[R-SIG-Mac] memory allocation problems

[Kasper Daniel Hansen]

Thanks for the clarification. How did you get that output?

Kasper

On Jun 30, 2008, at 10:23 AM, Simon Urbanek wrote:

>
> 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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>>
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