Re: [R] help with parallel processing code

2011-10-31 Thread Max Kuhn
I'm not sure what you mean by full code or the iteration. This uses foreach to parallelize the loops over different tuning parameters and resampled data sets. The only way I could set to split up the parallelism is if you are fitting different models to the same data. In that case, you could launc

Re: [R] help with parallel processing code

2011-10-28 Thread 1Rnwb
the part of the question dawned on me now is, should I try to do the parallel processing of the full code or only the iteration part? if it is full code then I am at the complete mercy of the R help community or I giveup on this and let the computation run the serial way, which is continuing from p

Re: [R] help with parallel processing code

2011-10-27 Thread Max Kuhn
I have had issues with some parallel backends not finding functions within a namespace for packages listed in the ".packages" argument or explicitly loaded in the body of the foreach loop. This has occurred with MPI but not with multicore. I can get around this to some extent by calling the functio

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
If i understand correctly you mean to write the line as below: foreach(icount(itr),.combine=combine,.options.smp=smpopts,.packages='MASS')%dopar% -- View this message in context: http://r.789695.n4.nabble.com/help-with-parallel-processing-code-tp3944303p3945954.html Sent from the R help mailin

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
yes the library(MASS) was loaded. -- View this message in context: http://r.789695.n4.nabble.com/help-with-parallel-processing-code-tp3944303p3945972.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list ht

Re: [R] help with parallel processing code

2011-10-27 Thread Dennis Murphy
Did you load the class package before calling lda()? Dennis On Thu, Oct 27, 2011 at 10:14 AM, 1Rnwb wrote: > my modification gives me error >>  rows<- c(1:nrow(mat)) >>  scores <- c() >>  labels <-c() >>  itr<-1000 >>  chnksz<-ceiling(itr/getDoParWorkers()) >> smpopt=list(chunkSize=chnksz) >>  f

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
my modification gives me error > rows<- c(1:nrow(mat)) > scores <- c() > labels <-c() > itr<-1000 > chnksz<-ceiling(itr/getDoParWorkers()) > smpopt=list(chunkSize=chnksz) > foreach(icount(itr),.combine=cbind,.options.smp=smpopts)%dopar% + { + train <- sample(rows, length(rows)-1) + label =

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
sorry for noise the simulated data should be like this d=data.frame(replicate(9, rnorm(40)+10),rep(c('y','n'),20)) colnames(d)<-c("LEPTIN","SAA","PTH","sEGFR","IGFBP6","MMP2","OPG","IGFBP3","PDGFAABB","group") -- View this message in context: http://r.789695.n4.nabble.com/help-with-parallel-pr

[R] help with parallel processing code

2011-10-27 Thread 1Rnwb
Hello R gurus, I have the code below for which i need help and pointers to make it run in parallel on a dual core win7 computer with R 2.13.x, using foreach, iterators,doMC. library(scatterplot3d) # Loads 3D library. library(fields) library(MASS) library(ROCR) library(verification) library(caret)