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

[Matthew Knepley]

On Tue, Dec 13, 2022 at 1:14 AM Yuyun Yang <yyang85 at alumni.stanford.edu>
wrote:

> 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);
>

d_nnz and o_nnz are pointers, and they are supposed to hold arrays of the
number of nonzero in each row,
You seem to be passing integers.

  Thanks,

     Matt


> 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/>
>>
>

-- 
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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