Question: memory limit
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gravatar for Noemi Andor
9.1 years ago by
Noemi Andor100
Noemi Andor100 wrote:
Hi, I have a problem with the R memory limits. First, I use R on a 64 bit system under windows 7. I start R with the following options: --min-vsize=10M --max-vsize=3G --min-nsize=500k --max-nsize=900M Yet somewhere within the program I use, I get the error report: "can not allocate vector of size 370.8 MB". Now, what I try to do while getting this message is to use RAE, a program for analysis of CGH data. It is very time consuming, and I have to wait for ca. 2 hours till the message appears. Also, it seems to appear earlier as I keep trying: at my second trial the error message appeared sooner then in the first trial. It is also worth mentioning, that I used RAE before, on ca 3/4 of the same data I'm using now, and it worked. I also tried to restart my pc, yet no improval. ********before RAE: memory.size(max=TRUE) [1] 16.94 memory.limit() [1] 3583 memory.size() [1] 6.89 gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 119268 3.2 500000 13.4 25200.0 500000 13.4 Vcells 78210 0.6 1310720 10.0 24576.1 426021 3.3 ******** ***********After error message within RAE: memory.size(max=TRUE) [1] 3583.88 memory.size() [1] 511.92 memory.limit() [1] 3583 gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 285631 7.7 633250 17 25200.0 633250 17.0 Vcells 65059765 496.4 274195172 2092 24576.1 462143052 3525.9 ************ sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.20.0 I would be very greatfull for a solution to my problem. best, Noemi
cgh trigger • 641 views
ADD COMMENTlink modified 9.1 years ago by Steve Lianoglou12k • written 9.1 years ago by Noemi Andor100
Answer: memory limit
0
gravatar for Steve Lianoglou
9.1 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Wed, Oct 6, 2010 at 6:13 PM, Noemi Andor <noemi.andor at="" campus.lmu.de=""> wrote: > Hi, > > I have a problem with the R memory limits. > First, I use R on a 64 bit system under windows 7. > I start R with the following options: > --min-vsize=10M --max-vsize=3G --min-nsize=500k --max-nsize=900M Although your system is 64bit, it looks as if the version of R you are running is only 32 bit. Look at the output of your sessionInfo() you pasted below: sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 > Yet somewhere within the program I use, I get the error report: > > "can not allocate vector of size 370.8 MB". As someone in R-help once put it, this 370.8 MB is the straw that broke the camel's back. R has been chewing up memory while your process is running, and now wanted to get 370MB more memory, but there wasn't that much (contiguous) memory left. > It is also worth mentioning, that I used RAE before, on ca 3/4 of the same data I'm using now, and it worked. On the same machine? With the same setup? > I would be very greatfull for a solution to my problem. You can try running a 64bit version of R to see if you can access more memory (how much RAM does your machine have, anyway?). It seems that R-2.11 was the first R version that had a 64bit capable version available for windows: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-use-R-on- 64_002dbit-Windows_003f -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 9.1 years ago by Steve Lianoglou12k
I applied RAE on the 64 bit version of R and it worked! Thank's a lot! ________________________________ Von: Steve Lianoglou <mailinglist.honeypot@gmail.com> An: Noemi Andor <noemi.andor@campus.lmu.de> CC: bioconductor@stat.math.ethz.ch Gesendet: Mittwoch, den 6. Oktober 2010, 16:04:00 Uhr Betreff: Re: [BioC] memory limit Hi, On Wed, Oct 6, 2010 at 6:13 PM, Noemi Andor <noemi.andor@campus.lmu.de> wrote: > Hi, > > I have a problem with the R memory limits. > First, I use R on a 64 bit system under windows 7. > I start R with the following options: > --min-vsize=10M --max-vsize=3G --min-nsize=500k --max-nsize=900M Although your system is 64bit, it looks as if the version of R you are running is only 32 bit. Look at the output of your sessionInfo() you pasted below: sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 > Yet somewhere within the program I use, I get the error report: > > "can not allocate vector of size 370.8 MB". As someone in R-help once put it, this 370.8 MB is the straw that broke the camel's back. R has been chewing up memory while your process is running, and now wanted to get 370MB more memory, but there wasn't that much (contiguous) memory left. > It is also worth mentioning, that I used RAE before, on ca 3/4 of the same data >I'm using now, and it worked. On the same machine? With the same setup? > I would be very greatfull for a solution to my problem. You can try running a 64bit version of R to see if you can access more memory (how much RAM does your machine have, anyway?). It seems that R-2.11 was the first R version that had a 64bit capable version available for windows: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-use-R-on- 64_002dbit-Windows_003f -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]
ADD REPLYlink written 9.1 years ago by Noe Andor70
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