[petsc-users] Seg fault in gdb but program runs

[Yuyun Yang]

Hello team,

I’m debugging my code using gdb. The program runs just fine if I don’t debug it, but when I use gdb, it seg faults at a place where it never experienced any seg fault when I debugged it 1-2 years ago. I wonder if this might be caused by the PETSc version change? Or something wrong with gdb itself? I’ve included the code block that is problematic for you to take a look at what might be wrong – seg fault happens when this function is called. For context, Spmat is a class of sparse matrices in the code:


// calculate the exact nonzero structure which results from the kronecker outer product of left and right

// d_nnz = diagonal nonzero structure, o_nnz = off-diagonal nonzero structure

void kronConvert_symbolic(const Spmat &left, const Spmat &right, Mat &mat, PetscInt* d_nnz, PetscInt* o_nnz)

{

  size_t rightRowSize = right.size(1);

  size_t rightColSize = right.size(2);



  PetscInt Istart,Iend; // rows owned by current processor

  PetscInt Jstart,Jend; // cols owned by current processor



  // allocate space for mat

  MatGetOwnershipRange(mat,&Istart,&Iend);

  MatGetOwnershipRangeColumn(mat,&Jstart,&Jend);

  PetscInt m = Iend - Istart;



  for (int ii=0; ii<m; ii++) { d_nnz[ii] = 0; }

  for (int ii=0; ii<m; ii++) { o_nnz[ii] = 0; }



  // iterate over only nnz entries

  Spmat::const_row_iter IiL,IiR;

  Spmat::const_col_iter JjL,JjR;

  double valL=0, valR=0, val=0;

  PetscInt row,col;

  size_t rowL,colL,rowR,colR;


  // loop over all values in left
  for (IiL=left._mat.begin(); IiL!=left._mat.end(); IiL++) {
    for (JjL=(IiL->second).begin(); JjL!=(IiL->second).end(); JjL++) {
      rowL = IiL->first;
      colL = JjL->first;
      valL = JjL->second;
      if (valL==0) { continue; }

      // loop over all values in right
      for (IiR=right._mat.begin(); IiR!=right._mat.end(); IiR++) {
        for (JjR=(IiR->second).begin(); JjR!=(IiR->second).end(); JjR++) {
          rowR = IiR->first;
          colR = JjR->first;
          valR = JjR->second;

          // the new values and coordinates for the product matrix
          val = valL*valR;
          row = rowL*rightRowSize + rowR;
          col = colL*rightColSize + colR;

          PetscInt ii = row - Istart; // array index for d_nnz and o_nnz
          if (val!=0 && row >= Istart && row < Iend && col >= Jstart && col < Jend) { d_nnz[ii]++; \
}
          if ( (val!=0 && row >= Istart && row < Iend) && (col < Jstart || col >= Jend) ) { o_nnz[i\
i]++; }
        }
      }
    }
  }
}



Thank you,
Yuyun
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