Thank you all for your answers. I think I have enough to keep going:

As pointed out it is probably not growing a list of objects each of size
6824 bytes that is the source of the problem per se (even if the list is not
pre-allocated), but rather a "memory leak" with the function fun within the
loop. I'm not providing the full example here because the code spans several
files.

Nonetheless the body of fun itself contains deeply nested lists, some which
are temporary and others which are part of the return value. So i'm now
trying to see what to do about these nested lists instead. About memory
leak: my assumption was that the memory needed for a temporary object (i.e.
defined within the body of a function) would be redeemed after the function
call, but perhaps i'm wrong about that (no automatic garbage collection)?


On Fri, Nov 14, 2008 at 6:37 AM, Patrick Burns <pburns@pburns.seanet.com>wrote:

> The recommended technique is to create objects
> as their final size and then subscript into them
> with your data.
>
> My intuition (which is often brutally wrong) tells
> me that your case should not be overly traumatic.
> So I'm suspicious that you are fragmenting memory
> in other ways as well.
>
> Patrick Burns
> patrick@burns-stat.com
> +44 (0)20 8525 0696
> http://www.burns-stat.com
> (home of S Poetry and "A Guide for the Unwilling S User")
>
>
> erwann rogard wrote:
>
>> hello,
>>
>> i have something like:
>>
>> out<-list()
>>
>> for(i in 1:n){
>>  data<-gen(...) #fixed size data
>>  out[[i]]<- fun(data)
>> }
>>
>>
>>
>>> object.size(out[[1]])
>>>
>>>
>> 6824
>>
>> In principle 1 GB should allow
>>
>> n = 1024^3/6824 = 157347?
>>
>> i have about 2GB are not taken by other processes. however, I can see the
>> memory shrinking quite rapidly on my system monitor and have to stop the
>> simulation after only n=300. why such a discrepancy? any remedy?
>>
>> x86_64-pc-linux/RKWard/R2.8.0/ 4GB
>>
>> thanks.
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>>
>>
>>
>

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