Collapsing preallocated memory of sparse matrix

I used sparse matrix for some calculation, and I roughly know how many nnz will be stored. So I preallocated a slightly larger memory when I initialize that sparse matrix.

reserveRate = 1.2 % 120%
A = spalloc(n,m,estimated_nnz * reserveRate);

After finishing the calculation, since the memory has some unfilled margin, I would like to remove those space. Is there any way to do so?

Answer 1

[Bjorn Gustavsson]

Is there a particular reason you dont collect the non-zero values and their matrix indices into 3 arrays and then after all those are completed first then generating the sparse array? That is the general advice to not over-allocate.

HTH

[Hyeokjin Jho]

It's a quite big data. The array takes memory over 50%, so duplicating it will lead to shortage of memory.

[Bjorn Gustavsson]

But if your arrays with the non-zero values and the corresponding row and column indices take up over 50% of your memory wouldn't you rapidly run into problems as soon as you start doing operations on the sparse array?

Sad follow-up suggestion: read the indices first, then you candetermine the exact size needed so you can allocate the minimal A, and then do another read to fill it? If it is so that you just get the values and indices in some calculation maybe another way would be to store them in arrays, save to file(s) - then you might be able to wiggle your way around by determining the size of A and then populate it. I know these are "not pretty" suggestions...