[R] memory error

[Sharpie]

Janet Choate-2 wrote:
> 
> Thanx for clarification on stating my problem, Charlie.
> 
> I am attempting to merge to files, i.e.:
> hi39 = merge(comb[,c("hillID","geo")], hi.h39, by=c("hillID"))
> 
> if this is relevant or helps to explain:
> the file 'comb' is 3 columns and 1127 rows
> the file 'hi.h39' is 5 columns and 19758564 rows
> 
> i started a new clean R session in which i was able to read those 2 files
> in, but get the following error when i try to merge them:
> 
> R(2175) malloc: *** mmap(size=79036416) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=79036416) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=158068736) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=158068736) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=158068736) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Error: cannot allocate vector of size 150.7 Mb
> 
> so the final error is "Cannot allocate vector of size 150.7 Mb", as
> suggested when R runs out of memory.
> 
> i am running R version 2.9.2, on mac os X 10.5 - leopard.
> 
> any suggestion on how to increase R's memory on a mac?
> thanx for any much needed help!
> Janet
> 

Ah, so it is indeed a shortage of memory problem.  With R 2.9.2, you are
likely running a 32 bit version of R which will be limited to accessing at
most 4 GB of RAM.  You may want to try the newest version of R, 2.10.1, as
it includes a 64 bit version that will allow you to access significantly
more memory- provided you have the RAM installed on your system.

I'm not too hot on memory usage calculation, but someone else on this list
may be able to give you a ballpark estimate of how much RAM this merge would
require.  If it turns out to be a ridiculous amount, you will need to
consider breaking the merge up into chunks or finding an out-of-core (i.e.
not dependent on RAM for storage) merge tool.

Hope this helps!

-Charlie

-----
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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