Performance Notes

Matrix Performance Notes

While the matrix interface is always identical, performance characteristics are implementation dependent. In general, performance of a matrix operation is a function of {data structure, density, type and kind of method arguments}. This library takes great care about performance. When in doubt about the detailed character of an operation, have a look at the source code.

In practice, sparse matrices are used for one of two reasons: To safe memory or to speed up computation. Hash based sparse matrices (SparseDoubleMatrix2D) are neither the smallest possible matrix representation nor the fastest. They implement a reasonable trade-off between performance and memory: Very good average performance on get/set operations at quite small memory footprint. They are also suited for special-purpose algorithms exploiting explicit knowledge about what regions are zero and non-zero, but not quite as good as other sparse matrix representations. For example, sparse linear algebraic matrix multiplies, inversions, etc. better work on sparse row compressed (RCDoubleMatrix2D). However, alternative sparse matrix representations are really only usable for special purposes, because their get/set performance can be very bad. In contrast, hash based sparse matrices are more generally applicable data structures.

Here is a list describing which combinations are particularly optimized. (F is used as shortcut for cern.jet.math.Functions)

General Remarks

Matrix-matrix and matrix-vector multiplication C = alpha*AxB + beta*C :

For good performance B,C may have any type. For A={SparseDoubleMatrix2D,RCDoubleMatrix2D} this is only fast if the density of A is small. For A={DenseDoubleMatrix2D} density does not matter. If A is dense and B is sparse, this is no problem, because even then the quick sparse mult is used.

DenseDoubleMatrix2D

Dense row major format. Essentially all methods highly optimized. This is almost always the implementation type to go for. It is also most easily to understand. The types below are only useful for very specific use cases.

RCDoubleMatrix2D

Sparse row-compressed format. Special-purpose implementation. Thus some operations very efficient, others quite slow. Essentially designed to support the fastest possible sparse matrix-matrix and matrix-vector multiplications as well as sparse linear algebra. Efficient methods are:
Operation Method Comment
read get,getQuick always
write set,setQuick

only fast if the matrix is really sparse and in a loop iterating upwards:
for (int i=0; i<rows; i++) { for (int j=0; j<columns; j++) { setQuick(i,j,...) ... }}

matrix-matrix and matrix-vector multiplication zMult see above in Section "General"
elementwise scaling assign(f) where f is one of {F.mult(a),F.div(a)} x[i,j] = x[i,j] {*,/} a
elementwise scaling assign(y,f) where f is one of {F.plus,F.minus, F.mult,F.div, F.plusMult(a),F.minusMult(a)} x[i,j] = x[i,j] {+,-,*,/} y[i,j]
x[i,j] = x[i,j] {+,-} y[i,j] {*,/} a
copying assign(othermatrix) always fast, best if othermatrix is a RCDoubleMatrix2D
iteration forEachNonzero(function) most of the time the preferred way for iteration and modification
     

SparseDoubleMatrix2D

Sparse hash format. General-purpose sparse implementation. Designed for efficient random access to sparse structures. Thus, performance more balanced than RCDoubleMatrix2D. Never really slow, often faster than RCDoubleMatrix2D, sometimes slightly slower. Efficient methods are:
Operation Method Comment
read get,getQuick always
write set,setQuick

always

matrix-matrix and matrix-vector multiplication zMult slightly slower than RCDoubleMatrix when size is large
elementwise scaling assign(f) where f is one of {F.mult(a),F.div(a)} x[i,j] = x[i,j] {*,/} a
elementwise scaling assign(y,f) where f is one of {F.plus,F.minus, F.mult,F.div, F.plusMult(a),F.minusMult(a)} x[i,j] = x[i,j] {+,-,*,/} y[i,j]
x[i,j] = x[i,j] {+,-} y[i,j] {*,/} a
copying assign(othermatrix) best if othermatrix is a SparseDoubleMatrix2D
iteration forEachNonzero(function) often the preferred way for iteration and modification