#18834: Use Sage to compute clustering coefficient
-------------------------+-------------------------------------------------
Reporter: | Owner:
ncohen | Status: needs_review
Type: | Milestone: sage-6.8
enhancement | Resolution:
Priority: major | Merged in:
Component: graph | Reviewers:
theory | Work issues:
Keywords: | Commit:
Authors: | 6274bff716b13f4ef7b3e1745d8dcbf761336826
Nathann Cohen | Stopgaps:
Report Upstream: N/A |
Branch: |
u/ncohen/18834 |
Dependencies: |
#18811 |
-------------------------+-------------------------------------------------
Comment (by dcoudert):
Also, I have an issue:
{{{
sage: g = graphs.RandomGNP(1000,.1)
sage: N = 1000
sage: g = graphs.RandomGNP(N, log(N)/N)
sage: g.order(), g.size()
(1000, 3567)
sage: %timeit _=g.clustering_coeff(implementation="boost")
100 loops, best of 3: 2.78 ms per loop
sage: %timeit _=g.clustering_coeff(implementation="dense_copy")
---------------------------------------------------------------------------
ZeroDivisionError Traceback (most recent call
last)
<ipython-input-31-cd519bf674aa> in <module>()
----> 1 get_ipython().magic(u'timeit
_=g.clustering_coeff(implementation="dense_copy")')
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/IPython/core/interactiveshell.pyc in magic(self, arg_s)
2305 magic_name, _, magic_arg_s = arg_s.partition(' ')
2306 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2307 return self.run_line_magic(magic_name, magic_arg_s)
2308
2309
#-------------------------------------------------------------------------
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/IPython/core/interactiveshell.pyc in run_line_magic(self,
magic_name, line)
2226 kwargs['local_ns'] =
sys._getframe(stack_depth).f_locals
2227 with self.builtin_trap:
-> 2228 result = fn(*args,**kwargs)
2229 return result
2230
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/IPython/core/magics/execution.pyc in timeit(self, line, cell)
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/IPython/core/magic.pyc in <lambda>(f, *a, **k)
191 # but it's overkill for just that one bit of state.
192 def magic_deco(arg):
--> 193 call = lambda f, *a, **k: f(*a, **k)
194
195 if callable(arg):
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/IPython/core/magics/execution.pyc in timeit(self, line, cell)
1034 number = 1
1035 for _ in range(1, 10):
-> 1036 time_number = timer.timeit(number)
1037 worst_tuning = max(worst_tuning, time_number /
number)
1038 if time_number >= 0.2:
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/IPython/core/magics/execution.pyc in timeit(self, number)
130 gc.disable()
131 try:
--> 132 timing = self.inner(it, self.timer)
133 finally:
134 if gcold:
<magic-timeit> in inner(_it, _timer)
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/sage/graphs/generic_graph.pyc in clustering_coeff(self, nodes,
weight, implementation, return_vertex_weights)
12437 from sage.rings.integer import Integer
12438 return
{v:Integer(count)/((self.degree(v)*(self.degree(v)-1))/2)
> 12439 for v,count in
triangles_count(self).iteritems()}
12440
12441 def cluster_transitivity(self):
/Users/dcoudert/sage/local/lib/python2.7/site-
packages/sage/graphs/generic_graph.pyc in <dictcomp>((v, count))
12437 from sage.rings.integer import Integer
12438 return
{v:Integer(count)/((self.degree(v)*(self.degree(v)-1))/2)
> 12439 for v,count in
triangles_count(self).iteritems()}
12440
12441 def cluster_transitivity(self):
/Users/dcoudert/sage/src/sage/structure/element.pyx in
sage.structure.element.RingElement.__div__
(/Users/dcoudert/sage/src/build/cythonized/sage/structure/element.c:17310)()
1991 if have_same_parent_c(self, right):
1992 return (<RingElement>self)._div_(<RingElement>right)
-> 1993 return coercion_model.bin_op(self, right, div)
1994
1995 cpdef RingElement _div_(self, RingElement right):
/Users/dcoudert/sage/src/sage/structure/coerce.pyx in
sage.structure.coerce.CoercionModel_cache_maps.bin_op
(/Users/dcoudert/sage/src/build/cythonized/sage/structure/coerce.c:8195)()
994 try:
995 xy = self.canonical_coercion(x,y)
--> 996 return PyObject_CallObject(op, xy)
997 except TypeError as err:
998 if xy is not None:
/Users/dcoudert/sage/src/sage/structure/element.pyx in
sage.structure.element.RingElement.__div__
(/Users/dcoudert/sage/src/build/cythonized/sage/structure/element.c:17293)()
1990 """
1991 if have_same_parent_c(self, right):
-> 1992 return (<RingElement>self)._div_(<RingElement>right)
1993 return coercion_model.bin_op(self, right, div)
1994
/Users/dcoudert/sage/src/sage/rings/integer.pyx in
sage.rings.integer.Integer._div_
(/Users/dcoudert/sage/src/build/cythonized/sage/rings/integer.c:11621)()
1728 # This is vastly faster than doing it here, since here
1729 # we can't cimport rationals.
-> 1730 return the_integer_ring._div(self, right)
1731
1732 def __floordiv__(x, y):
/Users/dcoudert/sage/src/sage/rings/integer_ring.pyx in
sage.rings.integer_ring.IntegerRing_class._div
(/Users/dcoudert/sage/src/build/cythonized/sage/rings/integer_ring.c:4894)()
420 cdef rational.Rational x =
rational.Rational.__new__(rational.Rational)
421 if mpz_sgn(right.value) == 0:
--> 422 raise ZeroDivisionError('Rational division by zero')
423 mpz_set(mpq_numref(x.value), left.value)
424 mpz_set(mpq_denref(x.value), right.value)
ZeroDivisionError: Rational division by zero
}}}
I'll send you the graph by mail if you want to investigate.
--
Ticket URL: <http://trac.sagemath.org/ticket/18834#comment:12>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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