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install lightgbm failed on macos m2 pro #5876

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nzhsta opened this issue May 8, 2023 · 3 comments
Closed

install lightgbm failed on macos m2 pro #5876

nzhsta opened this issue May 8, 2023 · 3 comments
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@nzhsta
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nzhsta commented May 8, 2023 •
edited
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Description

install lightgbm failed

Environment info

py3.6

Command(s) you used to install LightGBM

git clone --recursive https://github.com/microsoft/LightGBM
cd LightGBM
sh build-python.sh install

output

building lightgbm
--- building wheel ---
INFO:root:running bdist_wheel
setup.py:195: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer, pypa/build or
        other standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  install.initialize_options(self)
INFO:root:running build
INFO:root:running build_py
INFO:root:creating build
INFO:root:creating build/lib
INFO:root:creating build/lib/lightgbm
INFO:root:copying lightgbm/callback.py -> build/lib/lightgbm
INFO:root:copying lightgbm/compat.py -> build/lib/lightgbm
INFO:root:copying lightgbm/plotting.py -> build/lib/lightgbm
INFO:root:copying lightgbm/__init__.py -> build/lib/lightgbm
INFO:root:copying lightgbm/engine.py -> build/lib/lightgbm
INFO:root:copying lightgbm/dask.py -> build/lib/lightgbm
INFO:root:copying lightgbm/basic.py -> build/lib/lightgbm
INFO:root:copying lightgbm/libpath.py -> build/lib/lightgbm
INFO:root:copying lightgbm/sklearn.py -> build/lib/lightgbm
INFO:root:running egg_info
INFO:root:creating lightgbm.egg-info
INFO:root:writing lightgbm.egg-info/PKG-INFO
INFO:root:writing dependency_links to lightgbm.egg-info/dependency_links.txt
INFO:root:writing requirements to lightgbm.egg-info/requires.txt
INFO:root:writing top-level names to lightgbm.egg-info/top_level.txt
INFO:root:writing manifest file 'lightgbm.egg-info/SOURCES.txt'
INFO:root:reading manifest file 'lightgbm.egg-info/SOURCES.txt'
INFO:root:reading manifest template 'MANIFEST.in'
WARNING:root:no previously-included directories found matching 'build'
WARNING:root:warning: no files found matching '*.txt'
WARNING:root:warning: no files found matching '*.so' under directory 'lightgbm'
WARNING:root:warning: no files found matching '*.so' under directory 'compile'
WARNING:root:warning: no files found matching '*.dll' under directory 'compile/Release'
WARNING:root:warning: no files found matching '*.dll' under directory 'compile/windows/x64/DLL'
WARNING:root:warning: no previously-included files matching '*.py[co]' found anywhere in distribution
WARNING:root:warning: no previously-included files found matching 'compile/external_libs/compute/.git'
INFO:root:adding license file 'LICENSE'
INFO:root:writing manifest file 'lightgbm.egg-info/SOURCES.txt'
INFO:root:copying lightgbm/VERSION.txt -> build/lib/lightgbm
INFO:root:copying lightgbm/py.typed -> build/lib/lightgbm
INFO:root:installing to build/bdist.macosx-10.9-x86_64/wheel
INFO:root:running install
INFO:LightGBM:Starting to compile the library.
INFO:LightGBM:Starting to compile with CMake.
Traceback (most recent call last):
  File "setup.py", line 61, in silent_call
    subprocess.check_call(cmd, stderr=log, stdout=log)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', '_lightgbm', '-I/Users/jarven/LightGBM/lightgbm-python/build_cpp', '-j4']' returned non-zero exit status 2.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "setup.py", line 355, in <module>
    'Typing :: Typed'])
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/__init__.py", line 107, in setup
    return distutils.core.setup(**attrs)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/dist.py", line 1244, in run_command
    super().run_command(command)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 259, in run
    self.run_command('install')
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
    self.distribution.run_command(command)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/dist.py", line 1244, in run_command
    super().run_command(command)
  File "/Users/jarven/environment/anaconda3/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "setup.py", line 228, in run
    time_costs=self.time_costs)
  File "setup.py", line 175, in compile_cpp
    error_msg='An error has occurred while building lightgbm library file')
  File "setup.py", line 65, in silent_call
    raise Exception("\n".join((error_msg, LOG_NOTICE)))
Exception: An error has occurred while building lightgbm library file
The full version of error log was saved into /Users/jarven/LightGBM_compilation.log
@nzhsta nzhsta changed the title install lightgbm failed in macos m2 pro install lightgbm failed on macos m2 pro May 8, 2023
@nzhsta
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nzhsta commented May 8, 2023

log as follows:

[ 98%] Building CXX object CMakeFiles/lightgbm_objs.dir/src/treelearner/voting_parallel_tree_learner.cpp.o
In file included from /Users/jarven/LightGBM/lightgbm-python/compile/src/treelearner/serial_tree_learner.cpp:5:
In file included from /Users/jarven/LightGBM/lightgbm-python/compile/src/treelearner/serial_tree_learner.h:8:
In file included from /Users/jarven/LightGBM/lightgbm-python/compile/include/LightGBM/dataset.h:8:
In file included from /Users/jarven/LightGBM/lightgbm-python/compile/include/LightGBM/config.h:15:
In file included from /Users/jarven/LightGBM/lightgbm-python/compile/include/LightGBM/meta.h:9:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/functional:515:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/__memory/shared_ptr.h:28:
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/__memory/unique_ptr.h:48:5: warning: delete called on non-final 'LightGBM::GradientDiscretizer' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/__memory/unique_ptr.h:305:7: note: in instantiation of member function 'std::default_delete<LightGBM::GradientDiscretizer>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Users/jarven/LightGBM/lightgbm-python/compile/src/treelearner/serial_tree_learner.cpp:65:27: note: in instantiation of member function 'std::unique_ptr<LightGBM::GradientDiscretizer>::reset' requested here
    gradient_discretizer_.reset(new GradientDiscretizer(config_->num_grad_quant_bins, config_->num_iterations, config_->seed, is_constant_hessian, config_->stochastic_rounding));
                          ^
1 warning generated.
[ 98%] Built target lightgbm_objs
[100%] Linking CXX shared library /Users/jarven/LightGBM/lightgbm-python/compile/lib_lightgbm.so
ld: warning: ignoring file /opt/homebrew/opt/libomp/lib/libomp.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
Undefined symbols for architecture x86_64:
  "___kmpc_barrier", referenced from:
      _.omp_outlined..15 in linear_tree_learner.cpp.o
      _.omp_outlined..87 in linear_tree_learner.cpp.o
  "___kmpc_dispatch_init_4", referenced from:
      _.omp_outlined..65 in dataset.cpp.o
      _.omp_outlined..80 in dataset.cpp.o
      _.omp_outlined. in dataset_loader.cpp.o
      _.omp_outlined..60 in dataset_loader.cpp.o
      _.omp_outlined..86 in dataset_loader.cpp.o
      _.omp_outlined..87 in dataset_loader.cpp.o
      _.omp_outlined..116 in metric.cpp.o
      ...
  "___kmpc_dispatch_next_4", referenced from:
      _.omp_outlined..65 in dataset.cpp.o
      _.omp_outlined..80 in dataset.cpp.o
      _.omp_outlined. in dataset_loader.cpp.o
      _.omp_outlined..60 in dataset_loader.cpp.o
      _.omp_outlined..86 in dataset_loader.cpp.o
      _.omp_outlined..87 in dataset_loader.cpp.o
      _.omp_outlined..116 in metric.cpp.o
      ...
  "___kmpc_end_master", referenced from:
      _.omp_outlined. in c_api.cpp.o
      _.omp_outlined..36 in gbdt.cpp.o
      _.omp_outlined. in gbdt_model_text.cpp.o
      _.omp_outlined. in sample_strategy.cpp.o
      _.omp_outlined. in bin.cpp.o
      _.omp_outlined..68 in dataset.cpp.o
      _.omp_outlined..103 in dataset_loader.cpp.o
      ...
  "___kmpc_end_reduce_nowait", referenced from:
      _.omp_outlined..35 in metadata.cpp.o
      _.omp_outlined. in metric.cpp.o
      _.omp_outlined..25 in metric.cpp.o
      _.omp_outlined..27 in metric.cpp.o
      _.omp_outlined..29 in metric.cpp.o
      _.omp_outlined..31 in metric.cpp.o
      _.omp_outlined..33 in metric.cpp.o
      ...
  "___kmpc_end_serialized_parallel", referenced from:
      LightGBM::ScoreUpdater::ScoreUpdater(LightGBM::Dataset const*, int) in gbdt.cpp.o
      LightGBM::ScoreUpdater::AddScore(double, int) in gbdt.cpp.o
      LightGBM::ScoreUpdater::MultiplyScore(double, int) in gbdt.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, true, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, true, 16>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, true, true, 16>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      ...
  "___kmpc_for_static_fini", referenced from:
      _.omp_outlined..17 in c_api.cpp.o
      _.omp_outlined..23 in c_api.cpp.o
      _.omp_outlined..24 in c_api.cpp.o
      _.omp_outlined..26 in c_api.cpp.o
      _.omp_outlined..27 in c_api.cpp.o
      _.omp_outlined..32 in c_api.cpp.o
      _.omp_outlined..33 in c_api.cpp.o
      ...
  "___kmpc_for_static_init_4", referenced from:
      _.omp_outlined..17 in c_api.cpp.o
      _.omp_outlined..23 in c_api.cpp.o
      _.omp_outlined..24 in c_api.cpp.o
      _.omp_outlined..26 in c_api.cpp.o
      _.omp_outlined..27 in c_api.cpp.o
      _.omp_outlined..32 in c_api.cpp.o
      _.omp_outlined..33 in c_api.cpp.o
      ...
  "___kmpc_for_static_init_4u", referenced from:
      _.omp_outlined..119 in gbdt_model_text.cpp.o
      _.omp_outlined..7 in serial_tree_learner.cpp.o
      _.omp_outlined..8 in serial_tree_learner.cpp.o
  "___kmpc_for_static_init_8", referenced from:
      _.omp_outlined..137 in c_api.cpp.o
      _.omp_outlined..138 in c_api.cpp.o
      _.omp_outlined. in gbdt.cpp.o
      _.omp_outlined..46 in gbdt.cpp.o
      _.omp_outlined..23 in metadata.cpp.o
  "___kmpc_fork_call", referenced from:
      _LGBM_DatasetCreateFromFile in c_api.cpp.o
      _LGBM_DatasetCreateFromSampledColumn in c_api.cpp.o
      _LGBM_DatasetCreateFromSerializedReference in c_api.cpp.o
      LightGBM::Dataset::InitStreaming(int, int, int, int, int, int, int) in c_api.cpp.o
      _LGBM_DatasetPushRows in c_api.cpp.o
      _LGBM_DatasetPushRowsWithMetadata in c_api.cpp.o
      _LGBM_DatasetPushRowsByCSR in c_api.cpp.o
      ...
  "___kmpc_global_thread_num", referenced from:
      LightGBM::ScoreUpdater::ScoreUpdater(LightGBM::Dataset const*, int) in gbdt.cpp.o
      LightGBM::ScoreUpdater::AddScore(double, int) in gbdt.cpp.o
      LightGBM::ScoreUpdater::MultiplyScore(double, int) in gbdt.cpp.o
      int LightGBM::ParallelPartitionRunner<int, false>::Run<true>(int, std::__1::function<int (int, int, int, int*, int*)> const&, int*) in sample_strategy.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<false, false, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, true, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      ...
  "___kmpc_master", referenced from:
      _.omp_outlined. in c_api.cpp.o
      _.omp_outlined..36 in gbdt.cpp.o
      _.omp_outlined. in gbdt_model_text.cpp.o
      _.omp_outlined. in sample_strategy.cpp.o
      _.omp_outlined. in bin.cpp.o
      _.omp_outlined..68 in dataset.cpp.o
      _.omp_outlined..103 in dataset_loader.cpp.o
      ...
  "___kmpc_push_num_threads", referenced from:
      int LightGBM::ParallelPartitionRunner<int, false>::Run<true>(int, std::__1::function<int (int, int, int, int*, int*)> const&, int*) in sample_strategy.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<false, false, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, true, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<false, true, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, true, 16>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<false, false, true, 16>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      ...
  "___kmpc_reduce_nowait", referenced from:
      _.omp_outlined..35 in metadata.cpp.o
      _.omp_outlined. in metric.cpp.o
      _.omp_outlined..25 in metric.cpp.o
      _.omp_outlined..27 in metric.cpp.o
      _.omp_outlined..29 in metric.cpp.o
      _.omp_outlined..31 in metric.cpp.o
      _.omp_outlined..33 in metric.cpp.o
      ...
  "___kmpc_serialized_parallel", referenced from:
      LightGBM::ScoreUpdater::ScoreUpdater(LightGBM::Dataset const*, int) in gbdt.cpp.o
      LightGBM::ScoreUpdater::AddScore(double, int) in gbdt.cpp.o
      LightGBM::ScoreUpdater::MultiplyScore(double, int) in gbdt.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, true, false, 0>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, false, true, 16>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      void LightGBM::Dataset::ConstructHistogramsInner<true, true, true, 16>(std::__1::vector<signed char, std::__1::allocator<signed char> > const&, int const*, int, float const*, float const*, float*, float*, LightGBM::TrainingShareStates*, double*) const in dataset.cpp.o
      ...
  "_omp_get_max_threads", referenced from:
      LightGBM::LinearTreeLearner::InitLinear(LightGBM::Dataset const*, int) in linear_tree_learner.cpp.o
  "_omp_get_num_threads", referenced from:
      _.omp_outlined. in c_api.cpp.o
      _.omp_outlined..36 in gbdt.cpp.o
      _.omp_outlined. in gbdt_model_text.cpp.o
      _.omp_outlined. in sample_strategy.cpp.o
      _.omp_outlined. in bin.cpp.o
      _.omp_outlined..68 in dataset.cpp.o
      _.omp_outlined..103 in dataset_loader.cpp.o
      ...
  "_omp_get_thread_num", referenced from:
      _.omp_outlined..17 in c_api.cpp.o
      _.omp_outlined..23 in c_api.cpp.o
      _.omp_outlined..24 in c_api.cpp.o
      _.omp_outlined..26 in c_api.cpp.o
      _.omp_outlined..27 in c_api.cpp.o
      _.omp_outlined..32 in c_api.cpp.o
      _.omp_outlined..33 in c_api.cpp.o
      ...
  "_omp_set_num_threads", referenced from:
      _LGBM_DatasetCreateFromFile in c_api.cpp.o
      _LGBM_DatasetCreateFromSampledColumn in c_api.cpp.o
      _LGBM_DatasetCreateFromSerializedReference in c_api.cpp.o
      _LGBM_DatasetCreateFromMats in c_api.cpp.o
      _LGBM_DatasetCreateFromCSR in c_api.cpp.o
      _LGBM_DatasetCreateFromCSRFunc in c_api.cpp.o
      _LGBM_DatasetCreateFromCSC in c_api.cpp.o
      ...
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [/Users/jarven/LightGBM/lightgbm-python/compile/lib_lightgbm.so] Error 1
make[2]: *** [CMakeFiles/_lightgbm.dir/all] Error 2
make[1]: *** [CMakeFiles/_lightgbm.dir/rule] Error 2
make: *** [_lightgbm] Error 2

@jameslamb
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Thanks for using LightGBM.

I'm closing this and marking it as a duplicate of #5700. This is the exact same issue and error message as was reported there. In the future, please search the open issues in this project before opening a new one.

See my response there for why this has not yet been fixed: #5700 (comment). I'm sorry for the inconvenience, and I hope we'll be able to get LightGBM working on the new Macs soon.

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This issue has been automatically locked since there has not been any recent activity since it was closed.
To start a new related discussion, open a new issue at https://github.com/microsoft/LightGBM/issues
including a reference to this.

@github-actions github-actions bot locked as resolved and limited conversation to collaborators Aug 15, 2023
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@jameslamb @nzhsta