Thanks all for the tips. So if I'm summarizing right:

 * Hama and Spark are designed for distributed computing. Given that
   our need is for small matrices (usually no more than 5x5),
   distributed computing would probably be too much. However I keep
   Hama and Spark in mind for the SIS "Grid Coverage" (or Raster)
   processing part, to come later.
 * JBlas seems to be JNI wrappers around LAPACK and BLAS Fortran
   libraries. For small matrix, the JNI cost may be larger than the
   benefit. I will keep JBlas in mind for some computations that
   require large matrix, but those computations are not expected to
   occur in the "referencing" part of SIS.
 * Other libraries under compatible license include Apache Commons Math
   [1] and JAMA [2].


Given that Apache Commons is a large library (the JAR file is 1.6 Mb) while JAMA is very small and focused on Matrix only (a 36.5 kb file), I would be tempted to propose JAMA. Is there any though on that?


    Martin


[1] http://commons.apache.org/proper/commons-math/
[2] http://math.nist.gov/javanumerics/jama/

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