Filling Sparse Matrices in Kratos

[DanielB]

Dear all,

I have a given a medium-sized sparse matrix as follows. In the process of factorizing the matrix, I very often need to access and add values to single positions of the matrix (refer to the following code). Now I realize that filling the matrix in such a way becomes very slow the bigger the matrix gets, I guess because I did not specify any sparsity pattern or so. Hence the very general question: What is the most efficient way in Kratos to fill sparse matrices assuming I can not loop just over all lines and columns in a nested form but I need to access entries more or less randomly:

Code: [Select]


typedef UblasSpace<double, CompressedMatrix, Vector> SparseSpaceType;
typedef typename SparseSpaceType::MatrixType SparseMatrixType;

SparseMatrixType A_Matrix;
A_Matrix.resize(100000,100000);
A_Matrix.clear();

for(int some_itr=0; some_itr<some_big_number; some_itr++)
{
for(int i=0; i<some_rows_of_A_Matrix;i++)
{
for(int j=0; j<some_collums_of_A_Matrix;j++)
{
                    A_Matrix(i,j) += some_value;
                }
        }
}

Any advice is appreciated. Thank you very much in advance.

Best regards,
Daniel

[pooyan]

Sparse Matrices are very slow in new allocation. So the way to go is to create a correct graph before filling it. This process consists in allocating the memory for non-zeros in each row of the matrix. you can find an example in ConstructMatrixStructure in the BuilderAndSolvers.

So first you should count nonzeros and create your matrix with

Code: [Select]

SparseMatrixType A_Matrix(100000,100000, number_of_nonzeros); 

Then you should add the your entries in ordered way as you were doing.