Error in UseMethod("stopCluster") : no applicable method for 'stopCluster' ...

That's interesting, the same script (with the same call) fails for me. I had to
put sessionInfo() earlier in the script so that it is printed. Below is the
output of the script. 

I further experimented with it, it runs if I additionally put in
'library(snow)'. I thought I don't need that if I use 'parallel' (?). Hmmm...

Cheers,

Marius

library(parallel)

sessionInfo()

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-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] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

ex <- function() {

+      cl <- makeCluster(detectCores(), type="MPI")
+      stopCluster(cl)
+ }

res <- ex()

Loading required package: Rmpi
	4 slaves are spawned successfully. 0 failed.
Error in NextMethod() : 'NextMethod' called from an anonymous function
Calls: ex ... stopCluster.spawnedMPIcluster -> <Anonymous> -> NextMethod
Execution halted


Martin Morgan <mtmorgan at fhcrc.org> writes:

On 09/22/2012 08:52 AM, Marius Hofert wrote:

Dear Martin,

Thanks for your help. I tried to put in library(parallel) in your example (see
below), but I still obtain

,----
| Error in NextMethod() : 'NextMethod' called from an anonymous function
`----

Do you know why?

Cheers,

Marius

grid <- expand.grid(a=1:4, b=2:10)
ngrid <- nrow(grid)
f <- function(x) sum(x)

library(parallel)

ex <- function() {
     cl <- makeCluster(detectCores(), type="MPI")
     stopCluster(cl)
}

res <- ex()

For the file script.R

library(parallel)
ex <- function() {
    cl <- makeCluster(detectCores(), type="MPI")
    stopCluster(cl)
}
res <- ex()
sessionInfo()

The command

  R --vanilla -f script.R

'works for me' with

sessionInfo()

R version 2.15.1 Patched (2012-08-26 r60438)
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] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Rmpi_0.6-1

loaded via a namespace (and not attached):
[1] snow_0.3-10

Martin Morgan <mtmorgan at fhcrc.org> writes:

On 9/21/2012 12:16 PM, Marius Hofert wrote:

Dear Martin,

thanks for helping. Is there a solution without explicitly loading snow/parallel
with library()/require()? I forgot to say, I was hoping for such a solution.

Not that I know of. Write a package and importFrom(parallel, stopCluster)?
Martin

Cheers,

Marius

Martin Morgan <mtmorgan at fhcrc.org> writes:

On 09/21/2012 12:47 AM, Marius Hofert wrote:

Dear expeRts,

If I run the minimal example below, I obtain:

Loading required package: Rmpi
Loading required package: grDevices
Loading required package: grDevices
Loading required package: grDevices
Loading required package: grDevices
	4 slaves are spawned successfully. 0 failed.
Error in UseMethod("stopCluster") :
     no applicable method for 'stopCluster' applied to an object of class "c('spawnedMPIcluster', 'MPIcluster', 'cluster')"

However, if I run the body of the function (linewise; without calling the
function), everything works. Why is that so?

Cheers,

Marius


grid <- expand.grid(a=1:4, b=2:10)
ngrid <- nrow(grid)
f <- function(x) sum(x)

ex <- function() {
       cl <- snow::makeCluster(parallel::detectCores(), type="MPI")
       on.exit(snow::stopCluster(cl))
       RNGkind("L'Ecuyer-CMRG")
       parallel::clusterExport(cl, varlist=c("f", "grid"))
       parallel::clusterApply(cl, seq_len(ngrid), function(i) f(grid[i,]))
}

res <- ex()

An even more minimal example is

    ex <- function() {
        cl <- snow::makeCluster(parallel::detectCores(), type="MPI")
        snow::stopCluster(cl)
    }
    res <- ex()

To be clear, there is no library(snow) in the script, and on.exit() is not
relevant. The reason is that snow::stopCluster is an S3 generic, and on the help
page ?NextMethod we have


       Namespaces can register methods for generic functions.  To support
       this, 'UseMethod' and 'NextMethod' search for methods in two
       places: first in the environment in which the generic function is
       called, and then in the registration data base for the environment
       in which the generic is defined (typically a namespace).  So
       methods for a generic function need to be available in the
       environment of the call to the generic, or they must be
       registered.  (It does not matter whether they are visible in the
       environment in which the generic is defined.)

There are no stopCluster methods defined in the calling namespace (i.e., your
script) and since there has been no call to library(snow), there is no snow
namespace to search and hence no method to be found.

The solution is to add

    library(snow)

to the script (or better library(parallel) and use the 'parallel' library
throughout).

Martin