fmorlin's profile - activity

Thank you for your answer! I verified and in fact there was no memory leak occurring in the first code snippet I posted. The issue appears to be related with the 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 False