[BioC] FYI from apple employee RE: [R] Memory error in Mac OS X

stefano iacus stefano.iacus at unimi.it
Thu Apr 14 16:36:01 CEST 2005

Dear David,
we cannot discuss Tiger-related stuff publicly until release (which is 
planned for april 29).
But yes, R builds out of the box on Tiger and Simon Urbanek has also 
obtained a successful 64bit build.
We will surely talk about this in R-sig-Mac
p.s. btw, Tiger is 10.4 (only!)

On 13/apr/05, at 20:44, David Williamson wrote:

> Stefano,
> I saw this thread and would like to know how the tiger/64bit
> R/bioconductor compile is coming along.  I'm interested in using the
> hopach package to run memory intensive jobs that are currently limited
> by the OSX 10.8 memory ceiling.
> Have you been able to use  the new TIGER kernel or the new Xtools 2.0
> libraries to compile R in 64-bit, or are you waiting for the release?
> Are there another threads or newsgroups dedicated to this topic?
> Thanks for your assistance.
> ~david
> 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
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David Williamson
> The J. David Gladstone Institutes
> Gladstone Institute of Cardiovascular Disease
> 1650 Owens Street, room 571 Y2
> San Francisco, CA 94158
> UCSF mailbox 1230
> Work:   	415.734.4945 (voice mail 6136)
> Fax:    	415.285.5632
> Home:	http://dww.ucsf.edu/~david/
> Email: 	dwilliamson at gladstone.ucsf.edu
> 	[[alternative text/enriched version deleted]]
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