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

[stefano iacus]

On Feb 24, 2005, at 1:43 AM, Betty Gilbert wrote:

> 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.
>

and we are going to release a G5 Tiger compliant version of R indeed 
after Tiger will be officially released. We are working on this.
stefano

>
> 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
>
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