[BioC] FYI from apple employee RE: [R] Memory error in Mac OS X Aqua GUI v1.01 with cluster

[Betty Gilbert]

Please ignore this is you're not interested in what my friend who 
works for apple had to say regarding my issue which is explained in 
detail at the bottom of this exchange...

me:
  The data from this simulation has to be processed at several stages 
of data processing so at some point I do have to have to make a 
dissimilarity matrix from this large matrix, as well as ones that I 
have filtered.

appleguy:
>>>Your matrix is too big; adding more memory, or killing off other 
>>>processes won't help.  R is clearly not very smart when it comes 
>>>to dealing with large chunks of data, and you're running into a 
>>>fundamental upper limit on the amount of data that it can deal 
>>>with.
>>>
>>>The only hope you have of dealing with this is to find a 64-bit 
>>>system (many Unix boxes fit this description) and use the text or 
>>>X-windows based R there.  If you have a login on a Unix machine at 
>>>work that has R installed, try your program there.  In a few 
>>>months, when Tiger is out and about, the G5 Macs will also be able 
>>>to run 64-bit R.


me:
>>Yeah I was unsuccesful trying to download the unix version of r 
>>last night(which is also the windows version). Christopher said it 
>>needed the fortran compiler(?). According to takao the linux we use 
>>doesn't have any gui capability so I'm not sure I can make the 
>>dendograms I'm gonna need if I installed R on it. It Linux 2.6.7. 
>>and is some version of red hat(?). Oh well...

appleguy:

>Being Linnex, it is probably running on a PC, so it won't be a 
>64-bit system anyway.   What sort of timeframe do you have on this? 
>I might be able to track down a 64-bit system, but it may take a 
>little while.
>>
If time is tight, then you should ask around to see a) whether anyone 
has a 64-bit unix machine; i.e. a Sun, SGI or Alpha box, and b) 
whether they know how to generate the graphs without the GUI (I 
suspect the GUI is not required to generate them, only view them).
Until then, you're going to need to reduce the size of your dataset 
I'm afraid. 8(


OG message to rhelp:

I'm sorry if the answer to my problem is buried in the archives. I 
have limited experience with R  and I couldn't find a solution to my 
particular problem. I am running  Mac OS X Aqua GUI v1.01 on a new G5 
running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just 
downloaded bioconducter a week ago and I'm trying to cluster a matrix 
I created with a simulation with dimensions
dim(nca35)
[1] 10481    12

with size
>  object.size(nca352)
[1] 1426204

I checked my ulimits variable on the unix terminal and it says it's 
unlimited as does
>  mem.limits()
nsize vsize
    NA    NA
But I'm still getting errors like the following with funtions in the 
cluster package
>  daisy(nca352, metric= "euclidean", stand=FALSE)->dnca35
Error: cannot allocate vector of size 858213 Kb
*** malloc: vm_allocate(size=878813184) failed (error code=3)
*** malloc[599]: error: Can't allocate region
if it helps i also checked
>  gc()
          used (Mb) gc trigger   (Mb)
Ncells 448662 12.0     741108   19.8
Vcells 847630  6.5  135357901 1032.7

I tried the suggested unix command in the memory help doc but that 
doesn't work in the Aqua GUI. Can someone tell me how to change the 
Vcells? Although to the best of my understanding (which is limited) I 
shouldn't have to do that. Any suggestions would be greatly 
appreciated.
thanks,
betty

-- 
Betty Gilbert
lgilbert at berkeley.edu
Taylor Lab
Plant and Microbial Biology
321 Koshland Hall
U.C. Berkeley
Berkeley, Ca 94720