Question

I am using mex bridge to perform some operations on Sparse matrices from Matlab.
For that I need to convert input matrix into CSR (compressed row storage) format, since Matlab stores the sparse matrices in CSC (compressed column storage).

I was able to get value array and column_indices array. However, I am struggling to get row_pointer array for CSR format.Is there any C library that can help in conversion from CSC to CSR ?

Further, while writing a CUDA kernel, will it be efficient to use CSR format for sparse operations or should I just use following arrays :- row indices, column indices and values?

Which on would give me more control over the data, minimizing the number for-loops in the custom kernel?

Answer 1

I ended up converting CSC format from Matlab to CSR using CUSP library as follows.

After getting the matrix A from matlab and I got its row,col and values vectors and I copied them in respective thrust::host_vector created for each of them.

After that I created two cusp::array1d of type Indices and Values as follows.

    typedef typename cusp::array1d<int,cusp::host_memory>Indices;   
    typedef typename cusp::array1d<float,cusp::host_memory>Values;
    Indices row_indices(rows.begin(),rows.end());
    Indices col_indices(cols.begin(),cols.end());
    Values  Vals(Val.begin(),Val.end());

where rows, cols and Val are thrust::host_vector that I got from Matlab.

After that I created a cusp::coo_matrix_view as given below.

typedef cusp::coo_matrix_view<Indices,Indices,Values>HostView;
HostView Ah(m,n,NNZa,row_indices,col_indices,Vals);

where m,n and NNZa are the parameters that I get from mex functions of sparse matrices.

I copied this view matrix to cusp::csr_matrixin device memory with proper dimensions set as given below.

    cusp::csr_matrix<int,float,cusp::device_memory>CSR(m,n,NNZa);
    CSR = Ah;   

After that I just copied the three individual content arrays of this CSR matrix back to the host using thrust::raw_pointer_cast where arrays with proper dimension are already mxCalloced as given below.

 cudaMemcpy(Acol,thrust::raw_pointer_cast(&CSR.column_indices[0]),sizeof(int)*(NNZa),cudaMemcpyDeviceToHost);
 cudaMemcpy(Aptr,thrust::raw_pointer_cast(&CSR.row_offsets[0]),sizeof(int)*(n+1),cudaMemcpyDeviceToHost);
 cudaMemcpy(Aval,thrust::raw_pointer_cast(&CSR.values[0]),sizeof(float)*(NNZa),cudaMemcpyDeviceToHost);

Hope this is useful to anyone who is using CUSP with Matlab