Re: [R] sparse matrix tools

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Mon 03 Jul 2006 - 17:44:38 EST

>>>>> "JJTh" == Thaden, John J <ThadenJohnJ@uams.edu>
>>>>> on Sun, 2 Jul 2006 07:38:21 -0500 writes:

    JJTh> Dear R-Help list: I'm using the Matrix library to
    JJTh> operate on 600 X ~5000 element unsymmetrical sparse
    JJTh> arrays. So far, so good, but if I find I need more
    JJTh> speed or functionality, 

Can you be more specific?
Functionality:

   For asymmetric matrices, in our view, the most important gap to    fill is the LU decomposition and hence solve() features.

Speed: Are you sure the time your R code spends is spent in

       functions from "Matrix"?  {Did you use 'Rprof()' ?}
       If yes, which ones?


    JJTh> how hard would it be to
    JJTh> utilize other sparse matrix toolsets from within R,
    JJTh> say MUMPS, PARDISO or UMFPACK, that do not have
    JJTh> explicit R interfaces? More information on these is     JJTh> available here
    JJTh> www.cise.ufl.edu/research/sparse/umfpack/
    JJTh> www.computational.unibas.ch/cs/scicomp/software/pardiso
    JJTh> www.enseeiht.fr/lima/apo/MUMPS/ 

>From these, only the first one is open source.
Unfortunately, the PARDISO people seem to believe in money making with scientific software -- a particular shame for since they only work at most an hour away from me. MUMPS is said to be "public domain", but then you only get it after filling out a web form and only for a specific hardware. Also, it is about massively parallel computation, very interesting for sparse matrices, but AFAIK not yet in our main focus.

UMFPACK is different, and even ships with the Matrix package, because we have planned to interface to it, but haven't yet got to that. What parts of UMFPACK functionality would you be interested in ?

    JJTh> and in these reviews

    JJTh> ftp://ftp.numerical.rl.ac.uk/pub/reports/ghsNAGIR20051r1.pdf     JJTh> http://www.cise.ufl.edu/research/sparse/codes/

    JJTh> neither of which reviewed the R Matrix package, unfortunately.

    JJTh> Thanks, - John Thaden, Ph.D., U. Arkansas for     JJTh> Med. Sci., Little Rock.

Regards,
Martin Maechler, ETH Zurich



R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Jul 03 17:48:11 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Tue 04 Jul 2006 - 00:13:55 EST.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.