[R-SIG-Mac] Memory error

[stefano iacus]

I don't think this is necessarily a user problem of allocating big  
chunks of memory, or at least I did experienced last days the same  
kind of issue by iterating some linear optimization problem of very  
small dimension (something like 5 rows x 5 columns matrix).
In my particular problem it was a sequence on independent calls to  
lpSolve on very small problems. Looking at "top" command on the  
shell, I've seen a growing number of vmem (VSIZE?) almost linearly  
with iteration up to 3.5 giga.
This is also occurring after forcing gc(). If i stop the iteration  
before the alloc failure, the previously allocated ram never gets  
back until I quit R itself.
I'm not able to debug myself, but I can try to provide a reproducible  
example (not these days, but later on)
I've faced the same problem on a G4 and a dual G5.

I'm curious to see the dimension of the data Alan is using, but I'm  
confident that this is not where the problem lies.

stefano


On Nov 28, 2005, at 1:31 AM, Simon Urbanek wrote:

>
> On Nov 27, 2005, at 4:37 PM, Alan Olav Bergland wrote:
>
>> When I attempt to run a rather hefty lme model, I get the following
>> error message:
>>
>>> clinal7.lme<-lme(ovn~tlc+geno+log(food), clinal, random=~tlc+geno
>> +log(food)|block/lat)
>> Error in logLik.lmeStructInt(lmeSt, lmePars) :
>> 	Calloc could not allocate (500237956 of 8) memory
>> R(1049,0xa000ed68) malloc: *** vm_allocate(size=4001906688) failed
>> (error code=3)
>> R(1049,0xa000ed68) malloc: *** error: can't allocate region
>> R(1049,0xa000ed68) malloc: *** set a breakpoint in szone_error to
>> debug
>>
>>
>> I'm running R Version 2.2.0  (2005-10-06 r35749) on a iMac running
>> OS  10.4.3
>>
>>
>> Any suggestions?
>
> Reformulate your problem.
> The lme you run with that data attempts to allocate 4GB of memory
> which is a bit too much. Even if you put 8GB in a G5 and run 64-bit
> version of R it's likely to run out of memory or to take forever ...
> Maybe someone will be able to help you to solve your problem in a
> different way if you specify more precisely what you are trying to do
> (including size of the data etc.).
>
> Cheers,
> Simon
>
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