Question

I am having difficulty finding this memory leak.

I believe it has something to do with basin

int numbasinsx(int size, double *f)
{
    int maxBasin, maxRelabel, bcnt;
    unsigned int newgene;
    int *basin, *relabel;
    int relabelcnt;

    //
    // find the basins
    //
    maxBasin = 1<<size;
    basin = new int [maxBasin];
    for (int gene=0; gene<maxBasin; gene++) basin[gene] = 0;

    bool change = true;
    bcnt = 0;
    while (change) {
        change = false;

        for (int gene=0; gene<maxBasin; gene++) {

            bool dominated = false;
            for (int i=0; i<size; i++) {               // for all neighbors
                newgene = gene ^ (1<<i);               // newgene is a neighbor 1 bit away

                if (f[newgene] > f[gene]) dominated = true;  // if neighbor is better mark it

                if (basin[newgene]!=0) {                                        // something to copy
                    if (f[newgene] > f[gene]) {                                // gene is dominated
                        if (basin[gene]==0 || basin[gene]<basin[newgene]) {    // if not labeled or not lowest number
                            basin[gene] = basin[newgene];                      // then label or relabel
                            change = true;
                        }
                    }
                    else if (f[newgene] == f[gene]) {
                        if (basin[gene]<basin[newgene]) {
                            basin[gene] = basin[newgene];
                            change = true;
                        }
                    }
                }
            }

            if (! dominated && basin[gene]==0) {
//                printf("max: %d %lg\n", gene, f[gene]);
                basin[gene] = ++bcnt;
                change = true;
            }
        }
    }


    //
    // relabel the basins
    //
    maxRelabel = maxBasin/2+1;
    relabel = new int [maxRelabel];
    for (int gene=0; gene<maxRelabel; gene++) relabel[gene] = 0;

    relabelcnt = 1;
    for (int gene=0; gene<maxBasin; gene++) {
        if (basin[gene]>=maxRelabel) printf("ERROR: trying to index %d into relabel array with max index of %d\n", basin[gene], maxRelabel-1);

        if (relabel[basin[gene]]==0) {
            relabel[basin[gene]] = relabelcnt++;
        }
//        printf("%d %lg %d\n", gene, f[gene], relabel[basin[gene]]);
    }
//    printf("%d\n", relabelcnt-1);

    delete basin;
    delete relabel;

    return relabelcnt-1;
}

I will leave the above up as to help others, but the new code with vectors is now at http://codepad.org/KiV85Brw. The vector run time is much slower than the delete[] version, and it is even segfaulting for large inputs. I am doing something wrong

Answer 1

If you use operator new[] to allocate a bunch of bytes, then you must use operator delete[] to destroy them:

basin = new int [maxBasin];
//.....
delete[] basin;

Note that you’re doing the same thing with relabel.

Anyway, for this kind of tasks, you should use std::vector:

std::vector<int> basin(maxBasin), relabel(maxRelabel); // We haz no leaks