On Nov 18, 2009, at 12:35 PM, Max Kuhn wrote:

On Tue, Nov 17, 2009 at 6:01 PM, raluca <uca...@hotmail.com> wrote:

Hello,

Is the first time I am using SNOW package and I am trying to tune the cost parameter for a linear SVM, where the cost (variable cost1) takes 10 values
between 0.5 and 30.

I have a large dataset and a pc which is not very powerful, so I need to
tune the parameters using both CPUs of the pc.

Somehow I cannot manage to do it. It seems that both CPUs are fitting the model for the same values of cost1, I guess the first 5, but not for the
last 5.

Please, can anyone help me! :-((

This is pretty easy to do with the train() funciton in the caret
package. From ?train, here is an example for a different data set

library(caret)
library(snow)
library(mlbench)

data(BostonHousing)

mpiCalcs <- function(X, FUN, ...)
+   {
+     theDots <- list(...)
+     parLapply(theDots$cl, X, FUN)
+   }

library(snow)
cl <- makeCluster(5, "MPI")

## 50 bootstrap models distributed across 5 workers
mpiControl <- trainControl(workers = 5,
+                            number = 50,
+                            computeFunction = mpiCalcs,
+                            computeArgs = list(cl = cl))
set.seed(1)
usingMPI <-  train(medv ~ .,
+                    data = BostonHousing,
+                    "svmLinear",
+ tuneGrid = data.frame(.C = seq(.5, 30, length = 10)),
+                    trControl = mpiControl)

stopCluster(cl)
[1] 1


Well, that _was_ interesting. I submitted this job modified to set the number of clusters and workers set to eight on a Mac Pro (with 8 cores and 16 GB) and watched the cpu usage as reported by Activity Monitor.app. The cpu activity is divided into system and user and over the course of that run (which took a several minutes) the system proportion gradually rose o about 75% of total.

Was it your expectation that this task was comparable in complexity to that offered by the OP?

And should I be looking for a tangible result? Looking at usingMPI with str() I see a 50 x 506 matrix, no it's a list, usingMPI%control $index, of integers as well as quite a bit of other material that looks like input and side-effects of the multi-processor activity or setup.

--
David


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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