I cannot really be sure what you are trying to do, but doing a bit of
"surgery" on your code lets it run on a multicore Mac:
library(e1071)
library(snow)
library(pls)
data(gasoline)
X=gasoline$NIR
Y=gasoline$octane
NR=10
cost1=seq(0.5,30, length=NR)
sv.lin<- function(c) {
for (i in 1:NR) {
ind=sample(1:60,50)
gTest<- data.frame(Y=I(Y[-ind]),X=I(X[-ind,]))
gTrain<- data.frame(Y=I(Y[ind]),X=I(X[ind,]))
svm.lin <- svm(gTrain$X,gTrain$Y, kernel="linear",cost=c[i],
cross=5)
results.lin <- predict(svm.lin, gTest$X)
e.test.lin <- sqrt(sum((results.lin-gTest$Y)^2)/length(gTest$Y))
return(e.test.lin)
}
}
cl<- makeCluster(2, type="SOCK" )
clusterEvalQ(cl, library(e1071))
cost1=seq(0.5,30, length=NR)
clusterExport(cl,c("NR","Y","X", "cost1"))
# Pretty sure you need a copy of cost1 on each node.
RMSEP<-clusterApply(cl, cost1, sv.lin)
# I thought the second argument was the matrix or vector over which to
iterate.
stopCluster(cl)
# Since I don't know what the model meant, I cannot determine whehter
this result is interpretable>
> RMSEP
[[1]]
[1] 0.1921887
[[2]]
[1] 0.1924917
[[3]]
[1] 0.1885066
[[4]]
[1] 0.1871466
[[5]]
[1] 0.3550932
[[6]]
[1] 0.1226460
[[7]]
[1] 0.2426345
[[8]]
[1] 0.2126299
[[9]]
[1] 0.2276286
[[10]]
[1] 0.2064534
--
David Winsemius, MD
On Nov 18, 2009, at 7:09 AM, raluca wrote:
Hi Charlie,
Yes, you are perfectly right, when I make the clusters I should put
2, not
10 (it remained 10 from previous trials with 10 slaves).
cl<- makeCluster(2, type="SOCK" )
To tell the truth I do not understand very well what the 2nd
parameter for
clusterApplyLB() has to be.
If the function sv.lin has just 1 parameter, sv.lin(c), where c is
the cost,
how should I call clusterApplyLB?
? clusterApply LB(cl, ?,sv.lin, c=cost1) ?
Below, I am providing a working example, using the gasoline data
that comes
in the pls package.
Thank you for your time!
library(e1071)
library(snow)
library(pls)
data(gasoline)
X=gasoline$NIR
Y=gasoline$octane
NR=10
cost1=seq(0.5,30, length=NR)
sv.lin<- function(c) {
for (i in 1:NR) {
ind=sample(1:60,50)
gTest<- data.frame(Y=I(Y[-ind]),X=I(X[-ind,]))
gTrain<- data.frame(Y=I(Y[ind]),X=I(X[ind,]))
svm.lin <- svm(gTrain$X,gTrain$Y, kernel="linear",cost=c[i],
cross=5)
results.lin <- predict(svm.lin, gTest$X)
e.test.lin <- sqrt(sum((results.lin-gTest$Y)^2)/length(gTest$Y))
return(e.test.lin)
}
}
cl<- makeCluster(2, type="SOCK" )
clusterEvalQ(cl,library(e1071))
clusterExport(cl,c("NR","Y","X"))
RMSEP<-clusterApplyLB(cl,?,sv.lin,c=cost1)
stopCluster(cl)
cls59 wrote:
raluca 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!
Here is the code:
data <- data.frame(Y=I(Y),X=I(X))
data.X<-data$X
data.Y<-data$Y
Helping you will be difficult as we're only three lines into your
example
and already I have no idea what the data you are using looks like.
Example code needs to be fully reproducible-- that means a small
slice of
representative data needs to be provided or faked using an
appropriate
random number generator.
Some things did jump out at me about your approach and I've made some
notes below.
raluca wrote:
NR=10
cost1=seq(0.5,30, length=NR)
sv.lin<- function(cl,c) {
for (i in 1:NR) {
ind=sample(1:414,276)
hogTest<- data.frame(Y=I(data.Y[-ind]),X=I(data.X[-ind,]))
hogTrain<- data.frame(Y=I(data.Y[ind]),X=I(data.X[ind,]))
svm.lin <- svm(hogTrain$X,hogTrain$Y,
kernel="linear",cost=c[i],
cross=5)
results.lin <- predict(svm.lin, hogTest$X)
e.test.lin <- sqrt(sum((results.lin-hogTest$Y)^2)/
length(hogTest$Y))
return(e.test.lin)
}
}
cl<- makeCluster(10, type="SOCK" )
If your machine has two cores, why are you setting up a cluster
with 10
nodes? Usually the number of nodes should equal the number of
cores on
your machine in order to keep things efficient.
raluca wrote:
clusterEvalQ(cl,library(e1071))
clusterExport(cl,c("data.X","data.Y","NR","cost1"))
RMSEP<-clusterApplyLB(cl,cost1,sv.lin)
Are you sure this evaluation even produces results? sv.lin() is a
function
you defined above that takes two parameters-- "cl" and "c".
clusterApplyLB() will feed values of cost1 into sv.lin() for the
argument
"cl", but it has nothing to give for "c". At the very least, it
seems
like you would need something like:
RMSEP <- clusterApplyLB( cl, cost1, sv.lin, c = someVector )
raluca wrote:
stopCluster(cl)
Sorry I can't be very helpful, but with no data and no apparent way
to
legally call sv.lin() the way you have it set up, I can't
investigate the
problem to see if I get the same results you described. If you could
provide a complete working example, then there's a better chance that
someone on this list will be able to help you.
Good luck!
-Charlie
--
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