[BioC] snow library, question on clusterExport

[mattia pelizzola]

Hi,

I have a simple function:

> library(snow)
> fun2=function() {
+ cl=makeCluster(3)
+ Mat=matrix(2:10,3,3)
+ fun3=function(startInd, endInd=3, data=Mat) {Mat[startInd:endInd,]}
+ print(clusterApplyLB(cl, 1:3, fun3))
+ stopCluster(cl)
+ }

that is working fine:

> fun2()
[[1]]
     [,1] [,2] [,3]
[1,]    2    5    8
[2,]    3    6    9
[3,]    4    7   10

[[2]]
     [,1] [,2] [,3]
[1,]    3    6    9
[2,]    4    7   10

[[3]]
[1]  4  7 10

now, if I run the same commands outside the function:

> cl=makeCluster(3)
> Mat=matrix(2:10,3,3)
> fun3=function(startInd, endInd=3, data=Mat) {Mat[startInd:endInd,]}
> print(clusterApplyLB(cl, 1:3, fun3))
Error in checkForRemoteErrors(val) :
  3 nodes produced errors; first error: object 'Mat' not found

so I figured out I have to export 'Mat' on the cluster nodes:

> clusterExport(cl, 'Mat')
> print(clusterApplyLB(cl, 1:3, fun3))
[[1]]
     [,1] [,2] [,3]
[1,]    2    5    8
[2,]    3    6    9
[3,]    4    7   10

[[2]]
     [,1] [,2] [,3]
[1,]    3    6    9
[2,]    4    7   10

[[3]]
[1]  4  7 10

I still do not understand why clusterExport is NOT necessary within
the function 'fun2' and actually it would give an error:

> rm(Mat)
> fun2=function() {
+ cl=makeCluster(3)
+ Mat=matrix(2:10,3,3)
+ clusterExport(cl, 'Mat')
+ fun3=function(startInd, endInd=3, data=Mat) {Mat[startInd:endInd,]}
+ print(clusterApplyLB(cl, 1:3, fun3))
+ stopCluster(cl)
+ }
> fun2()
Error in get(name, env = .GlobalEnv) : object 'Mat' not found


I found clusterExport to be the solution for a more complex example,
can I can't make it working within a function.
What is it happening here with clusterExport? and how can I export an
object that is not on my globalEnv but rather is created within a
function?

many thanks!

mattia

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] snow_0.3-3