svd() very slow for wide matrix X but not for t(X) (PR#1761)
gregory_r_warnes@groton.pfizer.com
gregory_r_warnes@groton.pfizer.com
Tue, 9 Jul 2002 17:40:08 +0200 (MET DST)
Hi All,
A colleague has just pointed out to me prcomp is *much* slower and memory
intensive when applied to very wide matrixes than when applied to the
transpose of the same matrix. In looking for the reason, I discovered that
that the singular value decomposition function svd is the primary culprit:
On my Solaris workstation, under R 1.5.1:
> nr <- 50
> nc <- 1000
> x <- matrix( rnorm( nr*nc), nrow=nr, ncol=nc )
> tx <- t(x)
>
> # SVD directly on matrix is SLOW
> system.time( val.x <- svd(x)$u )
[1] 5.41 0.00 5.62 0.00 0.00
>
> # SVD directly on t(matrix) is FAST
> system.time( val.tx <- svd(tx)$v )
[1] 0.60 0.00 0.61 0.00 0.00
>
> # but the results are (essentially) identical
> max( abs(val.x) - abs(val.tx) )
[1] 4.201361e-13
The speed difference gets worse as the number of columns grows.
Here is a simple patch to $R_SRC/src/library/base/R/svd.R that works around
the problem. It simply checks whether the matrix is wider than it is long,
and if so, calls itself on the transpose of the matrix, and then exchanges
the returned u and v matrixes.
*** svd.R.orig Tue Jul 9 11:06:46 2002
--- svd.R Tue Jul 9 11:06:49 2002
***************
*** 5,10 ****
--- 5,17 ----
n <- dx[1]
p <- dx[2]
if(!n || !p) stop("0 extent dimensions")
+
+ if( p > n ) # compute on the transpose if wide
+ {
+ s <- svd( t(x), nv=nu, nu=nv)
+ return( d=s$d, u=s$v, v=s$u )
+ }
+
if (is.complex(x)) {
res <- La.svd(x, nu, nv)
return(list(d = res$d, u = if(nu) res$u, v = if(nv)
Conj(t(res$vt))))
With this patch the speed is almost the same whether called on x or tx:
> system.time( val.x <- svd(x)$u )
[1] 0.62 0.00 0.66 0.00 0.00
> system.time( val.tx <- svd(tx)$v )
[1] 0.60 0.00 0.86 0.00 0.00
> identical( val.x, val.tx )
[1] TRUE
This is fine for my purposes, but perhaps someone familiar with the FORTRAN
code should see why its performance is so unbalanced.
Extra details:
> version
_
platform sparc-sun-solaris2.8
arch sparc
os solaris2.8
system sparc, solaris2.8
status Patched
major 1
minor 5.1
year 2002
month 06
day 18
language R
>
-Greg Warnes
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