[R] parSapply can't find function

[David Winsemius]

On Apr 29, 2013, at 11:16 AM, 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")')

Are you sure those outer single quote marks are not the problem?

-- 
David.


> 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.zhong at erasmusmc.nl
> kindlychung at gmail.com
> 
> 
> On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges <ligges at 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.zhong at erasmusmc.nl <mailto:k.zhong at erasmusmc.nl>
>>> kindlychung at gmail.com <mailto:kindlychung at gmail.com>
>>> 
>>> 
>>> 
>>> On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
>>> <ligges at statistik.tu-dortmund.**de <ligges at statistik.tu-dortmund.de>
>>> <mailto:ligges at statistik.tu-**dortmund.de<ligges at 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.zhong at erasmusmc.nl <mailto:k.zhong at erasmusmc.nl>
>>>        kindlychung at gmail.com <mailto:kindlychung at gmail.com>
>>> 
>>>                 [[alternative HTML version deleted]]
>>> 
>>>        ______________________________**__________________
>>>        R-help at r-project.org <mailto:R-help at r-project.org> mailing list
>>>        https://stat.ethz.ch/mailman/_**_listinfo/r-help<https://stat.ethz.ch/mailman/__listinfo/r-help>
>>> 
>>>        <https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>>>> 
>>>        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.
>>> 
>>> 
>>> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA