[Rd] Exporting a method to a cluster object
Philip Leifeld
philip.leifeld at ipw.unibe.ch
Tue Nov 17 18:18:03 CET 2015
Hi,
This is my first message to this list. It would be great if people here
could help me with the following problem (self-contained code example
below):
I have a list of matrices and would like to apply a summary function to
the matrices in the list. The matrices represent social networks,
therefore I need to apply some specialized summary functions provided by
the ergm package. These summary statistics are contained in a summary
method. I can write a function as a wrapper around this summary method
and use lapply to apply the function to the list of matrices. This gives
me the result I want:
[,1] [,2] [,3] [,4] [,5]
edges 94 94 94 94 94
dsp1 227 227 227 227 227
However, when I try to parallelize this by using parLapply or parSapply
from the parallel package, the results look weird:
[,1] [,2] [,3] [,4] [,5]
Length "3" "3" "3" "3" "3"
Class "formula" "formula" "formula" "formula" "formula"
Mode "call" "call" "call" "call" "call"
And when I export summary.statistics, which is used inside my wrapper
function, I get an error message:
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: could not find function
"summary.statistics"
Do I have to export the summary method that is provided by the ergm
package to the cluster object? If so, how? The following code is a
self-contained example.
##########
library("ergm")
library("parallel")
# create list of matrices
m <- matrix(rbinom(900, 1, 0.1), nrow = 30)
l <- list(m, m, m, m, m)
# write wrapper function that computes results
fun <- function(mat) {
s <- summary(mat ~ edges + dsp(1))
return(s)
}
cl <- makePSOCKcluster(2) # create cluster object
test1 <- sapply(l, fun) # works!
test2 <- parSapply(cl, l, fun) # problem: results look weird!
clusterExport(cl, varlist = "summary.statistics")
test3 <- parSapply(cl, l, fun) # error!
##########
I found a solution somewhere in a forum:
clusterCall(cl, function() library("ergm"))
However, as I'd like to use the code in a package, the CRAN check tells
me that using library calls inside a package is uncool. So I guess there
must be another solution?
Thanks in advance for any hints.
Best,
Philip
(University of Bern)
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