Axel Ruhe
September  15, 2006
2D1252, Computational Algebra, Fall 2006, 

Programming Assignment 2

Hand in by Ocober 5 at lecture!

Sparse Matrices, direct algorithms

A short introduction given in the lecture notes Chapter 2!

The Matlab command
help/ MATLAB/Using Matlab/Mathematics/Sparse matrices
gives an instructive description. Some details are given in  Extra tips.

If you are really interested, read the  original paper:
Gilbert, John R., Cleve Moler, and Robert Schreiber, "Sparse Matrices in MATLAB: Design and Implementation," SIAM J. Matrix Anal. Appl., Vol. 13, No. 1, January 1992, pp. 333-356.  gilbert92sparse.ps gilbert92sparse.pdf

Test matrices are found in Matrix Market  at National Institute of Standards and Technology (NIST).

1. Simple example: Compare reorderings!

Start with the matrix you get from a finite difference approximation of the Laplace equation. You get a grid by the command  G=numgrid and a matrix by  A=delsq(G)! Look at the matrix with spy(A).

Take an appropriate size, start with an L-membrane. This is the one that you see as logo for Matlab. Look at the grid matrix G and see how the points are ordered by columns.

You will get  permutation vectors for band width reduction (RCM) and minimal degree (MMD) by the calls pr=symrcm(A) and pm=symmmd(A). Substructuring, nested dissection, is not implemented, but there is an option in numgrid that gives that order for a square. Look at the reordered matrices with spy  and compare to what I showed in the lecture!

Look at the grid G reordered by Reversed Cuthill Mc Kee. You can use the routine  vector2grid as described in Extra tips.
Note that it cannot be used directly on the permutation vector pr, it must have the inverse permutation. It is simple to get the inverse permutation by doing the call
iv=1:n ; rp(pr)=iv ;
which gives the inverse permutation in the vector rp.

Does your result look like what I showed in the lecture?

Note: The Minimum Degree ordering of G does not look as I have described.


2. When is sparse factorization of advantage?

The sparse factorization will use much less storage space and fewer arithmetic operations than a full matrix code. On the other hand, it needs quite a lot of book keeping to track at which places fill in occurs.

Now we want to see when it is of advantage to use a sparse matrix code.

Matrix:  Take the matrix A as finite difference matrices over a L-membrane as in previous task.
Right hand side b: Take the vector b as a 1 (one) in one or a set of contigous positions in the center of the grid G.
Solution x: Plotted over the membrane, it will look like a tent with poles in those positions where b is one.
You can use the routine
X=v2g(x,G);
to get a matrix with the vector x spread over the grid G and plot it by the command mesh(X).

Experiment with sparse code: Let the number of grid points vary. Make up a table of the number of nonzeros in the original matrix A and the Cholesky factors for the original ordering and the reorderings RCM and MMD. Determine the permutations and measure the time needed for
  1. Factorization:    Compute the LU factors of the reordered matrix
  2. Solution:     Solve a system for a new right hand side b
Check the solution: Compute the residual r=Ax-b and list ||r||

Start with a moderate grid, say 20*20 points. When your code works increase the grid size until you either run out of memory or the experiment takes more than say 3 minutes. Record for which n that happens, and report which machine you use! It may be different on different workstations or PC:s.

Compare to a full matrix code
: Just call
     AF=full(A); 
and you get a full matrix. Do the same computations as in the previous task. Record the time and space needed, and report for which matrix sizes the full matrix code is faster than the sparse one. Be careful, the full matrix may need too much memory for a much smaller n than a sparse matrix! On my account, I got Out of memory for n just above 4000.

A note on timing: The Matlab clock ticks very slowly. You might need to run the shorter operations several times and divide the total time by the number of repeats.

3. General Sparse Matrices

I have stored some quite large matrices as Matlab files. Look at them and see how much fill in there is in Gaussian elimination with different reorderings. Note that these matrices are too large to store as full matrices! Do not print the result of the spy command in the report, it can be very space consuming.

Note that:

 Take one or more of the matrices:

  1. fleigAB.mat A twodimensional finite element stiffness and mass matrix generated by FEMLAB. It will probably behave like the finite difference matrices of previous task.
  2. A power network for western  USA bcspwr
  3. A VLSI circuit of a clock clock.mat Only one of the matrices, G, has many elements enough to be interesting, I think each element stands for a resistor. A VLSI circuit has a tree like structure with few cycles. This makes the matrices very sparse and algorithms that are built on level structures like RCM will give very little fill in.
  4. You may find another interesting matrix on Matrix Market. Get it and study it!
Good Tour!


Finished September 15, 2006 by Axel Ruhe