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rth opened this issue Oct 4, 2019 · 1 comment
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Building scikit-learn with gcc 9.2 in a conda env fails #15129

rth opened this issue Oct 4, 2019 · 1 comment
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rth commented Oct 4, 2019 •
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When building scikit-learn in a clean conda environement,

conda create -n sklearn-dev scipy nomkl cython python=3.7

with gcc 9.2, I get the following error,

$ pip install -e .                                                              
Obtaining file:///home/rth/src/scikit-learn
Requirement already satisfied: numpy>=1.11.0 in /home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages (from scikit-learn==0.22.dev0) (1.17.2)
Requirement already satisfied: scipy>=0.17.0 in /home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages (from scikit-learn==0.22.dev0) (1.3.1)
Requirement already satisfied: joblib>=0.11 in /home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages (from scikit-learn==0.22.dev0) (0.14.0)
Installing collected packages: scikit-learn
  Running setup.py develop for scikit-learn
    ERROR: Command errored out with exit status 1:
     command: /home/rth/.miniconda3/envs/sklearn-dev/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/rth/src/scikit-learn/setup.py'"'"'; __file__='"'"'/home/rth/src/scikit-learn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps         
         cwd: /home/rth/src/scikit-learn/                                                                                              
    Complete output (56 lines):                                                                                                        
    C compiler: gcc -pthread -B /home/rth/.miniconda3/envs/sklearn-dev/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC                                                                                                 
                                                                                                                                       
    compile options: '-c'                                                                                                              
    extra options: '-fopenmp'                                                                                                          
    gcc: test_openmp.c                                                                                                                 
    gcc -pthread -B /home/rth/.miniconda3/envs/sklearn-dev/compiler_compat -Wl,--sysroot=/ objects/test_openmp.o -o test_openmp -fopenmp                                                                                                                                      
    /home/rth/.miniconda3/envs/sklearn-dev/compiler_compat/ld: objects/test_openmp.o: unable to initialize decompress status for section .debug_info                                                                                                                          
    /home/rth/.miniconda3/envs/sklearn-dev/compiler_compat/ld: objects/test_openmp.o: unable to initialize decompress status for section .debug_info                                                                                                                          
    /home/rth/.miniconda3/envs/sklearn-dev/compiler_compat/ld: objects/test_openmp.o: unable to initialize decompress status for section .debug_info                                                                                                                          
    /home/rth/.miniconda3/envs/sklearn-dev/compiler_compat/ld: objects/test_openmp.o: unable to initialize decompress status for section .debug_info                                                                                                                          
    objects/test_openmp.o: file not recognized: file format not recognized                                                             
    collect2: error: ld returned 1 exit status                                                                                         
    Partial import of sklearn during the build process.                                                                                
    Traceback (most recent call last):                                                                                                 
      File "<string>", line 1, in <module>                                                                                             
      File "/home/rth/src/scikit-learn/setup.py", line 290, in <module>                                                                
        setup_package()                                                                                                                
      File "/home/rth/src/scikit-learn/setup.py", line 286, in setup_package                                                           
        setup(**metadata)                                                                                                              
      File "/home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages/numpy/distutils/core.py", line 137, in setup            
        config = configuration()                                                                                                       
      File "/home/rth/src/scikit-learn/setup.py", line 174, in configuration                                                           
        config.add_subpackage('sklearn')                                                                                               
      File "/home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1035, in add_subpackage                                                                                                                                    
        caller_level = 2)                                                                                                              
      File "/home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1004, in get_subpackage                                                                                                                                    
        caller_level = caller_level + 1)                                                                                               
      File "/home/rth/.miniconda3/envs/sklearn-dev/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 941, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "sklearn/setup.py", line 78, in configuration
        maybe_cythonize_extensions(top_path, config)
      File "/home/rth/src/scikit-learn/sklearn/_build_utils/__init__.py", line 43, in maybe_cythonize_extensions
        with_openmp = check_openmp_support()
      File "/home/rth/src/scikit-learn/sklearn/_build_utils/openmp_helpers.py", line 140, in check_openmp_support
        raise CompileError(err_message)
    distutils.errors.CompileError:
                        ***
    
    It seems that scikit-learn cannot be built with OpenMP support.
    
    - Make sure you have followed the installation instructions:
    
        https://scikit-learn.org/dev/developers/advanced_installation.html
    
    - If your compiler supports OpenMP but the build still fails, please
      submit a bug report at:
    
        https://github.com/scikit-learn/scikit-learn/issues
    
    - If you want to build scikit-learn without OpenMP support, you can set
      the environment variable SKLEARN_NO_OPENMP and rerun the build
      command. Note however that some estimators will run in sequential
      mode and their `n_jobs` parameter will have no effect anymore.
    
                        ***
    
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/rth/.miniconda3/envs/sklearn-dev/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/rth/src/scikit-learn/setup.py'"'"'; __file__='"'"'/home/rth/src/scikit-learn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

with,

$ gcc --version                                                                 
gcc (Gentoo 9.2.0-r1 p2) 9.2.0

if I remember correctly, @tomMoral was getting the same error on Arch also with a recent gcc.

I would rather not install conda compilers as a workaround, build should work with recent system gcc..

The root cause is that conda ships its own ld that doesn't work with recent gcc ContinuumIO/anaconda-issues#11152
If anyone has constructive comments to add there that might also help.

Removing or renaming compiler_compat/ld in the conda folder is a hacky workaround.

Opening issue to raise attention to this, it's a problem for sprints in particular.

cc @jeremiedbb Currently the error message is confusing. Maybe we should fist check that gcc works, before checking if it works with OpenMP as otherwise users always get a message about OpenMP not being available which is a red herring.

Slightly related to #14968
@rth rth added the Build / CI label Oct 4, 2019
@rth rth mentioned this issue Oct 10, 2019
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@jeremiedbb jeremiedbb mentioned this issue Oct 10, 2019
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@jeremiedbb jeremiedbb mentioned this issue Nov 5, 2019
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rth commented Jun 3, 2020

Closing as likely outdated and related to openmp issues addressed since.

@rth rth closed this as completed Jun 3, 2020
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