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Problems with big objects in R-2.5 x86_64
6 messages · Eric Blanc, Simon Urbanek, Simon de Bernard
Eric, unless you tell us more precisely what you do and what machine you have we can't really help you. If you don't have enough RAM (>4GB) 64- bit R won't really help you as it ends up swapping all the time anyway (just look at the resource usage). Cheers, Simon
On May 23, 2007, at 11:15 AM, Eric Blanc wrote:
Hi, I encountered problems in using the experimental build R 2.5 for x86_64 architecture. I have downloaded the framework from http://r.research.att.com/R-25-br-quad.tar.gz I tried to load large objects, (about 2GB each), but it hangs at random points, apparently always after the 4GB mark (i.e. while loading the 3rd object). I am monitoring the resources usage from another terminal window (top), and the R process never completes loading the 3rd object, the memory usage stops increasing before reaching 6GB, even though the CPU usage by R is 100%. The time required to load the 1st and 2nd objects are about 1 minute each, while I stopped R after 30 minutes (without completing loading the 3rd object). I had similar problems last december, when I tried to compile R 2.4 from scratch using the instructions in https://stat.ethz.ch/pipermail/r-sig-mac/2006-November/003384.html Here is the sessionInfo(): R version 2.5.0 Patched (2007-05-02 r41420) x86_64-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" Has anybody tried to use large amounts of memory with R 2.5 x86_64 ? I must add that I tried to load the same objects, on the same machine, but using Ubuntu 7.4 x86_64, and it works on Ubuntu. It seems to be a OS X problem (I am using 10.4.9). Thanks, Eric [[alternative HTML version deleted]]
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Based on what Eric says (symptoms and the fact that it works on the SAME machine under ubuntu), it looks a lot like what I reported on april the 7th... Best, Simon de Bernard. Le 23 mai 07 ? 19:03, Simon Urbanek a ?crit :
Eric, unless you tell us more precisely what you do and what machine you have we can't really help you. If you don't have enough RAM (>4GB) 64- bit R won't really help you as it ends up swapping all the time anyway (just look at the resource usage). Cheers, Simon On May 23, 2007, at 11:15 AM, Eric Blanc wrote:
Hi, I encountered problems in using the experimental build R 2.5 for x86_64 architecture. I have downloaded the framework from http://r.research.att.com/R-25-br-quad.tar.gz I tried to load large objects, (about 2GB each), but it hangs at random points, apparently always after the 4GB mark (i.e. while loading the 3rd object). I am monitoring the resources usage from another terminal window (top), and the R process never completes loading the 3rd object, the memory usage stops increasing before reaching 6GB, even though the CPU usage by R is 100%. The time required to load the 1st and 2nd objects are about 1 minute each, while I stopped R after 30 minutes (without completing loading the 3rd object). I had similar problems last december, when I tried to compile R 2.4 from scratch using the instructions in https://stat.ethz.ch/pipermail/r-sig-mac/2006-November/003384.html Here is the sessionInfo(): R version 2.5.0 Patched (2007-05-02 r41420) x86_64-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" Has anybody tried to use large amounts of memory with R 2.5 x86_64 ? I must add that I tried to load the same objects, on the same machine, but using Ubuntu 7.4 x86_64, and it works on Ubuntu. It seems to be a OS X problem (I am using 10.4.9). Thanks, Eric [[alternative HTML version deleted]]
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On May 23, 2007, at 1:19 PM, Simon de Bernard wrote:
Based on what Eric says (symptoms and the fact that it works on the SAME machine under ubuntu), it looks a lot like what I reported on april the 7th...
What you reported was a crash, what he reports is ... I don't know what ;). And that's why I need more info ... Cheers, Simon
Le 23 mai 07 ? 19:03, Simon Urbanek a ?crit :
Eric, unless you tell us more precisely what you do and what machine you have we can't really help you. If you don't have enough RAM (>4GB) 64- bit R won't really help you as it ends up swapping all the time anyway (just look at the resource usage). Cheers, Simon On May 23, 2007, at 11:15 AM, Eric Blanc wrote:
Hi, I encountered problems in using the experimental build R 2.5 for x86_64 architecture. I have downloaded the framework from http://r.research.att.com/R-25-br-quad.tar.gz I tried to load large objects, (about 2GB each), but it hangs at random points, apparently always after the 4GB mark (i.e. while loading the 3rd object). I am monitoring the resources usage from another terminal window (top), and the R process never completes loading the 3rd object, the memory usage stops increasing before reaching 6GB, even though the CPU usage by R is 100%. The time required to load the 1st and 2nd objects are about 1 minute each, while I stopped R after 30 minutes (without completing loading the 3rd object). I had similar problems last december, when I tried to compile R 2.4 from scratch using the instructions in https://stat.ethz.ch/pipermail/r-sig-mac/2006-November/003384.html Here is the sessionInfo(): R version 2.5.0 Patched (2007-05-02 r41420) x86_64-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" Has anybody tried to use large amounts of memory with R 2.5 x86_64 ? I must add that I tried to load the same objects, on the same machine, but using Ubuntu 7.4 x86_64, and it works on Ubuntu. It seems to be a OS X problem (I am using 10.4.9). Thanks, Eric [[alternative HTML version deleted]]
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Actually, I reported an example that consistently crashes but it is
pretty easy to construct one that gets into an infinite loop:
> l<-list(1)
> while(1) { print(object.size(l)/1024/1024); l<-c(l,l) }
(Just duplicate the list instead of triplicating it)
That's why I think we are facing the same ugly bug :-(
Best,
Simon.
Le 23 mai 07 ? 19:56, Simon Urbanek a ?crit :
On May 23, 2007, at 1:19 PM, Simon de Bernard wrote:
Based on what Eric says (symptoms and the fact that it works on the SAME machine under ubuntu), it looks a lot like what I reported on april the 7th...
What you reported was a crash, what he reports is ... I don't know what ;). And that's why I need more info ... Cheers, Simon
Le 23 mai 07 ? 19:03, Simon Urbanek a ?crit :
Eric, unless you tell us more precisely what you do and what machine you have we can't really help you. If you don't have enough RAM (>4GB) 64- bit R won't really help you as it ends up swapping all the time anyway (just look at the resource usage). Cheers, Simon On May 23, 2007, at 11:15 AM, Eric Blanc wrote:
Hi, I encountered problems in using the experimental build R 2.5 for x86_64 architecture. I have downloaded the framework from http://r.research.att.com/R-25-br-quad.tar.gz I tried to load large objects, (about 2GB each), but it hangs at random points, apparently always after the 4GB mark (i.e. while loading the 3rd object). I am monitoring the resources usage from another terminal window (top), and the R process never completes loading the 3rd object, the memory usage stops increasing before reaching 6GB, even though the CPU usage by R is 100%. The time required to load the 1st and 2nd objects are about 1 minute each, while I stopped R after 30 minutes (without completing loading the 3rd object). I had similar problems last december, when I tried to compile R 2.4 from scratch using the instructions in https://stat.ethz.ch/pipermail/r-sig-mac/2006-November/003384.html Here is the sessionInfo(): R version 2.5.0 Patched (2007-05-02 r41420) x86_64-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" Has anybody tried to use large amounts of memory with R 2.5 x86_64 ? I must add that I tried to load the same objects, on the same machine, but using Ubuntu 7.4 x86_64, and it works on Ubuntu. It seems to be a OS X problem (I am using 10.4.9). Thanks, Eric [[alternative HTML version deleted]]
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