Eigen Sparse Matrix

Question

I am trying to multiply two large sparse matrices of size 300k * 1000k and 1000k*300k using Eigen. The matrices are highly sparse ~0.01% non zero entries, however there's no block or other structure in their sparsity.

It turns out that Eigen chokes and ends up taking 55-60G of memory. Actually, it makes the final matrix dense which explains why it takes so much memory.

I have tried multiplying matrices of similar sizes when one of the matrix is diagonal and the multiplication works fine, with ~2-3 G of memory.

Any thoughts on whats going wrong?

Answer 1

Even though your matrices are sparse, the result might be completely dense. You can try to remove smallest entries with (A*B).prune(ref,eps); where ref is a reference value for what is not a zero and eps is a tolerance value. Basically, all entries smaller than ref*eps will be removed during the computation of the product, thus reducing both the memory usage and size of the result. A better option would be to find a way to avoid performing this product.