ASKSAGE: Sage Q&A Forum - RSS feedhttps://ask.sagemath.org/questions/Q&A Forum for SageenCopyright Sage, 2010. Some rights reserved under creative commons license.Thu, 12 Sep 2019 11:20:58 +0200Memory leak with matroid is_connected methodhttps://ask.sagemath.org/question/47839/memory-leak-with-matroid-is_connected-method/Hello.
I've been using Graphic Matroids to deal with some enumeration problems, where I filter a list of graphs based on their flats. Even without really undestanding what happens at low level, I could verify that the computation is faster when I build the equivalent representation of each graphic matroid using the Incidence matrix of the graph over GF(2).
One big issue that I am facing is that some memory leak is ocurring. As the size of my list of graphs grows, the ram memory got consumed until a point that my computer breaks down and restarts. My way out has been to use a bash script to keep calling the main program until I reach the end of an external text file (the input).
To force the `gc.collect()` seems to not be an option, because the program becomes really slow.
EDIT 1:
The memory leak seems to be related with the `is_connected` method. Here is a piece of my code showing two different situations:
With the use of `is_connected`:
sage: G = [g for g in graphs.nauty_geng("12 16:16 -Ct")]
sage: len(G)
11771
sage: print(get_memory_usage())
....:
....: for g in G:
....: A = g.incidence_matrix()
....: M = Matroid(A, ring = GF(2))
....: if M.is_connected():
....: pass
....: print(get_memory_usage())
....:
3396.38671875
3418.06640625
and without:
sage: print(get_memory_usage())
....: for g in G:
....: A = g.incidence_matrix()
....: M = Matroid(A, ring = GF(2))
....: for r in range(M.corank()):
....: for F in M.coflats(r):
....: pass
....:
....: print(get_memory_usage())
....:
3490.53515625
3490.53515625
EDIT 2:
Ok, I solved my problem by just explicitly declaring the function `is_connected` in the body of my code, instead of using the method present in the abstract matroid class. I'm not sure about why it really worked, I tried this approach because I thought it had something to do with the lists that are created by the `components` method, however I stopped investigating when I notice the memory leak vanished just by using the function. To be honest, I changed the script to not return any output (there was an option to input a certificate flag and return the components).
I'm letting the code below for the case someone faces a similar problem or has any better solution or clue about why it happened:
cpdef components(self):
B = self.basis()
components = [frozenset([e]) for e in self.groundset()]
for e in self.groundset() - B:
C = self.circuit(B | set([e]))
components2 = []
for comp in components:
if len(C & comp) != 0:
C = C | comp
else:
components2.append(comp)
components2.append(C)
components = components2
return components
cpdef is_connected(self):
comp = components(self)
if len(comp) == 1:
return True
else:
return FalsefmorlinThu, 12 Sep 2019 11:20:58 +0200https://ask.sagemath.org/question/47839/