[R-SIG-Mac] memory allocation problems

[Simon Urbanek]

On Jun 30, 2008, at 1:04 PM, Kasper Daniel Hansen wrote:

> Like Sean is aying, you most likely are using _way_ more memory than  
> 1.2 GB.
>
> However, if you a re running 32bit R (which is the case if you use  
> the CRAN binary) R can only access 2GB,

That's not true, 32-bit process can use up to about 3.5GB of RAM:

Virtual Memory Map of process 2849 (R)
Output report format:  2.2  -- 32-bit process
[...]
ReadOnly portion of Libraries: Total=72.9M resident=36.6M(50%)  
swapped_out_or_unallocated=36.3M(50%)
Writable regions: Total=3.4G written=3.4G(100%) resident=3.4G(99%)  
swapped_out=3352K(0%) unallocated=19.3M(1%)

so it should make no real difference for Antonio (unless he doesn't  
mind waiting while the machine swaps). Nonetheless using 64-bit R is  
fine as well, especially on Leopard - albeit that doesn't fix  
incorrect use of memory by users :).

Cheers,
S


> so you can squeeze a little more out of your machine by switching to  
> a 64bit version of R. You can check what version you have by typing
> R> .Machine
> and look for sizeof.pointer - if it is 4 you are using 32bit, if it  
> is 8 you are using 64 bit.
>
> If you want the 64 bit version of R you can download a binary from  
> Simon's page: r.research.att.com , but you need to also get the  
> preview build of GCC 4.2 which is available from Apple's developer  
> site (although hard to find these days).
>
> Kasper
>
> On Jun 30, 2008, at 3:23 AM, Sean Davis wrote:
>
>> On Sun, Jun 29, 2008 at 6:35 AM, Antonio P. Ramos
>> <ramos.grad.student at gmail.com> wrote:
>>> Hi everybody,
>>>
>>> I have a memory allocation problem while using  R in my macbook pro,
>>> which runs the latest leopard. I'm trying to run a monte carlo
>>> simulation with 500,000 interactions, but the machine failed:
>>>
>>>
>>> Starting MCMC Iterations...
>>> Error: cannot allocate vector of size 1.2 Gb
>>> R(176,0xa0640fa0) malloc: *** mmap(size=1239990272) failed (error  
>>> code=12)
>>> *** error: can't allocate region
>>> *** set a breakpoint in malloc_error_break to debug
>>> R(176,0xa0640fa0) malloc: *** mmap(size=1239990272) failed (error  
>>> code=12)
>>> *** error: can't allocate region
>>> *** set a breakpoint in malloc_error_break to debug
>>>
>>>
>>> Since my machine has 4 Gb of memory, and since I'm not running  
>>> nothing
>>> in addition to the simulation, I found it strange. This is my  
>>> machine:
>>>
>>> Model Identifier:     MacBookPro3,1
>>> Processor Name:       Intel Core 2 Duo
>>> Processor Speed:      2.4 GHz
>>> Memory:       4 GB
>>>
>>>
>>> Unfortunately, I could figure it out how to solve it. Any help?
>>
>> The error message above means that R failed to allocate a vector of
>> size 1.2Gb.  That doesn't mean that R was using only 1.2 Gb, but that
>> it was trying to allocate a new block of memory of that size in
>> addition to the memory that was already in use.  The system on the  
>> Mac
>> uses a fair amount of memory; R was probably using memory as well.   
>> In
>> short, you probably need more memory or be more clever about how you
>> are using the memory you have.  Without more details about what you
>> are doing, it is difficult to know how to change the latter.
>>
>> Sean
>>
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