[R-sig-hpc] Error in UseMethod("stopCluster") : no applicable method for 'stopCluster' ...

[Martin Morgan]

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
>>>>
>>>>
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-hpc mailing list
>>>>> R-sig-hpc at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>>
>>>
>
> --
> ETH Zurich
> Dr. Marius Hofert
> RiskLab, Department of Mathematics
> HG E 65.2
> Rämistrasse 101
> 8092 Zurich
> Switzerland
>
> Phone +41 44 632 2423
> http://www.math.ethz.ch/~hofertj
>


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