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

[Kort, Eric]

Yes...unfortunately it looks like the lab that owns the irix does not have a license for Sun's compilers which are required for compiling a 64bit R (I used gcc to compile the 32 bit version, but have not had success compiling a 64 bit R with gcc on the irix).  But I am sure we will manage to compile a 64 bit R somewhere sometime soon.
 
Thanks,
Eric

	-----Original Message----- 
	From: Paul Gilbert [mailto:pgilbert at bank-banque-canada.ca] 
	Sent: Fri 7/2/2004 10:39 AM 
	To: Kort, Eric 
	Cc: Tae-Hoon Chung; r-help at stat.math.ethz.ch 
	Subject: Re: [R] Absolute ceiling on R's memory usage = 4 gigabytes?
	
	

	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 at tgen.org]
	>       Sent: Thu 7/1/2004 7:52 PM
	>       To: Kort, Eric
	>       Cc: r-help at 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}}
	>       >
	>       > ______________________________________________
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	>       > 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
	>      
	>      
	>
	>
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	>
	>______________________________________________
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	>
	> 
	>
	
	


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