In an assignment for a parallel computing class we have been assigned to program Sparse Binary Matrix-Matrix multiplication (SpGEMM) in C. Julia has a relatively easy to follow implementation based on Gustavson's algorithm that works great.
Thing is we also need to do the multiplication in block form, which I already did, but I don't really see any speedup in doing so. From what I understand you're supposed to use
the result of A(i,k)*B(k,j), where (i,j) are coordinates in the block matrix, as a mask/filter for the next block multiplication in the sum C(i,j) = Σ( A(i,k)*B(k,j) ).
Julia's implementation though, which I followed, already has a dense boolean array when computing each row that acts as a "flag" for when not to add something again in the resulting matrix.
My question is, is there any merit in turning this into block matrix multiplication or is there something that I might be doing wrong myself.
Keep in mind my C code currently runs in half the time Matlab takes in multiplying a 5,000,000 x 5,000,000 sparse matrix. The blocked version, which I really tried to optimize and I'm also doing in the Gustavson order, gets slower and slower the smaller the block-size is set.
Here is my current code
//C=D+(A*B) (basically OR)
bool SpGEMM_dor(int *Acol, int *Arow, int An,
int *Bcol, int *Brow, int Bm,
int **Ccol, int *Crow, int *Csize,//output
int *Dcol, int *Drow)//previous
{
//printCSR(Arow,Acol,An,An,An);
int nnzcum=0;
bool *xb = calloc(An,sizeof(bool)); //boolean flag
for(int i=0; i<An; i++){
int nnzpv = nnzcum;//nnz of previous row;
Crow[i] = nnzcum;
if(nnzcum + An > *Csize){ //make sure theres enough space
*Csize += MAX(An, *Csize/4);
*Ccol = realloc(*Ccol,*Csize*sizeof(int));
}
//---OR---
//add previous row items in order to exist in the next block
for(int jj=Drow[i]; jj<Drow[i+1]; jj++){
int j = Dcol[jj];
xb[j] = true;
(*Ccol)[nnzcum] = j;
nnzcum++;
}
//--------
//add new row items
for(int jj=Arow[i]; jj<Arow[i+1]; jj++){
int j = Acol[jj];
for(int kp=Brow[j]; kp<Brow[j+1]; kp++){
int k = Bcol[kp];
if(!xb[k]){
xb[k] = true;
(*Ccol)[nnzcum] = k;
nnzcum++;
}
}
}
if(nnzcum > nnzpv){
quickSort(*Ccol,nnzpv,nnzcum-1);
for(int p=nnzpv; p<nnzcum; p++){
xb[ (*Ccol)[p] ] = false;
}
}
}
Crow[An] = nnzcum;
free(xb);
return Crow[An];
}
The part of code that I have inside of the ----OR---- section only happens in the block version in order to add the previous block to the now-calculating one. It basically does C = D+(A*B). I've also tried calculating the next block and then merging the 2 sorted arrays of each row of the 2 CSR matrices, which seems to be slower. Also all matrices are in CSR format.