[Rd] problem using rJava with parallel::mclapply

[Simon Urbanek]

On Nov 11, 2013, at 12:40 PM, Karl Forner <karl.forner at gmail.com> wrote:

> Dear all,
> 
> I got an issue trying to parse excel files in parallel using XLConnect, the
> process hangs forever.
> Martin Studer, the maintainer of XLConnect kindly investigated the issue,
> identified rJava as a possible cause of the problem:
> 
> This does not work (hangs):
> library(parallel)
> require(rJava)
> .jinit()
> res <- mclapply(1:2, function(i) {
>      J("java.lang.Runtime")$getRuntime()$gc()
>      1
>  }, mc.cores = 2)
> 
> but this works:
> library(parallel)
> res <- mclapply(1:2, function(i) {
>  require(rJava)
>  .jinit()
>  J("java.lang.Runtime")$getRuntime()$gc()
>  1
> }, mc.cores = 2)
> 
> To cite Martin, it seems to work with mclapply when the JVM process is
> initialized after forking.
> 
> Is this a bug or a limitation of rJava ?

It’s a limitation of the Java runtime - you cannot fork a JVM. This is true for most libraries that use long-lived threads or any kind if UI (see the warnings in mcfork).

Cheers,
Simon



> Or is there a good practice for rJava clients to avoid this problem ?
> 
> Best,
> Karl
> 
> P.S.
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 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
> 
> loaded via a namespace (and not attached):
> [1] tools_3.0.1
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>