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

[Martin Morgan]

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
>>
>>
>>>
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>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109