Re: [R] Absolute ceiling on R's memory usage = 4 gigabytes?

From: Paul Gilbert <pgilbert_at_bank-banque-canada.ca>
Date: Sat 03 Jul 2004 - 00:39:37 EST

It looks like you have R compiled as a 32 bit application, and you will need to compile it as a 64 bit application if you want to address more than 4G memory. I am not familiar with the sgi irix machine, but you can do this on many workstations that have processors with a 64 bit architecture and an OS that supports it. The R-admin notes have some hints about how to do this for various platforms.

Paul Gilbert

Kort, Eric wrote:

>Yes, we are using the HGU-133plus2 chips with 50,000+ probes, and I suppose that the memory requirements increase geometrically as the chip size increases.
>
>Thanks for your email...I can let you know if we have any success if you are interested for future reference.
>
>-Eric
>
> -----Original Message-----
> From: Tae-Hoon Chung [mailto:thchung@tgen.org]
> Sent: Thu 7/1/2004 7:52 PM
> To: Kort, Eric
> Cc: r-help@stat.math.ethz.ch
> Subject: Re: [R] Absolute ceiling on R's memory usage = 4 gigabytes?
>
>
>
> Hi, Eric.
> It seems a little bit puzzling to me. Which Affymetrix chip do you use?
> The reason I'm asking this is that yesterday I was able to normalize
> 150 HU-133A CEL files (containing 22283 probes) using R 1.9.1 in Mac OS
> X 10.3.3 with 1.5 GB memory. If your chip has more probes than this,
> then it must be understandable ...
>
> On Jul 1, 2004, at 2:59 PM, Kort, Eric wrote:
>
> > Hello. By way of background, I am running out of memory when
> > attempting to normalize the data from 160 affymetrix microarrays using
> > justRMA (from the affy package). This is despite making 6 gigabytes
> > of swap space available on our sgi irix machine (which has 2 gigabytes
> > of ram). I have seen in various discussions statements such as "you
> > will need at least 6 gigabytes of memory to normalize that many
> > chips", but my question is this:
> >
> > I cannot set the memory limits of R (1.9.1) higher than 4 gigabytes as
> > attempting to do so results in this message:
> >
> > WARNING: --max-vsize=4098M=4098`M': too large and ignored
> >
> > I experience this both on my windows box (on which I cannot allocate
> > more than 4 gigabytes of swap space anyway), and on an the above
> > mentioned sgi irix machine (on which I can). In view of that, I do
> > not see what good it does to make > 4 gigabytes of ram+swap space
> > available. Does this mean 4 gigabytes is the absolute upper limit of
> > R's memory usage...or perhaps 8 gigabytes since you can set both the
> > stack and the heap size to 4 gigabytes?
> >
> > Thanks,
> > Eric
> >
> >
> > This email message, including any attachments, is for the
> > so...{{dropped}}
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html
> >
> >
> Tae-Hoon Chung, Ph.D
>
> Post-doctoral Research Fellow
> Molecular Diagnostics and Target Validation Division
> Translational Genomics Research Institute
> 1275 W Washington St, Tempe AZ 85281 USA
> Phone: 602-343-8724
>
>
>
>
>This email message, including any attachments, is for the so...{{dropped}}
>
>______________________________________________
>R-help@stat.math.ethz.ch mailing list
>https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>
>



R-help@stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jul 03 00:44:38 2004

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