R help - Nov 2005 - random forests and memory allocation

Dear all,

I am trying to run a random forest on a 4-class dataset with 10 215 variables.
Whatever the number of trees (I was thinking of combining the trees), I 
first got the error on Windows:

Error: cannot allocate vector of size 407562 Kb
In addition: Warning messages:
1: Reached total allocation of 511Mb: see help(memory.size)
2: Reached total allocation of 511Mb: see help(memory.size)

We did then try on linux on a super calculator with 130 Go of RAM and 68 
processors of 1.5Ghz each.

We then got the following error:
Error: protect(): protection stack overflow
Execution halted

Is there anything that can be done to run this random forest ? In the 
?Startup I did not understand how to increase the stack size...

Regards,

Kim-Anh

Please give more info on your problem, as the Posting Guide asked.  How
exactly did you call randomForest?  How many cases are in the data?  What
options did you request in randomForest?

People have run randomForest on data with more variables than that on lesser
machines without problem.  You should look in the archive for some hints.

Andy
> From: Kim Anh L?? Cao
> 
> Dear all,
> 
> I am trying to run a random forest on a 4-class dataset with 
> 10 215 variables.
> Whatever the number of trees (I was thinking of combining the 
> trees), I 
> first got the error on Windows:
> 
> Error: cannot allocate vector of size 407562 Kb
> In addition: Warning messages:
> 1: Reached total allocation of 511Mb: see help(memory.size)
> 2: Reached total allocation of 511Mb: see help(memory.size)
> 
> We did then try on linux on a super calculator with 130 Go of 
> RAM and 68 
> processors of 1.5Ghz each.
> 
> We then got the following error:
> Error: protect(): protection stack overflow
> Execution halted
> 
> Is there anything that can be done to run this random forest ? In the 
> ?Startup I did not understand how to increase the stack size...
> 
> Regards,
> 
> Kim-Anh
> 
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> 
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