[petsc-users] Various Questions Regarding PETSC
Mohammed Mostafa
mo7ammedmostafa at gmail.com
Wed Jul 17 08:50:59 CDT 2019
Sorry for the confusion
First I fully acknowledge that setting Matrix non-zeros or copying in
general is not cheap and memory access pattern can play an important role.
So to establish a baseline to compare with, I tried setting the same matrix
but in an Eigen Sparse Matrix and the timings are as follows
FillPetscMat_with_MatSetValues 100 1.0 3.8820e+00 1.1 0.00e+00
0.0 0.0e+00 0.0e+00 0.0e+00 23 0 0 0 0 * 96 * 0 0 0 0 0
FilEigenMat 100 1.0
2.8727e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 18 0 0 0 0 88 0
0 0 0 0
I used the same code but simply filled a different Matrix something like
for ( i =0; i < nRows;i++)
{
//
.......
// Some code to get j_index, coefvalues
// Method1
MatSetValues(A, 1, &cell_global_index, nnz_per_row, j_index, coefvalues,
INSERT_VALUES);
//Method2
for ( int k = 0;k < nnz_per_row; k++)
EigenMat.coeffRef(i, j_index[k] ) = coefvalues[k];
}
Please note that only one of the two methods is being used at a time. Also,
I separately time the code section used to < j_index, coefvalues> but
simpling disabling both Method1 and Method2.
I found the cost to be trivial in comparison to when either one of the
methods is used.
I used Eigen out of convenience since I used for some vector and tensor
arithmetics somewhere else in the code and it may not be the best choice.
Since in PetscMatrix we technically fill two matrices: diagonal and
off-diagonal so I expected some difference but is that normal or am I
missing something. ?
Maybe some setting or MatOption I should be using so far this what I have
been using
MatCreateMPIAIJWithArrays(PETSC_COMM_WORLD, local_size, local_size,
PETSC_DETERMINE,
PETSC_DETERMINE, ptr, j , v, A);
MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);
MatSetOption(A,MAT_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);
MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);
MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);
MatSetUp(A);
MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
Thanks,
Kamra
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