[petsc-users] Non zero entries

[Chung-Kan Huang]

Hi,

I have some confusion related to NONZERO in the matrix.
In my application I created Matrix using following procedure.

  MatCreate(* comm_, & J_);
  PetscInt * d_nnz = NULL;
  PetscInt * o_nnz = NULL;
  PetscMalloc(local_size * sizeof(PetscInt), & d_nnz);
  PetscMalloc(local_size * sizeof(PetscInt), & o_nnz);
  for (int i = 0; i < local_size; i++) {
    d_nnz[i] = d_nnz_v[i];
    o_nnz[i] = o_nnz_v[i];
  }
  MatSetType(J_, MATAIJ);
  MatSetSizes(J_,
       local_size,
       local_size,
       PETSC_DECIDE,
       PETSC_DECIDE);


  if (comm_->Get_size() > 1) {
    // MPI
    MatMPIAIJSetPreallocation(J_,
         max_d_nz,
         d_nnz,
         max_o_nz,
         o_nnz);
  } else {
    // Seq
    MatSeqAIJSetPreallocation(J_,
         PETSC_DEFAULT,
         d_nnz);
  }
  PetscFree(d_nnz);
  PetscFree(o_nnz);

The sructure of the matrix changes from time to time during the application
(as the connectivity list is varying) however  o_nnz d_nnz are made based
on the densest possible scenario.

In a recently test I noticed that matrix consturcion time become extremely
long when the sturucture changes (form less dense to denser).  I dug a
little and found out it become very slow in
  MatSetValues(J_,
        NumRows,
        idxm,
        NumCols,
        idxn,
        data,
        ADD_VALUES);
and it becomes normal again after the first chanaged matrix has been
assembled.

In my case I didn't do MatSetValues for the connection doesn't exisit in on
time connectivity list although I count them in d_nnz and o_nnz but I
started to suspect that PETSC was allocating memory for the new additional
entries base on previous matrix structure.

Any suggestions?


*Cheers*
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