner/work/1/s/src/boosting/gbdt_prediction.cpp:5:
2021-05-29T18:39:26.0030460Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: In function 'void* malloc(size_t)':
2021-05-29T18:39:26.0135830Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:39:7: error: '__align' was not declared in this scope
2021-05-29T18:39:26.0248500Z    39 |   if (__align & (__align - 1))
2021-05-29T18:39:26.0307170Z       |       ^~~~~~~
2021-05-29T18:39:26.0405210Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:54:9: error: '__align' was not declared in this scope
2021-05-29T18:39:26.0467260Z    54 |     if (__align < 2 * sizeof (void *))
2021-05-29T18:39:26.0569960Z       |         ^~~~~~~
2021-05-29T18:39:26.0689200Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h:57:35: error: '__align' was not declared in this scope
2021-05-29T18:39:26.0690590Z    57 |   __malloc_ptr = malloc (__size + __align);
2021-05-29T18:39:26.0759330Z       |                                   ^~~~~~~
2021-05-29T18:39:26.0838750Z In file included from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:26.0933390Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:8,
2021-05-29T18:39:26.1041030Z                  from /Users/runner/work/1/s/src/boosting/gbdt_prediction.cpp:5:
2021-05-29T18:39:26.1102160Z /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin18/10.2.0/include/mm_malloc.h: At global scope:
2021-05-29T18:39:26.1180760Z /Users/runner/work/1/s/include/LightGBM/utils/common.h:58:21: error: 'void free(void*)' was declared 'extern' and later 'static' [-fpermissive]
2021-05-29T18:39:26.1264090Z    58 | #define _mm_free(a) free(a)
2021-05-29T18:39:26.1360340Z       |                     ^~~~
2021-05-29T18:39:26.1424810Z In file included from /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:128,
2021-05-29T18:39:26.1526490Z                  from /usr/local/Cellar/gcc/10.2.0_4/include/c++/10.2.0/cstdlib:75,
2021-05-29T18:39:26.1625000Z                  from /Users/runner/work/1/s/include/LightGBM/utils/log.h:11,
2021-05-29T18:39:26.1726840Z                  from /Users/runner/work/1/s/include/LightGBM/utils/common.h:11,
2021-05-29T18:39:26.1773570Z                  from /Users/runner/work/1/s/include/LightGBM/config.h:16,
2021-05-29T18:39:26.1876180Z                  from /Users/runner/work/1/s/include/LightGBM/objective_function.h:8,
2021-05-29T18:39:26.1939010Z                  from /Users/runner/work/1/s/src/boosting/gbdt_prediction.cpp:5:
2021-05-29T18:39:26.2031870Z /Applications/Xcode_11.3.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc/_malloc.h:42:7: note: previous declaration of 'void free(void*)'
2021-05-29T18:39:26.2133960Z    42 | void  free(void *);
2021-05-29T18:39:26.2175010Z       |       ^~~~
2021-05-29T18:39:27.2086690Z cc1plus: note: unrecognized command-line option '-Wno-unused-private-field' may have been intended to silence earlier diagnostics
2021-05-29T18:39:27.2289360Z make[3]: *** [CMakeFiles/testlightgbm.dir/src/boosting/gbdt.cpp.o] Error 1
2021-05-29T18:39:27.7881930Z cc1plus: note: unrecognized command-line option '-Wno-unused-private-field' may have been intended to silence earlier diagnostics
2021-05-29T18:39:27.7908800Z make[3]: *** [CMakeFiles/testlightgbm.dir/src/boosting/gbdt_model_text.cpp.o] Error 1
2021-05-29T18:39:27.8775980Z cc1plus: note: unrecognized command-line option '-Wno-unused-private-field' may have been intended to silence earlier diagnostics
2021-05-29T18:39:27.8874510Z make[3]: *** [CMakeFiles/testlightgbm.dir/src/boosting/gbdt_prediction.cpp.o] Error 1
2021-05-29T18:39:27.8877080Z make[2]: *** [CMakeFiles/testlightgbm.dir/all] Error 2
2021-05-29T18:39:27.8879230Z make[1]: *** [CMakeFiles/testlightgbm.dir/rule] Error 2
2021-05-29T18:39:27.8881210Z make: *** [testlightgbm] Error 2
2021-05-29T18:39:27.8965200Z ##[error]Bash exited with code '255'.
2021-05-29T18:39:27.8983120Z ##[section]Finishing: Test
@StrikerRUS StrikerRUS mentioned this issue May 29, 2021
Merged
@StrikerRUS StrikerRUS mentioned this issue Jul 12, 2021
Closed
21 tasks
@StrikerRUS StrikerRUS mentioned this issue Apr 15, 2022
Closed
60 tasks
jameslamb added a commit that referenced this issue Feb 1, 2023
@jameslamb
[ci] use thread sanitizer in macOS cpp tests (fixes #4331)
4e3fe33
@jameslamb jameslamb mentioned this issue Feb 1, 2023
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@jameslamb
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jameslamb commented Feb 1, 2023 •
edited
Loading

Tested on my mac tonight and this is still an issue.

Providing a reproducible example here, to help anyone wanting to work on this in the future.

mkdir build
cd ./build

cmake \
    -DBUILD_CPP_TEST=ON \
    -DCMAKE_C_COMPILER='gcc-11' \
    -DCMAKE_CXX_COMPILER='g++-11' \
    -DUSE_OPENMP=OFF \
    -DUSE_SANITIZER=ON \
    -DUSE_DEBUG=ON \
    -DENABLED_SANITIZERS="thread" \
    ..

logs:

-- Sanitizers: thread
-- Sanitizers compile flags:  -fsanitize=thread
-- Performing Test MM_PREFETCH
-- Performing Test MM_PREFETCH - Failed
-- Performing Test MM_MALLOC
-- Performing Test MM_MALLOC - Failed
-- Could NOT find GTest (missing: GTest_DIR)
-- Did not find Google Test in the system root. Fetching Google Test now...
-- Found Python: /usr/local/Frameworks/Python.framework/Versions/3.11/bin/python3.11 (found version "3.11.1") found components: Interpreter
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - no
-- Could NOT find Threads (missing: Threads_FOUND)
-- Could NOT find Threads (missing: Threads_FOUND)
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/jlamb/repos/LightGBM/build

(notice MM_MALLOC - Failed)

And then built and tested

make testlightgbm -j3
./../testlightgbm

Logs:

[  1%] Building CXX object CMakeFiles/lightgbm_capi_objs.dir/src/c_api.cpp.o
[  3%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[  5%] Building CXX object CMakeFiles/lightgbm_objs.dir/src/boosting/boosting.cpp.o
In file included from /Users/jlamb/repos/LightGBM/include/LightGBM/config.h:16,
                 from /Users/jlamb/repos/LightGBM/include/LightGBM/boosting.h:8,
                 from /Users/jlamb/repos/LightGBM/src/c_api.cpp:7:
/Users/jlamb/repos/LightGBM/include/LightGBM/utils/common.h:53:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
   53 | #define _mm_malloc(a, b) malloc(a)
      |                          ^~~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/stdlib.h:128,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/cstdlib:75,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/string_conversions.h:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:6607,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:55,
                 from /Users/jlamb/repos/LightGBM/include/LightGBM/utils/json11.h:59,
                 from /Users/jlamb/repos/LightGBM/include/LightGBM/utils/common.h:8,
                 from /Users/jlamb/repos/LightGBM/include/LightGBM/config.h:16,
                 from /Users/jlamb/repos/LightGBM/include/LightGBM/boosting.h:8,
                 from /Users/jlamb/repos/LightGBM/src/c_api.cpp:7:
/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/malloc/_malloc.h:40:10: note: previous declaration of 'void* malloc(size_t)'
   40 | void    *malloc(size_t __size) __result_use_check __alloc_size(1);
      |          ^~~~~~

@tusharverma200

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@jameslamb
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@tusharverma200 sure, we'd welcome a contribution! Please put up a pull request if you believe you've found a fix for this issue.

@gxkevin
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gxkevin commented Jul 31, 2023

I am using the 3.0.0 version，compiled with gcc 10.5， how to fix the error with this lightgbm version？

@jameslamb jameslamb mentioned this issue Apr 28, 2024
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@hgminh95
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hgminh95 commented Jul 2, 2024

I am able to compile by removing all these __mm_malloc to malloc macros.

Personally, I don't think we should have a macro that change a global API like malloc in public header.

@hgminh95 hgminh95 mentioned this issue Jul 12, 2024
Merged
@StrikerRUS StrikerRUS mentioned this issue Jul 13, 2024
Closed
@bastistician
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FWIW, I get the same compilation error when trying to install lightgbm 4.5.0 (the R package) on Alpine Linux:

./include/LightGBM/utils/common.h:53:26: error: 'void* malloc(size_t)' was declared 'extern' and later 'static' [-fpermissive]
   53 | #define _mm_malloc(a, b) malloc(a)
      |                          ^~~~~~
./include/LightGBM/utils/common.h:54:21: error: 'void free(void*)' was declared 'extern' and later 'static' [-fpermissive]
   54 | #define _mm_free(a) free(a)
      |                     ^~~~

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