Hi,
On Sat, Apr 9, 2011 at 5:03 AM, Alaios <ala...@yahoo.com> wrote:
> Dear all,
> I would like to ask your help understand the subsequent steps for making my
> program faster.
>
> The following code:
> Gauslist<-array(data=NA,dim=c(dimx,dimy,dimz))
> for (i in c(1:dimz)){
> print(sprintf('Creating the %d map',i));
> Gauslist[,,i]<-f <- GaussRF(x=x, y=y, model=model,
> grid=TRUE,param=c(mean,variance,nugget,scale,Whit.alpha))
> }
>
>
> creates 100 GaussMaps (each map is of 256*256 dim) and stores them in a
> matrix called Gauslist.
>
> This process takes too long, so I was thinking if you can help me understand
> what should I do to make it run in parallel (in work there is a system with
> 16 cores).
>
> There is mclapply (parralel version of lapply) . If I make run my code run
> with lapply then I will be able to run it with mclapply also (they have same
> syntax).
> If I understand it correct the sequence for doing that is to understand the
> following:
>
> for..loop->lapply->mcapply
>
> Can you please help me understand if my for loop can be converted to lapply
> or not?
Your loop can be converted quite easily.
The lapply function simply takes an object to iterate over as its
first argument (this can be a list of things, a vector of things,
etc.) and a function to apply to each element in the iteration.
`lapply` will build a list of results that your function returns for
each element.
A simple example is to iterate over the words in a character vector
and return how many characters are in each word.
R> words <- c('cat', 'dog's, 'people')
R> sizes <- lapply(words, function(x) nchar(x))
R> sizes
[[1]]
[1] 3
[[2]]
[1] 4
[[3]]
[1] 6
So in your example:
> for (i in c(1:dimz)){
> print(sprintf('Creating the %d map',i));
> Gauslist[,,i]<-f <- GaussRF(x=x, y=y, model=model,
> grid=TRUE,param=c(mean,variance,nugget,scale,Whit.alpha))
> }
Could be something like:
gauslist <- lapply(1:dimz, function(i) {
GaussRF(x=x, y=y, model=model, ... WHATEVER ELSE)
})
using mclapply would be exactly the same, except replace lapply with mclapply.
Actually, is it correct that you aren't doing anything different in
the iterations of the for loop -- I mean, nothing in your code really
depends on your value for `i`, right?
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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