[adegenet-forum] sPCA - memory exceeded, can run in parallel?

[Roman Luštrik]

Hi, 

are you running the code on a 32 bit machine or 64? What OS are you on? When you monitor memory usage, does it exceed machine capacity (in my experience with Windows, system should slowly grinding to a halt)? Are there any error messages you receive? 

As for the parallel PCA. Current implementation of `spca` uses `ade4::dudi.pca` and I don't see it mentioned in the docs that it supports parallel execution. In any case, I'm not sure parallel execution would solve the memory problem, unless it's done in parallel sequentially (piece by piece). Perhaps someone else can chip in on this? 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 

----- Original Message -----

From: "Maybellene Gamboa" <maypgamboa at gmail.com> 
To: "Roman Luštrik" <roman.lustrik at biolitika.si> 
Sent: Friday, March 18, 2016 12:53:38 AM 
Subject: Re: [adegenet-forum] sPCA - memory exceeded, can run in parallel? 

Hi Roman, 

Thank you for your response. The actually Mac has 16GB of memory. I am using the most updated version of R. The memory in R itself is exceeded. How might I go about running the command in parallel? 

Thanks again! 

Best, 

Maybellene 

On Thu, Mar 17, 2016 at 5:41 AM, Roman Luštrik < roman.lustrik at biolitika.si > wrote: 



Hi, 

how much RAM does your machine have? Sometimes it's easier to just run the analysis on a more powerful machine. If you're already tipping the edge, parallelization would be a viable step. 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Maybellene Gamboa" < maypgamboa at gmail.com > 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 26, 2016 8:59:20 PM 
Subject: [adegenet-forum] sPCA - memory exceeded, can run in parallel? 


Hi, 

I am performing sPCA with 228 individuals and 9,273 SNPs. Every time I try to run it, the memory is exceeded in R. Can this command be run in parallel? Does it work for very large datasets? Any help would be greatly appreciated! 

Best, 

Maybellene Gamboa 

-- 
Maybellene P. Gamboa 
PhD Student, Department of Biology 
Graduate Degree Program in Ecology 
Colorado State University 
Office: Anatomy/Zoology E339 
Phone: (562) 676-6960 
E-mail: mgamboa at rams.colostate.edu 
Alt. e-mail: maypgamboa at gmail.com 

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-- 
Maybellene P. Gamboa 
PhD Student, Department of Biology 
Graduate Degree Program in Ecology 
Colorado State University 
Office: Anatomy/Zoology E339 
Phone: (562) 676-6960 
E-mail: mgamboa at rams.colostate.edu 
Alt. e-mail: maypgamboa at gmail.com 

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