[R] undefined S4 class in parallel computing at snowfall

[Martin Morgan]

Hi --

On 06/28/2012 04:51 PM, Edwin Sun wrote:
> Dear All,
>
> I have a question of how to export S4 class specification to
> clusters/workers in parallel computing. The package I used is snowfall. The
> problem is reproducible as follows. Any hint is greatly appreciated.
>
> Edwin Sun
>
> === begin ===========
> library(snowfall)
> sfInit(parallel = TRUE, cpus = 2)
> setClass("catt", representation(aa = "numeric"))
> setClass("dogg", representation(bb = 'character', cc = "catt"))
> f1<- function(y1) { new('catt', aa = y1 + 1) }
> f3<- function(y2, y3) { new('dogg', bb=c(y2, 'GA'), cc = f1(y3)) }
> dat<- 1:5
> f1(dat)
> f3('NY', dat)
> sapply(c("state1", 'state2', 'state3'), f3, dat)
> sfExportAll()

I think it makes sense to actually define the classes (and other 
cluster-specific objects) on the cluster;

   sfInit(parallel = TRUE, cpus = 2)
   sfClusterEval({
       setClass("catt", representation(aa = "numeric"))
       setClass("dogg", representation(bb = 'character', cc = "catt"))
       f1 <- function(y1) new('catt', aa = y1 + 1)
   })

   f3 <- function(y2, y3) { new('dogg', bb=c(y2, 'GA'), cc = f1(y3)) }
   dat <- 1:5
   sfSapply(c("s1", 's2', 's3'), f3, dat)

It's true that setClass creates variables in the global environment (see 
the .__C__* objects in the output of ls(all=TRUE)) and that sfExportAll 
seems not to export these, so that you could export them explicitly, 
e.g., sfExport(list=ls(all=TRUE)), but this assuming that these 
variables are the only side effect of calling setClass. Maybe the 
'setup' actions are defined in a separate script setup.R that 
sfClusterEval (and the main program, if that's relevant) source, 
sfClusterEval(source("setup.R")).

Martin

> sfClusterEval(ls())
> sfSapply(c("s1", 's2', 's3'), f3, dat)
> sfStop()
>
> # sfSapply generates the following error
> #    Error in checkForRemoteErrors(val) :
> #      2 nodes produced errors; first error: "dogg" is not a defined class
> === end =============
>
> --
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>
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