[R-sig-hpc] foreach package - Parallel Apply (Section 5.2 in Vignettes foreach Manual)

[Dirk Eddelbuettel]

On 10 December 2009 at 09:12, Debabrata Midya wrote:
| Dear hpc users,
|  
| Thanks in advance.
|  
| I am using R 2.10.0 on Windows XP, Intel(R) Core(TM) 2 Duo CPU E8400 @3.00GHz 2.99GHz, 1.96 of RAM.
|  
| I need you assistance to solve the problem below:
|  
| foreach package - Parallel Apply (Section 5.2 in Vignettes foreach Manual)
|  
| "Now we're only sending any given column of the matrix to one parallel execution worker. But it
| would be even more efficient if we sent the matrix in bigger chunks. To do that, we use a function
| called iblkcol that returns an iterator that will return multiple columns of the original matrix.
| That means that the R expression will need to execute the user's function once for every column in
| its submatrix".
|  
| The function below is from the above Vigenette:
|  
| applyKernel <- function(newX, FUN, d2, d.call, dn.call = NULL, ...) {
|  foreach(x = iblkcol(newX, 3), .combine = "c", .packages = "foreach") %dopar%
|  {
|     foreach(i = 1:ncol(x)) %do% FUN(array(x[, i], d.call, dn.call), ...)
|  }
| }
|  
| > applyKernel(matrix(1:16, 4), mean, 4, 4)
|  
| Error in eval(expr, envir, enclos) : could not find function "iblkcol"
|  
| How can I get this function?

I am not sure how familiar you are with vignettes but the key is that they
contain all the code.  So here it is, straight from the package sources. The
<<...>> and @ lines are the Sweave markers, R code is in-between.

<<ex13.iter, results=hide, echo=FALSE>>=
iblkcol <- function(a, chunks) {
  n <- ncol(a)
  i <- 1

  nextElem <- function() {
    if (chunks <= 0 || n <= 0) stop('StopIteration')
    m <- ceiling(n / chunks)
    r <- seq(i, length=m)
    i <<- i + m
    n <<- n - m
    chunks <<- chunks - 1
    a[,r, drop=FALSE]
  }

  structure(list(nextElem=nextElem), class=c('iblkcol', 'iter'))
}
nextElem.iblkcol <- function(obj) obj$nextElem()
@


Use the sources for R and its packages. They are a much-underused treasure.

Dirk

|  
| Once again, thank you very much for the time you have given.
| 
|  
| I am looking forward for your reply.
|  
| Regards,
|  
| Deb
| 
| 	[[alternative HTML version deleted]]
| 
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