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Fix scikit-learn build with Apple clang (#11496)

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* Fix scikit-learn build with Apple clang

* Update compiler unit tests

* Fix unit tests

* Fix OpenMP dep

* recursive=True no longer necessary

* Add myself as a maintainer

* Specify which versions require OpenMP

* Typo fixes

* LLVM-OpenMP is the correct dependency, no OMPT

* Flake8 fix

* Undo Apple Clang OpenMP flag change, split into a separate PR
This commit is contained in:
Adam J. Stewart 2019-07-17 21:27:16 -05:00 committed by GitHub
parent 1269256e25
commit 5d1f965e59
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 111 additions and 14 deletions
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16
var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
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@ -50,15 +50,19 @@ def cmake_args(self):
# CMAKE rpath variable prevents standalone error
# where this package wants the llvm tools path
if '+standalone' in self.spec:
cmake_args.extend(
['-DLIBOMP_STANDALONE_BUILD=true',
'-DCMAKE_BUILD_WITH_INSTALL_RPATH=true',
'-DLIBOMP_USE_DEBUGGER=false'])
cmake_args.extend(
['-DLIBOMP_STANDALONE_BUILD=true',
'-DCMAKE_BUILD_WITH_INSTALL_RPATH=true',
'-DLIBOMP_USE_DEBUGGER=false'])
# Build llvm-openmp-ompt using the tr6_forwards branch
# This requires the version to be 5.0 (50)
if '@tr6_forwards' in self.spec:
cmake_args.extend(
['-DLIBOMP_OMP_VERSION=50'])
cmake_args.extend(
['-DLIBOMP_OMP_VERSION=50'])
return cmake_args
@property
def libs(self):
return find_libraries('libomp', root=self.prefix, recursive=True)

27
var/spack/repos/builtin/packages/llvm-openmp/package.py Normal file
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@ -0,0 +1,27 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class LlvmOpenmp(CMakePackage):
"""The OpenMP subproject of LLVM contains the components required to build
an executable OpenMP program that are outside the compiler itself."""
homepage = "https://openmp.llvm.org/"
url = "https://releases.llvm.org/8.0.0/openmp-8.0.0.src.tar.xz"
version('8.0.0', sha256='f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5')
depends_on('cmake@2.8:', type='build')
def cmake_args(self):
# Disable LIBOMP_INSTALL_ALIASES, otherwise the library is installed as
# libgomp alias which can conflict with GCC's libgomp.
return ['-DLIBOMP_INSTALL_ALIASES=OFF']
@property
def libs(self):
return find_libraries('libomp', root=self.prefix, recursive=True)

4
var/spack/repos/builtin/packages/ompt-openmp/package.py
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@ -23,3 +23,7 @@ class OmptOpenmp(CMakePackage):
conflicts('%gcc@:4.7')
root_cmakelists_dir = 'runtime'
@property
def libs(self):
return find_libraries('libomp', root=self.prefix, recursive=True)

78
var/spack/repos/builtin/packages/py-scikit-learn/package.py
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@ -10,8 +10,29 @@ class PyScikitLearn(PythonPackage):
"""A set of python modules for machine learning and data mining."""
homepage = "https://pypi.python.org/pypi/scikit-learn"
url = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.18.1.tar.gz"
url = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.21.2.tar.gz"
maintainers = ['adamjstewart']
install_time_test_callbacks = ['install_test', 'import_module_test']
import_modules = [
'sklearn', 'sklearn.tree', 'sklearn.metrics', 'sklearn.ensemble',
'sklearn.experimental', 'sklearn.cluster',
'sklearn.feature_extraction', 'sklearn.__check_build',
'sklearn.semi_supervised', 'sklearn.gaussian_process',
'sklearn.compose', 'sklearn.datasets', 'sklearn.externals',
'sklearn.linear_model', 'sklearn.impute', 'sklearn.utils',
'sklearn.covariance', 'sklearn.neural_network',
'sklearn.feature_selection', 'sklearn.inspection', 'sklearn.svm',
'sklearn.manifold', 'sklearn.mixture', 'sklearn.preprocessing',
'sklearn.model_selection', 'sklearn._build_utils',
'sklearn.decomposition', 'sklearn.cross_decomposition',
'sklearn.neighbors', 'sklearn.metrics.cluster',
'sklearn.ensemble._hist_gradient_boosting'
]
version('0.21.2', sha256='0aafc312a55ebf58073151b9308761a5fcfa45b7f7730cea4b1f066f824c72db')
version('0.21.1', sha256='228d0611e69e5250946f8cd7bbefec75347950f0ca426d0c518db8f06583f660')
version('0.20.2', sha256='bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6')
version('0.20.0', sha256='97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18')
version('0.19.1', 'b67143988c108862735a96cf2b1e827a')
@ -21,12 +42,53 @@ class PyScikitLearn(PythonPackage):
version('0.17.1', 'a2f8b877e6d99b1ed737144f5a478dfc')
version('0.13.1', 'acba398e1d46274b8470f40d0926e6a4')
depends_on('python@2.6:2.8,3.3:', when='@:0.19.1')
depends_on('python@2.7:2.8,3.4:', when='@0.20.0:')
depends_on('py-numpy@1.6.1:', type=('build', 'run'), when='@:0.19.1')
depends_on('py-numpy@1.8.2:', type=('build', 'run'), when='@0.20.0:')
depends_on('py-scipy@0.9:', type=('build', 'run'), when='@:0.19.1')
depends_on('py-scipy@0.13.3:', type=('build', 'run'), when='@0.20.0:')
depends_on('python@2.6:2.8,3.3:', when='@:0.19')
depends_on('python@2.7:2.8,3.4:', when='@0.20.0:0.20.999')
depends_on('python@3.5:', when='@0.21:')
depends_on('py-numpy@1.6.1:', type=('build', 'run'), when='@:0.19')
depends_on('py-numpy@1.8.2:', type=('build', 'run'), when='@0.20.0:0.20.999')
depends_on('py-numpy@1.11.0:', type=('build', 'run'), when='@0.21:')
depends_on('py-scipy@0.9:', type=('build', 'run'), when='@:0.19')
depends_on('py-scipy@0.13.3:', type=('build', 'run'), when='@0.20.0:0.20.999')
depends_on('py-scipy@0.17.0:', type=('build', 'run'), when='@0.21:')
depends_on('py-joblib@0.11:', type=('build', 'run'))
depends_on('py-cython@0.23:', type='build')
depends_on('py-test@3.3.0:', type='test')
depends_on('py-cython@0.28.5:', type='build', when='@0.21:')
depends_on('py-pytest@3.3.0:', type='test')
depends_on('py-pandas', type='test')
depends_on('py-setuptools', type='build')
# Technically not correct, but currently no way to check if we
# are using Apple Clang or not.
depends_on('llvm-openmp', when='@0.21: %clang platform=darwin')
def setup_environment(self, spack_env, run_env):
# https://scikit-learn.org/stable/developers/advanced_installation.html#mac-osx
if self.spec.satisfies('@0.21: %clang platform=darwin'):
spack_env.append_flags(
'CPPFLAGS', '-Xpreprocessor -fopenmp')
spack_env.append_flags(
'CFLAGS', self.spec['llvm-openmp'].headers.include_flags)
spack_env.append_flags(
'CXXFLAGS',
self.spec['llvm-openmp'].headers.include_flags)
spack_env.append_flags(
'LDFLAGS', self.spec['llvm-openmp'].libs.ld_flags)
spack_env.append_flags(
'DYLD_LIBRARY_PATH',
self.spec['llvm-openmp'].libs.directories[0])
run_env.append_flags(
'DYLD_LIBRARY_PATH',
self.spec['llvm-openmp'].libs.directories[0])
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
if self.spec.satisfies('@0.21: %clang platform=darwin'):
spack_env.append_flags(
'DYLD_LIBRARY_PATH',
self.spec['llvm-openmp'].libs.directories[0])
def install_test(self):
# https://scikit-learn.org/stable/developers/advanced_installation.html#testing
with working_dir('spack-test', create=True):
pytest = which('pytest')
pytest(join_path(self.prefix, site_packages_dir, 'sklearn'))