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Updated somoclu for conda on Windows.
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Modified the setup process in Python
Possible fix for peterwittek#144
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@thompsonsed
thompsonsed committed Oct 2, 2019
1 parent b31dfbe commit 74e58c1
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Showing 8 changed files with 5,956 additions and 289 deletions.
5 changes: 5 additions & 0 deletions src/Python/.gitignore
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@@ -0,0 +1,5 @@
build/
dist/
somoclu.egg-info/
somoclu/src/

674 changes: 674 additions & 0 deletions src/Python/LICENSE
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277 changes: 151 additions & 126 deletions src/Python/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,42 +6,46 @@
import sys
import platform
import traceback

win_cuda_dir = None


def find_cuda():
if 'CUDAHOME' in os.environ:
home = os.environ['CUDAHOME']
nvcc = os.path.join(home, 'bin', 'nvcc')
if "CUDAHOME" in os.environ:
home = os.environ["CUDAHOME"]
nvcc = os.path.join(home, "bin", "nvcc")
else:
nvcc = None
for dir in os.environ['PATH'].split(os.pathsep):
binpath = os.path.join(dir, 'nvcc')
for dir in os.environ["PATH"].split(os.pathsep):
binpath = os.path.join(dir, "nvcc")
if os.path.exists(binpath):
nvcc = os.path.abspath(binpath)
if nvcc is None:
raise EnvironmentError('The nvcc binary could not be located in '
'your $PATH. Either add it to your path, or'
'set $CUDAHOME')
raise EnvironmentError(
"The nvcc binary could not be located in "
"your $PATH. Either add it to your path, or"
"set $CUDAHOME"
)
home = os.path.dirname(os.path.dirname(nvcc))
cudaconfig = {'home': home, 'nvcc': nvcc,
'include': os.path.join(home, 'include')}
cudaconfig = {"home": home, "nvcc": nvcc, "include": os.path.join(home, "include")}
for k, v in cudaconfig.items():
if not os.path.exists(v):
raise EnvironmentError('The CUDA %s path could not be located in '
'%s' % (k, v))
libdir = os.path.join(home, 'lib')
raise EnvironmentError(
"The CUDA %s path could not be located in " "%s" % (k, v)
)
libdir = os.path.join(home, "lib")
arch = int(platform.architecture()[0][0:2])
if sys.platform.startswith('win'):
os.path.join(libdir, "x"+str(arch))
if sys.platform.startswith("win"):
os.path.join(libdir, "x" + str(arch))
if os.path.exists(os.path.join(home, libdir + "64")):
cudaconfig['lib'] = libdir + "64"
cudaconfig["lib"] = libdir + "64"
elif os.path.exists(os.path.join(home, libdir)):
cudaconfig['lib'] = libdir
cudaconfig["lib"] = libdir
else:
raise EnvironmentError('The CUDA libraries could not be located')
raise EnvironmentError("The CUDA libraries could not be located")
return cudaconfig


try:
CUDA = find_cuda()
except EnvironmentError:
Expand All @@ -53,23 +57,25 @@ def find_cuda():
except AttributeError:
numpy_include = numpy.get_numpy_include()


def customize_compiler_for_nvcc(self):
'''This is a verbatim copy of the NVCC compiler extension from
"""This is a verbatim copy of the NVCC compiler extension from
https://github.com/rmcgibbo/npcuda-example
'''
self.src_extensions.append('.cu')
"""
self.src_extensions.append(".cu")
default_compiler_so = self.compiler_so
super = self._compile

def _compile(obj, src, ext, cc_args, extra_postargs, pp_opts):
if os.path.splitext(src)[1] == '.cu':
self.set_executable('compiler_so', CUDA['nvcc'])
postargs = extra_postargs['nvcc']
if os.path.splitext(src)[1] == ".cu":
self.set_executable("compiler_so", CUDA["nvcc"])
postargs = extra_postargs["nvcc"]
else:
postargs = extra_postargs['cc']
postargs = extra_postargs["cc"]

super(obj, src, ext, cc_args, postargs, pp_opts)
self.compiler_so = default_compiler_so

self._compile = _compile


Expand All @@ -79,122 +85,141 @@ def build_extensions(self):
customize_compiler_for_nvcc(self.compiler)
build_ext.build_extensions(self)


# class CustomExtension(Extension):
# def __init__(self, name, sourcedir="", **kwargs):
# Extension.__init__(self, name, **kwargs)
# self.sourcedir = os.path.abspath(sourcedir)


cmdclass = {}
if sys.platform.startswith('win') and win_cuda_dir is not None:
if sys.platform.startswith("win") and win_cuda_dir is not None:
if win_cuda_dir == "":
if 'CUDA_PATH' in os.environ:
win_cuda_dir = os.environ['CUDA_PATH']
if "CUDA_PATH" in os.environ:
win_cuda_dir = os.environ["CUDA_PATH"]
elif os.path.exists(win_cuda_dir):
pass
else:
win_cuda_dir = None
if win_cuda_dir:
arch = int(platform.architecture()[0][0:2])
somoclu_module = Extension('_somoclu_wrap',
sources=['somoclu/somoclu_wrap.cxx'],
extra_objects=[
'somoclu/src/denseCpuKernels.obj',
'somoclu/src/sparseCpuKernels.obj',
'somoclu/src/training.obj',
'somoclu/src/mapDistanceFunctions.obj',
'somoclu/src/uMatrix.obj',
'somoclu/src/denseGpuKernels.cu.obj'],
define_macros=[('CUDA', None)],
library_dirs=[win_cuda_dir+"/lib/x"+str(arch)],
libraries=['cudart', 'cublas'],
include_dirs=[numpy_include])
somoclu_module = Extension(
"somoclu._somoclu_wrap",
sources=["somoclu/somoclu_wrap.cxx"],
extra_objects=[
"somoclu/src/denseCpuKernels.obj",
"somoclu/src/sparseCpuKernels.obj",
"somoclu/src/training.obj",
"somoclu/src/mapDistanceFunctions.obj",
"somoclu/src/uMatrix.obj",
"somoclu/src/denseGpuKernels.cu.obj",
],
define_macros=[("CUDA", None)],
library_dirs=[win_cuda_dir + "/lib/x" + str(arch)],
libraries=["cudart", "cublas"],
include_dirs=[numpy_include],
)
else:
sources_files = ['somoclu/src/denseCpuKernels.cpp',
'somoclu/src/sparseCpuKernels.cpp',
'somoclu/src/mapDistanceFunctions.cpp',
'somoclu/src/training.cpp',
'somoclu/src/uMatrix.cpp',
'somoclu/somoclu_wrap.cxx']
if sys.platform.startswith('win'):
extra_compile_args = ['-openmp']
sources_files = [
"somoclu/src/denseCpuKernels.cpp",
"somoclu/src/sparseCpuKernels.cpp",
"somoclu/src/mapDistanceFunctions.cpp",
"somoclu/src/training.cpp",
"somoclu/src/uMatrix.cpp",
"somoclu/somoclu_wrap.cxx",
]
if sys.platform.startswith("win"):
extra_compile_args = ["-openmp"]
cmdclass = {}
somoclu_module = Extension('_somoclu_wrap',
sources=sources_files,
include_dirs=[numpy_include, 'src'],
extra_compile_args=extra_compile_args,
)
somoclu_module = Extension(
"somoclu._somoclu_wrap",
sourcedir="somoclu",
sources=sources_files,
include_dirs=[numpy_include, "src"],
extra_compile_args=extra_compile_args,
)
else:
extra_compile_args = ['-fopenmp']
if 'CC' in os.environ and 'clang-omp' in os.environ['CC']:
openmp = 'iomp5'
extra_compile_args = ["-fopenmp"]
if "CC" in os.environ and "clang-omp" in os.environ["CC"]:
openmp = "iomp5"
else:
openmp = 'gomp'
cmdclass = {'build_ext': custom_build_ext}
somoclu_module = Extension('_somoclu_wrap',
sources=sources_files,
include_dirs=[numpy_include, 'src'],
extra_compile_args={'cc': extra_compile_args},
libraries=[openmp],
)
openmp = "gomp"
cmdclass = {"build_ext": custom_build_ext}
somoclu_module = Extension(
"somoclu._somoclu_wrap",
sources=sources_files,
include_dirs=[numpy_include, "src"],
extra_compile_args={"cc": extra_compile_args},
libraries=[openmp],
)
if CUDA is not None:
somoclu_module.sources.append('somoclu/src/denseGpuKernels.cu')
somoclu_module.define_macros = [('CUDA', None)]
somoclu_module.include_dirs.append(CUDA['include'])
somoclu_module.library_dirs = [CUDA['lib']]
somoclu_module.libraries += ['cudart', 'cublas']
somoclu_module.runtime_library_dirs = [CUDA['lib']]
somoclu_module.extra_compile_args['nvcc']=['-use_fast_math',
'--ptxas-options=-v', '-c',
'--compiler-options','-fPIC ' +
extra_compile_args[0]]

somoclu_module.sources.append("somoclu/src/denseGpuKernels.cu")
somoclu_module.define_macros = [("CUDA", None)]
somoclu_module.include_dirs.append(CUDA["include"])
somoclu_module.library_dirs = [CUDA["lib"]]
somoclu_module.libraries += ["cudart", "cublas"]
somoclu_module.runtime_library_dirs = [CUDA["lib"]]
somoclu_module.extra_compile_args["nvcc"] = [
"-use_fast_math",
"--ptxas-options=-v",
"-c",
"--compiler-options",
"-fPIC " + extra_compile_args[0],
]


try:
setup(name='somoclu',
version='1.7.5',
license='GPL3',
author="Peter Wittek, Shi Chao Gao",
author_email="",
maintainer="shichaogao",
maintainer_email="[email protected]",
url="https://somoclu.readthedocs.io/",
platforms=["unix", "windows"],
description="Massively parallel implementation of self-organizing maps",
ext_modules=[somoclu_module],
packages=["somoclu"],
install_requires=['numpy', 'matplotlib', 'scipy'],
classifiers=[
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Operating System :: OS Independent',
'Development Status :: 5 - Production/Stable',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
'Topic :: Scientific/Engineering :: Visualization',
'Intended Audience :: Science/Research',
'Programming Language :: Python',
'Programming Language :: C++'
],
cmdclass=cmdclass,
test_suite="tests"
)
setup(
name="somoclu",
version="1.7.5",
license="GPL3",
author="Peter Wittek, Shi Chao Gao",
author_email="",
maintainer="shichaogao",
maintainer_email="[email protected]",
url="https://somoclu.readthedocs.io/",
platforms=["unix", "windows"],
description="Massively parallel implementation of self-organizing maps",
ext_modules=[somoclu_module],
packages=["somoclu"],
install_requires=["numpy", "matplotlib", "scipy"],
classifiers=[
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Development Status :: 5 - Production/Stable",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Visualization",
"Intended Audience :: Science/Research",
"Programming Language :: Python",
"Programming Language :: C++",
],
cmdclass=cmdclass,
test_suite="tests",
)
except:
traceback.print_exc()
setup(name='somoclu',
version='1.7.5',
license='GPL3',
author="Peter Wittek, Shi Chao Gao",
author_email="",
maintainer="shichaogao",
maintainer_email="[email protected]",
url="https://somoclu.readthedocs.io/",
platforms=["unix", "windows"],
description="Massively parallel implementation of self-organizing maps",
packages=["somoclu"],
classifiers=[
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Operating System :: OS Independent',
'Development Status :: 5 - Production/Stable',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
'Topic :: Scientific/Engineering :: Visualization',
'Intended Audience :: Science/Research',
'Programming Language :: Python',
'Programming Language :: C++'
],
install_requires=['numpy', 'matplotlib', 'scipy'],
test_suite="tests"
)
setup(
name="somoclu",
version="1.7.5",
license="GPL3",
author="Peter Wittek, Shi Chao Gao",
author_email="",
maintainer="shichaogao",
maintainer_email="[email protected]",
url="https://somoclu.readthedocs.io/",
platforms=["unix", "windows"],
description="Massively parallel implementation of self-organizing maps",
packages=["somoclu"],
classifiers=[
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Development Status :: 5 - Production/Stable",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Visualization",
"Intended Audience :: Science/Research",
"Programming Language :: Python",
"Programming Language :: C++",
],
install_requires=["numpy", "matplotlib", "scipy"],
test_suite="tests",
)
2 changes: 1 addition & 1 deletion src/Python/somoclu/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,6 @@
"""
__version = "1.7.5"

__all__ = ['Somoclu']
__all__ = ["Somoclu"]

from .train import Somoclu
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