On 29/04/2013 2:16 PM, Kaiyin Zhong (Victor Chung) wrote:
Hi, Uwe.
I still don't get how this can be done correctly. Here is what I tried.
In the file funcs.R, define these functions:
library('modeest')
x = vector(length=500)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (n>k) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
Then do the following:
library('snow')
cl = makeCluster(rep('localhost', 12), 'SOCK')
clusterSetupRNG(cl)
clusterEvalQ(cl, 'source("funcs.R")')
The expression being evaluated there is a string,
'source("funcs.R")'
You want an expression, e.g.
clusterEvalQ(cl, source("funcs.R"))
Duncan Murdoch
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
print(r)
}
testK()
stopCluster(cl)
The error still pops up:
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: could not find function "predR"
Best regards,
Kaiyin ZHONG
------------------------------
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges <lig...@statistik.tu-dortmund.de
> wrote:
>
>
> On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
>
>> Thanks for the reply.
>>
>> How can i make the functions known to all nodes?
>>
>
> See ?clusterEvalQ
>
> you may also want to try the parallel packages.
>
> Best,
> Uwe Ligges
>
>
>
>
>> Best regards,
>>
>> Kaiyin ZHONG
>> ------------------------------**------------------------------**
>> ------------
>> FMB, Erasmus MC
>> k.zh...@erasmusmc.nl <mailto:k.zh...@erasmusmc.nl>
>> kindlych...@gmail.com <mailto:kindlych...@gmail.com>
>>
>>
>>
>> On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
>> <lig...@statistik.tu-dortmund.**de <lig...@statistik.tu-dortmund.de>
>> <mailto:lig...@statistik.tu-**dortmund.de<lig...@statistik.tu-dortmund.de>>>
>> wrote:
>>
>>
>>
>> On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
>>
>> Here is the code, assuming 8 cores in the cpu.
>>
>> library('modeest')
>> library('snow')
>>
>> cl = makeCluster(rep('localhost', 8), 'SOCK')
>> x = vector(length=50)
>> x = sapply(x, function(i) i=sample(c(1,0), 1))
>>
>> pastK = function(n, x, k) {
>> if (n>k) { return(x[(n-k):(n-1)]) }
>> else {return(NA)}
>> }
>>
>> predR = function(x, k) {
>> pastList = lapply(1:length(x), function(n) pastK(n, x, k))
>> pred = sapply(pastList, function(v) mfv(v)[1])
>> ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
>> <http://is.na>(pred)))
>>
>> }
>>
>> testK = function() {
>> k = seq(3, 25, 2)
>> r = parSapply(cl, k, function(i) predR(x, i))
>> # r = sapply(k, function(i) predR(x, i))
>> }
>>
>> r = testK()
>> stopCluster(cl)
>>
>> Here is the error:
>> Error in checkForRemoteErrors(val) :
>> 8 nodes produced errors; first error: could not find
>> function "predR"
>>
>>
>>
>> predR is not yet known on all nodes, just on the master. You have to
>> tell the nodes about the definition first.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>>
>> Best regards,
>>
>> Kaiyin ZHONG
>> ------------------------------
>>
>> FMB, Erasmus MC
>> k.zh...@erasmusmc.nl <mailto:k.zh...@erasmusmc.nl>
>> kindlych...@gmail.com <mailto:kindlych...@gmail.com>
>>
>> [[alternative HTML version deleted]]
>>
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>> R-help@r-project.org <mailto:R-help@r-project.org> mailing list
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>>
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>> >
>> PLEASE do read the posting guide
>>
http://www.R-project.org/__**posting-guide.html<http://www.R-project.org/__posting-guide.html>
>>
>>
<http://www.R-project.org/**posting-guide.html<http://www.R-project.org/posting-guide.html>
>> >
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
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