Ah. Indeed, this is from the glmulti. I had not realized there would be
problems using Java. Is there a way around this to still use a multicore
approach? For what other packages that use multiple cores will this not be a
problem?
-Jarrett
On Aug 12, 2010, at 11:02 AM, Thomas Lumley wrote:
> On Thu, 12 Aug 2010, Jarrett Byrnes wrote:
>
>> I'm running r 2. on a mac running 10.6.4 and a dual-core macbook pro. I'm
>> having a funny time with multicore. When I run it with 2 cores, mclapply, R
>> borks with the following error.
>>
>> The process has forked and you cannot use this CoreFoundation functionality
>> safely. You MUST exec().
>> Break on
>> __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__()
>> to debug.
>>
>>
>> If, however, I crank the # of cores back to 1, it runs just fine.
>>
>> The code looks as follows:
>>
>>
>> mmi_fits<-mclapply(responses, function(a_response){
>> gmult<-glmulti(glm(make_formula(a_response, sp),
>> data=df, family=binomial))
>> return(gmult)
>> },
>> mc.cores=2)
>
> You don't say what glmulti() is. If you mean the function from glmulti
> package, that package uses Java and rjava, and it wouldn't be altogether
> surprising if the connection to Java or the Java environment reacted badly to
> being forked.
>
> -thomas
>
> Thomas Lumley
> Professor of Biostatistics
> University of Washington, Seattle
>
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