[BioC] Re: [R] Configuration of memory usage

[Peter Dalgaard]

Tae-Hoon Chung <thchung at tgen.org> writes:

> Hi, all;
> 
> I know there has been a lot of discussions on memory usage in R.
> However, I have some odd situation here. Basically, I have a rare
> opportunity to run R in a system with 64GB memory without any limit on
> memory usage for any person or process. However, I encountered the memory
> problem error message like this:
> 
> Error: cannot allocate vector of size 594075 Kb
....
> Although I have no idea of memory allocation in R, apparently something's
> wrong with this. The memory problem must have nothing to do with physical
> memory. My question is this. Is this memory problem due to some non-optimal
> configuration of memory usage? If so, then what will be the optimal
> configuration for this? If not, then there must be problems on actual
> implementations of functions I used here, right? The reason I am asking this
> is that, according to the reference manual, the error message I got can be
> brought up by roughly three reasons. First, when the system is unable to
> provide the R requested memory. Second, when the requested memory size
> exceeds the address-space limit for a process. Finally, when the length of a
> vector is larger than 2^31-1. 

Hmm, the length issue should not kick in before the length exceeds 2
billion or so and you are not beyond 75 or 150 million (counting 8 or
4 bytes per elements).

> I wonder the problem has anything to do with
> the third case. (If so, then I think I am hopeless unless the internal
> implementations change...)

Well, revolutionaries often find themselves just below the cutting
edge...

Just a sanity check: this is using a 64-bit compiled R on a 64-bit
operating system, right?

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907