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

[Yuyun Yang]

Here is the error message:

Program received signal SIGSEGV, Segmentation fault.
0x00005555555e73b7 in kronConvert (left=..., right=...,
    mat=@0x555555927e10: 0x555557791bb0, diag=5, offDiag=0)
    at /home/yuyun/scycle-2/source/spmat.cpp:265
265  kronConvert_symbolic(left,right,mat,d_nnz,o_nnz);

On Tue, Dec 13, 2022 at 12:41 PM Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Dec 12, 2022 at 9:56 PM Yuyun Yang <yyang85 at alumni.stanford.edu>
> wrote:
>
>> 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?
>>
>
> The only PETSc calls are the MatGetOwnershipRange() calls, which have not
> changed, so I think this is unlikely.
>
>
>> 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:
>>
>
> What is the debugger output?
>
>   Thanks,
>
>     Matt
>
>
>> // 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
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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