Running Cython in Jupyter iPython

Question

Running an iterative loop for a geometric progression for a time trial, using the Cython interface.

Get an error on compile (shift-enter): CompileError: command 'gcc' failed with exit status 1

%load_ext Cython

%%cython
def geo_prog_cython(double alpha, int n):
    cdef double current = 1.0
    cdef double sum = current
    cdef int i
    for i in range(n):
        current = current * alpha
        sum = sum + current
    return sum

The error:

//anaconda/lib/python3.5/distutils/command/build_ext.py in build_extension(self, ext)
    530                                          debug=self.debug,
    531                                          extra_postargs=extra_args,
--> 532                                          depends=ext.depends)
    533 
    534         # XXX outdated variable, kept here in case third-part code

DistutilsExecError //anaconda/lib/python3.5/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 — rrg, Feb 26 '16 at 17:46
Can you please paste the *whole* traceback,. not just the error. — hruske, Feb 26 '16 at 18:24
have you tried using cython outside of jupyter? I think this may just be an issue with your cython configuration — Tadhg McDonald-Jensen, Oct 27 '16 at 21:18

score 6 · Answer 1 · answered Oct 27 '16 at 21:09

I was able to reproduce this without error using Anaconda3:

%load_ext Cython
%%cython -a

def geo_prog_cython(double alpha, int n):
    cdef double current = 1.0
    cdef double sum = current
    cdef int i
    for i in range(n):
        current = current * alpha
        sum = sum + current
    return sum

Example:

geo_prog_cython(0.5, 5)
1.96875

The code seems fine. It must be an issue with your set up.

score 6 · Accepted Answer · answered Jan 12 '18 at 01:16

I know this question is quite old but I thought this may help some others.

I ran into this issue on Windows for an old Py2.7 project.

If on Windows, and using Py2.7 check that you have the MS Visual Studio C++ compiler for Python installed (download link). Not sure what changes are necessary for Py3.

For your anaconda environment, locate the Lib\distutils directory and create a distutils.cfg file (if not already there, otherwise just modify the current file as necessary).

You want the build config to look like below.

[build] compiler=msvc

If on linux, make sure you have the necessary devel packages available, e.g.

Ubuntu: apt-get install python-devel

Running Cython in Jupyter iPython

2 Answers2

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