Malloc and Calloc not freeing correctly

Question

Hello I seem to be having an issue with freeing some of my variables after creating them.

Little background on my program. My program is reading MatrixMarket files and building a Matrix Structure from the information read in. I am then using the matrices to do scalar and vector multiplication.

This is my structure for my matrix.

typedef struct {
    double *values;       // Value of each non-zero element.
    unsigned int *col_indices; // Corresponding column coordinate.
    unsigned int *row_ptr; // Initial position of each row.
    unsigned int nz;  // Total non-zero elements.
    unsigned int row_count; // Total row_count of matrix.
    unsigned int cols_count; // Total columns of matrix.
} CSRMatrix;

My goal here is to be able to manipulate my matrix and be able to multiply a vector to the CSR Matrix. (CSR is Compressed Sparse Row Matrix).

Here is how I am initializing my memory allocation.

    /**
    * Set the correct values to the struct and create the memory allocation.
    */
    csrMatrix.row_count = numberOfRows;
    csrMatrix.cols_count = numberOfColumn;
    csrMatrix.nz = numberOfNonZeros;
    csrMatrix.row_ptr = calloc(numberOfRows, 1);
    csrMatrix.values = (double *)malloc(numberOfRows * numberOfRows * 1);
    csrMatrix.col_indices = calloc(numberOfRows * numberOfRows, 1);

Here is where I think my issue is, I may be wrong. I'm terrible at troubleshooting memory issues.

Before I go more in-depth here is where the main multiplication and iteration to the matrix happens:

// Initialize vectors for multiplication

int x_size = numberOfRows * numberOfColumn;
int csr_x[x_size];
memset(csr_x, 0, sizeof(csr_x));
for(int h = 0; h < x_size; h++){
    csr_x[h] = 1;
}
double* csr_y;

printf("\nCalculating matrix-vector product of the CSR for %u iterations...\n", iterations);
clock_t begin = clock();
for(i=0; i < iterations; i++){
    csr_y = (double *)malloc(csrMatrix.row_count * csrMatrix.cols_count * 1);
    csrMVP(&csrMatrix, csr_x,csr_y);
    free(csr_y);
}
clock_t end = clock();
double time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
printf("for loop used %f seconds to complete the execution\n", time_spent);
fclose(file);
free(csr_x);
free(csr_y);
exit(EXIT_SUCCESS);

When I run my program strange things being to happen. The program will run for a few loops (total loops is 1000 iterations) then either exit incomplete with Process finished with exit code 0 or with exit code 11. This is where my troubleshooting started.

Since intellij is not throwing any memory issues or errors I have to go deeper.

I decided to ask a friend of mine who has used Valgrind to do a memcheck on my program. This was the result:

==5607== Memcheck, a memory error detector
==5607== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==5607== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==5607== Command: ./code
/home/tron/src/workspace/classes/cda5110/matrix/mat/ibm32/ibm32.mtx
==5607==
==5607== Invalid write of size 4
==5607==    at 0x109537: loadCSRMatrix (mainCSR.c:173)
==5607==    by 0x108F3A: main (mainCSR.c:72)
==5607==  Address 0x51f23b0 is 0 bytes after a block of size 128 alloc'd
==5607==    at 0x4C2EEF5: calloc (vg_replace_malloc.c:711)
==5607==    by 0x108EC5: main (mainCSR.c:64)
==5607==
==5607== Invalid read of size 4
==5607==    at 0x109300: csrMVP (mainCSR.c:140)
==5607==    by 0x109085: main (mainCSR.c:92)
==5607==  Address 0x51f23b0 is 0 bytes after a block of size 128 alloc'd
==5607==    at 0x4C2EEF5: calloc (vg_replace_malloc.c:711)
==5607==    by 0x108EC5: main (mainCSR.c:64)
==5607==
==5607== Invalid free() / delete / delete[] / realloc()
==5607==    at 0x4C2E10B: free (vg_replace_malloc.c:530)
==5607==    by 0x10910C: main (mainCSR.c:99)
==5607==  Address 0x1ffefff5a0 is on thread 1's stack
==5607==  in frame #1, created by main (mainCSR.c:24)
==5607==
==5607== Invalid free() / delete / delete[] / realloc()
==5607==    at 0x4C2E10B: free (vg_replace_malloc.c:530)
==5607==    by 0x10911B: main (mainCSR.c:100)
==5607==  Address 0x59d3bc0 is 0 bytes inside a block of size 8,192 free'd
==5607==    at 0x4C2E10B: free (vg_replace_malloc.c:530)
==5607==    by 0x109094: main (mainCSR.c:93)
==5607==  Block was alloc'd at
==5607==    at 0x4C2CEDF: malloc (vg_replace_malloc.c:299)
==5607==    by 0x109064: main (mainCSR.c:91)
==5607==
==5607==
==5607== HEAP SUMMARY:
==5607==     in use at exit: 12,416 bytes in 3 blocks
==5607==   total heap usage: 1,006 allocs, 1,005 frees, 8,213,160 bytes
allocated
==5607==
==5607== LEAK SUMMARY:
==5607==    definitely lost: 0 bytes in 0 blocks
==5607==    indirectly lost: 0 bytes in 0 blocks
==5607==      possibly lost: 0 bytes in 0 blocks
==5607==    still reachable: 12,416 bytes in 3 blocks
==5607==         suppressed: 0 bytes in 0 blocks
==5607== Rerun with --leak-check=full to see details of leaked memory
==5607==
==5607== For counts of detected and suppressed errors, rerun with: -v
==5607== ERROR SUMMARY: 1003 errors from 4 contexts (suppressed: 0 from 0)

There are few things that popped out at me. There are a few invaild write and read sizes. These are the following lines for each code called out by the errors:

• at 0x109537: loadCSRMatrix (mainCSR.c:173): m->row_ptr[row_index + 1] = pairIndex;
• by 0x108F3A: main (mainCSR.c:72): loadCSRMatrix(&csrMatrix, file);
• by 0x108EC5: main (mainCSR.c:64): csrMatrix.row_ptr = calloc(numberOfRows, 1);
• at 0x109300: csrMVP (mainCSR.c:140): y[i] += val[j] * x[col[j]];
• by 0x109085: main (mainCSR.c:92): free(csr_y);
• by 0x108EC5: main (mainCSR.c:64): csrMatrix.row_ptr = calloc(numberOfRows, 1);
• by 0x10910C: main (mainCSR.c:99): free(csr_y);
• by 0x10911B: main (mainCSR.c:100): exit(EXIT_SUCCESS);
• by 0x109094: main (mainCSR.c:93): }

• by 0x109064: main (mainCSR.c:91): csrMVP(&csrMatrix, csr_x,csr_y);

  From what I bring it down to is that I am not correctly utilizing malloc and calloc for my memory allocation.

So here's where I ask my question, I am not sure if malloc or calloc are used correctly. If anyone knows where I can start looking to fix this issue.

In case you're wondering what loadCSRMatrix and csrMVP functions are I will attach them below.

csrMVP

/**
 * Stores on vector y the product of matrix M and vector x:
 *   y = Mx
 */
void csrMVP(CSRMatrix *m, int x[], double *y){
    printf("\n\n\nValue of Y: \n ");

    unsigned int i,j,end;
    double *val = m->values;
    unsigned int *col = m->col_indices;
    unsigned int *ptr = m->row_ptr;
    end = 0;
    for(i = 0; i < m->row_count; i++){
        y[i] = 0.0;
        j = end;
        end = ptr[i+1];
        for( ; j < end; j++){
            y[i] += val[j] * x[col[j]];
            printf("%.f\t",  y[i]);
        }
    }printf("\n");

}

loadCSRMatrix

/**
 * Loads the matrix
 */
void loadCSRMatrix(CSRMatrix *m, FILE *f){
    unsigned int pairIndex = 0;
    for (int row_index = 0; row_index < m->row_count; row_index++) {
        for (unsigned int column_index = 0; column_index < m->row_count; column_index++) {
            double value;
            if(fscanf(f, "%lg", &value) != EOF){
                m->values[pairIndex] = value;
                m->col_indices[pairIndex] = column_index+1;
                //printf("Column: %d\t", matrixCSR.col_indices[pairIndex]);
                printf("%.f\t", m->values[pairIndex]);
                pairIndex++;
            }
            else {
                m->values[pairIndex] = 0;
                m->col_indices[pairIndex] = column_index+1;
                //printf("Column: %d\t", matrixCSR.col_indices[pairIndex]);
                printf("%.1f\t", m->values[pairIndex]);
                pairIndex++;
            }
        }
        if(pairIndex != 0) {
            m->row_ptr[row_index + 1] = pairIndex;
        }
        //printf("%zu\n", matrixCSR.row_indices[row_index]);
        printf("\n");
    }
}