AttributeError: 'list' object has no attribute 'rfind' using petsc4py
AttributeError: 'list' object has no attribute 'rfind' using petsc4py
我在结合使用 petsc4py 和 cython 时遇到错误：
AttributeError: 'list' 对象没有属性 'rfind'
以下代码是.../petsc4py/demo/wrap-cython/setup.py的一部分，项目示例，有错误：
def configuration(parent_package='',top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [#'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('_Bratu3D',
sources = ['Bratu3D.pyx',
'Bratu3Dimpl.c'],
depends = ['Bratu3Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
if __name__ == "__main__":
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())
错误信息是：
CC=/usr/local/openmpi-1.10.2/bin/mpicc F90=/usr/local/openmpi-1.10.2/bin/mpif90 LDSHARED='/usr/local/openmpi-1.10.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g3 -shared' \
python setup.py -q build_ext --inplace
Traceback (most recent call last):
File "setup.py", line 66, in <module>
setup(**configuration(top_path='').todict())
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_ext.py", line 82, in run
self.run_command('build_src')
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 147, in run
self.build_sources()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 164, in build_sources
self.build_extension_sources(ext)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
sources, py_files = self.filter_py_files(sources)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 389, in filter_py_files
return self.filter_files(sources, ['.py'])
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 398, in filter_files
(base, ext) = os.path.splitext(source)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/posixpath.py", line 122, in splitext
return genericpath._splitext(p, sep, None, extsep)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/genericpath.py", line 118, in _splitext
sepIndex = p.rfind(sep)
AttributeError: 'list' object has no attribute 'rfind'
make: *** [Bratu3D.so] Error 1
.../petsc4py/demo/wrap-swig/setup.py 的另一个示例具有几乎相同的代码，但没有任何错误。唯一的例外是：
config.add_extension('_Bratu3D',
sources = ['Bratu3D.i',
'Bratu3D.c'],
depends = ['Bratu3D.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
非常感谢。
您需要添加
from Cython.Build import cythonize
config.ext_modules[-1] = cythonize(config.ext_modules[-1])
就在 config.add_extension(...)
之后
问题是 sources 最终包含一个由 generate_a_pyrex_source. This is because it doesn't by itself know how to deal with cython files, so you need to run cythonize on the module to tell it how to (as demonstrated in the cython documentation 添加的空列表。
自己解决这个问题的方法是使用 python 调试器。 运行 python3 -m pdb setup.py -q build_ext --inplace，键入 cont 使其初始为 运行。你会得到例外。您可以键入 up 在堆栈中向上移动。
在第 (base, ext) = os.path.splitext(source) 行键入 print(source) 以查看它是一个空列表。
在第 sources, py_files = self.filter_py_files(sources) 行键入 print(sources) 以查看 [[], 'Bratu3Dimpl.c']。然后只是在第 329 行之前查看 distutils/build_src.py 的情况（其中调用 self.filter_py_files 以查看可能出错的地方。
我已经给代码编写者发了邮件，他说 NumPy distutils 支持得到了改进，现在代码被破坏了。然后安装文件被重写。我已经测试过它在我的系统中运行良好。
我在项目中遇到了同样的问题petsc4py/demo/wrap-cython
事实上，代码在这个文件上进行了一些猴子修补后运行良好：numpy/distutils/command/build_src.py
该方法在 numpy 1.11.0 上定义为：
def generate_a_pyrex_source(self, base, ext_name, source, extension):
"""Pyrex is not supported, but some projects monkeypatch this method.
That allows compiling Cython code, see gh-6955.
This method will remain here for compatibility reasons.
"""
return []
您必须用您自己的定义覆盖此方法。这是使用 python 3.5.1、petsc4py 2.0.0 测试的更新脚本：
wrap-cython/setup.py
#!/usr/bin/env python
# $ python setup.py build_ext --inplace
from numpy.distutils.command import build_src
# a bit of monkeypatching ...
import Cython.Compiler.Main
build_src.Pyrex = Cython
build_src.have_pyrex = True
def have_pyrex():
import sys
try:
import Cython.Compiler.Main
sys.modules['Pyrex'] = Cython
sys.modules['Pyrex.Compiler'] = Cython.Compiler
sys.modules['Pyrex.Compiler.Main'] = Cython.Compiler.Main
return True
except ImportError:
return False
build_src.have_pyrex = have_pyrex
##########################
# BEGIN additionnal code #
##########################
from numpy.distutils.misc_util import appendpath
from numpy.distutils import log
from os.path import join as pjoin, dirname
from distutils.dep_util import newer_group
from distutils.errors import DistutilsError
def generate_a_pyrex_source(self, base, ext_name, source, extension):
''' Monkey patch for numpy build_src.build_src method
Uses Cython instead of Pyrex.
Assumes Cython is present
'''
if self.inplace:
target_dir = dirname(base)
else:
target_dir = appendpath(self.build_src, dirname(base))
target_file = pjoin(target_dir, ext_name + '.c')
depends = [source] + extension.depends
if self.force or newer_group(depends, target_file, 'newer'):
import Cython.Compiler.Main
log.info("cythonc:> %s" % (target_file))
self.mkpath(target_dir)
options = Cython.Compiler.Main.CompilationOptions(
defaults=Cython.Compiler.Main.default_options,
include_path=extension.include_dirs,
output_file=target_file)
cython_result = Cython.Compiler.Main.compile(source, options=options)
if cython_result.num_errors != 0:
raise DistutilsError("%d errors while compiling %r with Cython" % (cython_result.num_errors, source))
return target_file
build_src.build_src.generate_a_pyrex_source = generate_a_pyrex_source
########################
# END additionnal code #
########################
def configuration(parent_package='', top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH:
pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [ # 'petscts', 'petscsnes', 'petscksp',
# 'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('Bratu3D',
sources=['Bratu3D.pyx', 'Bratu3Dimpl.c'],
depends=['Bratu3Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
if __name__ == "__main__":
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())
我在结合使用 petsc4py 和 cython 时遇到错误： AttributeError: 'list' 对象没有属性 'rfind'
以下代码是.../petsc4py/demo/wrap-cython/setup.py的一部分，项目示例，有错误：
def configuration(parent_package='',top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [#'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('_Bratu3D',
sources = ['Bratu3D.pyx',
'Bratu3Dimpl.c'],
depends = ['Bratu3Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
if __name__ == "__main__":
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())
错误信息是：
CC=/usr/local/openmpi-1.10.2/bin/mpicc F90=/usr/local/openmpi-1.10.2/bin/mpif90 LDSHARED='/usr/local/openmpi-1.10.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g3 -shared' \
python setup.py -q build_ext --inplace
Traceback (most recent call last):
File "setup.py", line 66, in <module>
setup(**configuration(top_path='').todict())
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_ext.py", line 82, in run
self.run_command('build_src')
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 147, in run
self.build_sources()
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 164, in build_sources
self.build_extension_sources(ext)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
sources, py_files = self.filter_py_files(sources)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 389, in filter_py_files
return self.filter_files(sources, ['.py'])
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/site-packages/numpy/distutils/command/build_src.py", line 398, in filter_files
(base, ext) = os.path.splitext(source)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/posixpath.py", line 122, in splitext
return genericpath._splitext(p, sep, None, extsep)
File "/home/zhangji/anaconda3/envs/obenv/lib/python3.5/genericpath.py", line 118, in _splitext
sepIndex = p.rfind(sep)
AttributeError: 'list' object has no attribute 'rfind'
make: *** [Bratu3D.so] Error 1
.../petsc4py/demo/wrap-swig/setup.py 的另一个示例具有几乎相同的代码，但没有任何错误。唯一的例外是：
config.add_extension('_Bratu3D',
sources = ['Bratu3D.i',
'Bratu3D.c'],
depends = ['Bratu3D.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
非常感谢。
您需要添加
from Cython.Build import cythonize
config.ext_modules[-1] = cythonize(config.ext_modules[-1])
就在 config.add_extension(...)
问题是 sources 最终包含一个由 generate_a_pyrex_source. This is because it doesn't by itself know how to deal with cython files, so you need to run cythonize on the module to tell it how to (as demonstrated in the cython documentation 添加的空列表。
自己解决这个问题的方法是使用 python 调试器。 运行 python3 -m pdb setup.py -q build_ext --inplace，键入 cont 使其初始为 运行。你会得到例外。您可以键入 up 在堆栈中向上移动。
在第 (base, ext) = os.path.splitext(source) 行键入 print(source) 以查看它是一个空列表。
在第 sources, py_files = self.filter_py_files(sources) 行键入 print(sources) 以查看 [[], 'Bratu3Dimpl.c']。然后只是在第 329 行之前查看 distutils/build_src.py 的情况（其中调用 self.filter_py_files 以查看可能出错的地方。
我已经给代码编写者发了邮件，他说 NumPy distutils 支持得到了改进，现在代码被破坏了。然后安装文件被重写。我已经测试过它在我的系统中运行良好。
我在项目中遇到了同样的问题petsc4py/demo/wrap-cython
事实上，代码在这个文件上进行了一些猴子修补后运行良好：numpy/distutils/command/build_src.py
该方法在 numpy 1.11.0 上定义为：
def generate_a_pyrex_source(self, base, ext_name, source, extension):
"""Pyrex is not supported, but some projects monkeypatch this method.
That allows compiling Cython code, see gh-6955.
This method will remain here for compatibility reasons.
"""
return []
您必须用您自己的定义覆盖此方法。这是使用 python 3.5.1、petsc4py 2.0.0 测试的更新脚本：
wrap-cython/setup.py
#!/usr/bin/env python
# $ python setup.py build_ext --inplace
from numpy.distutils.command import build_src
# a bit of monkeypatching ...
import Cython.Compiler.Main
build_src.Pyrex = Cython
build_src.have_pyrex = True
def have_pyrex():
import sys
try:
import Cython.Compiler.Main
sys.modules['Pyrex'] = Cython
sys.modules['Pyrex.Compiler'] = Cython.Compiler
sys.modules['Pyrex.Compiler.Main'] = Cython.Compiler.Main
return True
except ImportError:
return False
build_src.have_pyrex = have_pyrex
##########################
# BEGIN additionnal code #
##########################
from numpy.distutils.misc_util import appendpath
from numpy.distutils import log
from os.path import join as pjoin, dirname
from distutils.dep_util import newer_group
from distutils.errors import DistutilsError
def generate_a_pyrex_source(self, base, ext_name, source, extension):
''' Monkey patch for numpy build_src.build_src method
Uses Cython instead of Pyrex.
Assumes Cython is present
'''
if self.inplace:
target_dir = dirname(base)
else:
target_dir = appendpath(self.build_src, dirname(base))
target_file = pjoin(target_dir, ext_name + '.c')
depends = [source] + extension.depends
if self.force or newer_group(depends, target_file, 'newer'):
import Cython.Compiler.Main
log.info("cythonc:> %s" % (target_file))
self.mkpath(target_dir)
options = Cython.Compiler.Main.CompilationOptions(
defaults=Cython.Compiler.Main.default_options,
include_path=extension.include_dirs,
output_file=target_file)
cython_result = Cython.Compiler.Main.compile(source, options=options)
if cython_result.num_errors != 0:
raise DistutilsError("%d errors while compiling %r with Cython" % (cython_result.num_errors, source))
return target_file
build_src.build_src.generate_a_pyrex_source = generate_a_pyrex_source
########################
# END additionnal code #
########################
def configuration(parent_package='', top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH:
pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [ # 'petscts', 'petscsnes', 'petscksp',
# 'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('Bratu3D',
sources=['Bratu3D.pyx', 'Bratu3Dimpl.c'],
depends=['Bratu3Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
if __name__ == "__main__":
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())