Memory leak when using a C++ module for Python

Jaume Bonet jaume.bonet at gmail.com
Thu Dec 11 18:35:58 CET 2008


Sure, sorry...

This is the function that is visible from python and the one that the
python code calls:

static PyObject * IMFind (PyObject *self, PyObject *args, PyObject
*kwargs) {

	//Array for the detection of the parameters coming from Python
	static char *kwlist[] =
{"shareInt","root","prefix","lowerLimit",NULL};
	//Root protein code
	char *root;
	//Pefix for the output file
	char *prefix;
	//Incoming Python object
	PyObject *shareIntPy;
	//Number of proteins at level two from the root, that will appear in
the iMotifs' proteins
	int *pSize = new int;
	//Maximum number of common interactors
	int *max = new int;
	//Set relating each protein (integer) with their interactors...
	set<unsigned int>** shareInt;
	//Lower limit for iMotif search
	int lowLim;
	//Vector for the seed iMotifs from an specific threshold
	vector<iMotif> IMseed;
	//Vector of all the working iMotifs during the identification process
	vector<iMotif> IMarray;

        //Receiving data from python
	if (!PyArg_ParseTupleAndKeywords(args, kwargs, "Ossi", kwlist,
&shareIntPy, &root, &prefix,&lowLim)) {
		cerr << "Error in parameter transference from python to iMotif C++
module"<<endl;
		return Py_BuildValue("");
	}

	//The position of the name in the vector corresponds to the number by
which it is represented
        //Here we take the info coming from python and transform it
into a vector (will allow us to work with numbers instead of
        // strings) and shareInt which is an array of sets (form
std::set)
	vector<string> translator = string2int
(shareIntPy,root,shareInt,pSize,max);

	//Loop for iMotif search at threshold thr till the specified lower
limit
	for (int thr = *max; thr >= lowLim; thr--) {
		cout << "Checking threshold " << thr << endl;

		//Specifying the output file name
		stringstream filename;
		filename << prefix << "." << thr;

		//Getting the seed iMotifs for this threshold
		IMseed = getSeedIM(shareInt,*pSize,thr);

		//Adding the new seeds (if any) to those obtained from previous
rounds...
		if (!IMseed.size()) {
			IMseed.clear();
			vector<iMotif>().swap(IMseed); //This is how I try to free them
now, size & capacity gets to 0, but the
                                                       // memory is
not freed...
		} else {
			IMarray.insert(IMarray.end(),IMseed.begin(),IMseed.end());
			IMseed.clear();
			vector<iMotif>().swap(IMseed);
		}

                //Fuse those iMotifs sharing thr interactors
                // It also deletes the IMarray before giving it the
new data in the same way as I use here for IMseed
		processIMVector(IMarray,thr);
		writeIMVector(IMarray,translator,filename.str());

	}

	return Py_BuildValue("");
}

The object iMotif used here is composed by 2 sets and 3 strings just
like this: (the access is done by setters and getters)

class iMotif {
private:
	//Set of the proteins that shares the iMotif with the root
	set<unsigned int> proteins;
	//Set of the proteins to which the iMotifs interacts
	set<unsigned int> interactors;
	//iMotifs interactors signature
	string MD5Interactor;
	//iMotifs proteins signature
	string MD5Proteins;
	//Real MD5 according to the sequences names
	string signature;
...
}
and I specified the destructor as:
iMotif::~iMotif() {

	this->proteins.clear();
	set<unsigned int>().swap(this->proteins);

	this->interactors.clear();
	set<unsigned int>().swap(this->proteins);

}

The call to the function from python goes like this:

iMotifs.IMFind(shareInt=intersections_dict,
root=options.protein_problem, prefix=prefixOutFile, lowerLimit=1);

where intersections_dict is a dictionary and options.protein_problem
and prefixOutFile are strings. There is nothing to return from C++ to
python, the result is directly printed into several files.

Thanks,
J



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