Zach Oakes
Reputation: 183
Can't import cpplist into Cython?
I'm trying to figure out how to work lists/arrays in Cython, which seems impossibly complex, so I would prefer to just use C++ lists as I saw some people use on SO. However when I've ran their code, I'm getting a gcc+ compile error in ipynb. Cython data structures are infuriating.
When ran alone in a cell I get this error, I've tried importing with and without the %%cython magic call and both error...
'''
%%cython
from libcpp.list cimport list as cpplist
'''
def main(int t):
cdef cpplist[int] temp
for x in range(t):
if x> 0:
temp.push_back(x)
cdef int N = temp.size()
cdef list OutputList = N*[0]
for i in range(N):
OutputList[i] = temp.front()
temp.pop_front()
return OutputList
'''
'''
---------------------------------------------------------------------------
DistutilsExecError Traceback (most recent call last)
/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
117 self.spawn(compiler_so + cc_args + [src, '-o', obj] +
--> 118 extra_postargs)
119 except DistutilsExecError as msg:
/anaconda3/lib/python3.6/distutils/ccompiler.py in spawn(self, cmd)
908 def spawn(self, cmd):
--> 909 spawn(cmd, dry_run=self.dry_run)
910
/anaconda3/lib/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
35 if os.name == 'posix':
---> 36 _spawn_posix(cmd, search_path, dry_run=dry_run)
37 elif os.name == 'nt':
/anaconda3/lib/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
158 "command %r failed with exit status %d"
--> 159 % (cmd, exit_status))
160 elif os.WIFSTOPPED(status):
DistutilsExecError: command 'gcc' failed with exit status 1
During handling of the above exception, another exception occurred:
CompileError Traceback (most recent call last)
<ipython-input-6-70891eecfa66> in <module>()
----> 1 get_ipython().run_cell_magic('cython', '--cplus', '\n# distutils: language = c++\nfor i in range(10):\n print(i)\n \n\n\n#from libc.math cimport log\nfrom libcpp.list cimport list as cpplist')
/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
2165 magic_arg_s = self.var_expand(line, stack_depth)
2166 with self.builtin_trap:
-> 2167 result = fn(magic_arg_s, cell)
2168 return result
2169
<decorator-gen-127> in cython(self, line, cell)
/anaconda3/lib/python3.6/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in cython(self, line, cell)
327
328 self._build_extension(extension, lib_dir, pgo_step_name='use' if args.pgo else None,
--> 329 quiet=args.quiet)
330
331 module = imp.load_dynamic(module_name, module_path)
/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in _build_extension(self, extension, lib_dir, temp_dir, pgo_step_name, quiet)
437 if not quiet:
438 old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
--> 439 build_extension.run()
440 finally:
441 if not quiet and old_threshold is not None:
/anaconda3/lib/python3.6/distutils/command/build_ext.py in run(self)
337
338 # Now actually compile and link everything.
--> 339 self.build_extensions()
340
341 def check_extensions_list(self, extensions):
/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extensions(self)
446 self._build_extensions_parallel()
447 else:
--> 448 self._build_extensions_serial()
449
450 def _build_extensions_parallel(self):
/anaconda3/lib/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
471 for ext in self.extensions:
472 with self._filter_build_errors(ext):
--> 473 self.build_extension(ext)
474
475 @contextlib.contextmanager
/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
531 debug=self.debug,
532 extra_postargs=extra_args,
--> 533 depends=ext.depends)
534
535 # XXX outdated variable, kept here in case third-part code
/anaconda3/lib/python3.6/distutils/ccompiler.py in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
572 except KeyError:
573 continue
--> 574 self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
575
576 # Return *all* object filenames, not just the ones we just built.
/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
118 extra_postargs)
119 except DistutilsExecError as msg:
--> 120 raise CompileError(msg)
121
122 def create_static_lib(self, objects, output_libname,
CompileError: command 'gcc' failed with exit status 1
When ran alone in a cell I get this error, I've tried importing with and without the %%cython magic call and both error...
in Cython, I get the object of type 'None' has no length (the ONLY error message in Cython language)
or
invalid syntax
Please advise, Cython has me ready to rip my hair out 2 days in.
EDITS: I've tried using:
%%cython --cplus
#distutils: language = c++
same error message. Also, JUST RUNNING '%%cython --cplus' GIVES ME AN ERROR MESSAGE, SAME ONE? With anything in the cell, a simple print or anything. Something is wrong with my cpp extension I think... how do I resolve?
In terminal (using runipy -- don't know how else to run ipynb in terminal aside from compiling via a setup.py and distutils Build)
zacharys-mbp:Cython zoakes$ runipy CSTL.ipynb
08/08/2019 08:47:47 PM INFO: Reading notebook CSTL.ipynb
08/08/2019 08:47:49 PM INFO: Running cell:
%load_ext cython
08/08/2019 08:47:49 PM INFO: Cell returned
08/08/2019 08:47:49 PM INFO: Running cell:
%%cython
#distutils: language = c++
from libcpp.list cimport list as cpplist
warning: include path for stdlibc++ headers not found; pass '- stdlib=libc++' on
the command line to use the libc++ standard library instead
[-Wstdlibcxx-not-found]
/Users/zoakes/.ipython/cython/_cython_magic_5a0764b273da2aafc5775e4dd20b1249.cpp:592:10: fatal error:
'ios' file not found
#include "ios"
^~~~~
1 warning and 1 error generated.
08/08/2019 08:47:50 PM INFO: Cell raised uncaught exception:
---------------------------------------------------------------------------
DistutilsExecError Traceback (most recent call last)
/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
117 self.spawn(compiler_so + cc_args + [src, '-o', obj] +
--> 118 extra_postargs)
119 except DistutilsExecError as msg:
/anaconda3/lib/python3.6/distutils/ccompiler.py in spawn(self, cmd)
908 def spawn(self, cmd):
--> 909 spawn(cmd, dry_run=self.dry_run)
910
/anaconda3/lib/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
35 if os.name == 'posix':
---> 36 _spawn_posix(cmd, search_path, dry_run=dry_run)
37 elif os.name == 'nt':
/anaconda3/lib/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
158 "command %r failed with exit status %d"
--> 159 % (cmd, exit_status))
160 elif os.WIFSTOPPED(status):
DistutilsExecError: command 'gcc' failed with exit status 1
During handling of the above exception, another exception occurred:
CompileError Traceback (most recent call last)
<ipython-input-2-e4f283bb7389> in <module>()
----> 1 get_ipython().run_cell_magic('cython', '', '\n#distutils: language = c++\nfrom libcpp.list cimport list as cpplist')
/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
2165 magic_arg_s = self.var_expand(line, stack_depth)
2166 with self.builtin_trap:
-> 2167 result = fn(magic_arg_s, cell)
2168 return result
2169
<decorator-gen-127> in cython(self, line, cell)
/anaconda3/lib/python3.6/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in cython(self, line, cell)
327
328 self._build_extension(extension, lib_dir, pgo_step_name='use' if args.pgo else None,
--> 329 quiet=args.quiet)
330
331 module = imp.load_dynamic(module_name, module_path)
/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in _build_extension(self, extension, lib_dir, temp_dir, pgo_step_name, quiet)
437 if not quiet:
438 old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
--> 439 build_extension.run()
440 finally:
441 if not quiet and old_threshold is not None:
/anaconda3/lib/python3.6/distutils/command/build_ext.py in run(self)
337
338 # Now actually compile and link everything.
--> 339 self.build_extensions()
340
341 def check_extensions_list(self, extensions):
/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extensions(self)
446 self._build_extensions_parallel()
447 else:
--> 448 self._build_extensions_serial()
449
450 def _build_extensions_parallel(self):
/anaconda3/lib/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
471 for ext in self.extensions:
472 with self._filter_build_errors(ext):
--> 473 self.build_extension(ext)
474
475 @contextlib.contextmanager
/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
531 debug=self.debug,
532 extra_postargs=extra_args,
--> 533 depends=ext.depends)
534
535 # XXX outdated variable, kept here in case third-part code
/anaconda3/lib/python3.6/distutils/ccompiler.py in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
572 except KeyError:
573 continue
--> 574 self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
575
576 # Return *all* object filenames, not just the ones we just built.
/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
118 extra_postargs)
119 except DistutilsExecError as msg:
--> 120 raise CompileError(msg)
121
122 def create_static_lib(self, objects, output_libname,
CompileError: command 'gcc' failed with exit status 1
08/08/2019 08:47:50 PM INFO: Shutdown kernel
08/08/2019 08:47:50 PM WARNING: Exiting with nonzero exit status
Upvotes: 0
Views: 515
Answers (1)
DavidW
Reputation: 30912
I think this is a Mac issue, which limits my ability to help. However, the key error message seems to be:
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on
the command line to use the libc++ standard library instead
[-Wstdlibcxx-not-found]
If you search for (part of) this message it looks like it's related to XCode. At some point Apple switched the compiler from GCC to Clang, and this changed which implementation of the C++ standard library it uses.
I think the best solution is to install "stdlibc++" on XCode. Unfortunately I have no idea how you'd practically do this.
The second best solution involves adding the suggested command line argument for Cython - I think this is second-best because it's using a slightly mismatched implementation of the C++ standard library.
%%cython --compile-args=-stdlib=libc++ --link-args=-stdlib=libc++
I'm not sure if it needs to be in both compile and link args or just compile args.
Upvotes: 1
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