FYI from apple employee RE: [R] Memory error in Mac OS X Aqua GUI v1.01 with cluster
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@betty-gilbert-1120
Last seen 9.6 years ago
Please ignore this is you're not interested in what my friend who works for apple had to say regarding my issue which is explained in detail at the bottom of this exchange... me: The data from this simulation has to be processed at several stages of data processing so at some point I do have to have to make a dissimilarity matrix from this large matrix, as well as ones that I have filtered. appleguy: >>>Your matrix is too big; adding more memory, or killing off other >>>processes won't help. R is clearly not very smart when it comes >>>to dealing with large chunks of data, and you're running into a >>>fundamental upper limit on the amount of data that it can deal >>>with. >>> >>>The only hope you have of dealing with this is to find a 64-bit >>>system (many Unix boxes fit this description) and use the text or >>>X-windows based R there. If you have a login on a Unix machine at >>>work that has R installed, try your program there. In a few >>>months, when Tiger is out and about, the G5 Macs will also be able >>>to run 64-bit R. me: >>Yeah I was unsuccesful trying to download the unix version of r >>last night(which is also the windows version). Christopher said it >>needed the fortran compiler(?). According to takao the linux we use >>doesn't have any gui capability so I'm not sure I can make the >>dendograms I'm gonna need if I installed R on it. It Linux 2.6.7. >>and is some version of red hat(?). Oh well... appleguy: >Being Linnex, it is probably running on a PC, so it won't be a >64-bit system anyway. What sort of timeframe do you have on this? >I might be able to track down a 64-bit system, but it may take a >little while. >> If time is tight, then you should ask around to see a) whether anyone has a 64-bit unix machine; i.e. a Sun, SGI or Alpha box, and b) whether they know how to generate the graphs without the GUI (I suspect the GUI is not required to generate them, only view them). Until then, you're going to need to reduce the size of your dataset I'm afraid. 8( OG message to rhelp: I'm sorry if the answer to my problem is buried in the archives. I have limited experience with R and I couldn't find a solution to my particular problem. I am running Mac OS X Aqua GUI v1.01 on a new G5 running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just downloaded bioconducter a week ago and I'm trying to cluster a matrix I created with a simulation with dimensions dim(nca35) [1] 10481 12 with size > object.size(nca352) [1] 1426204 I checked my ulimits variable on the unix terminal and it says it's unlimited as does > mem.limits() nsize vsize NA NA But I'm still getting errors like the following with funtions in the cluster package > daisy(nca352, metric= "euclidean", stand=FALSE)->dnca35 Error: cannot allocate vector of size 858213 Kb *** malloc: vm_allocate(size=878813184) failed (error code=3) *** malloc[599]: error: Can't allocate region if it helps i also checked > gc() used (Mb) gc trigger (Mb) Ncells 448662 12.0 741108 19.8 Vcells 847630 6.5 135357901 1032.7 I tried the suggested unix command in the memory help doc but that doesn't work in the Aqua GUI. Can someone tell me how to change the Vcells? Although to the best of my understanding (which is limited) I shouldn't have to do that. Any suggestions would be greatly appreciated. thanks, betty -- Betty Gilbert lgilbert@berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720
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stefano iacus ▴ 430
@stefano-iacus-995
Last seen 9.6 years ago
On Feb 24, 2005, at 1:43 AM, Betty Gilbert wrote: > Please ignore this is you're not interested in what my friend who > works for apple had to say regarding my issue which is explained in > detail at the bottom of this exchange... > > me: > The data from this simulation has to be processed at several stages > of data processing so at some point I do have to have to make a > dissimilarity matrix from this large matrix, as well as ones that I > have filtered. > > appleguy: >>>> Your matrix is too big; adding more memory, or killing off other >>>> processes won't help. R is clearly not very smart when it comes to >>>> dealing with large chunks of data, and you're running into a >>>> fundamental upper limit on the amount of data that it can deal >>>> with. >>>> >>>> The only hope you have of dealing with this is to find a 64-bit >>>> system (many Unix boxes fit this description) and use the text or >>>> X-windows based R there. If you have a login on a Unix machine at >>>> work that has R installed, try your program there. In a few >>>> months, when Tiger is out and about, the G5 Macs will also be able >>>> to run 64-bit R. > and we are going to release a G5 Tiger compliant version of R indeed after Tiger will be officially released. We are working on this. stefano > > me: >>> Yeah I was unsuccesful trying to download the unix version of r last >>> night(which is also the windows version). Christopher said it needed >>> the fortran compiler(?). According to takao the linux we use doesn't >>> have any gui capability so I'm not sure I can make the dendograms >>> I'm gonna need if I installed R on it. It Linux 2.6.7. and is some >>> version of red hat(?). Oh well... > > appleguy: > >> Being Linnex, it is probably running on a PC, so it won't be a 64-bit >> system anyway. What sort of timeframe do you have on this? I might >> be able to track down a 64-bit system, but it may take a little >> while. >>> > If time is tight, then you should ask around to see a) whether anyone > has a 64-bit unix machine; i.e. a Sun, SGI or Alpha box, and b) > whether they know how to generate the graphs without the GUI (I > suspect the GUI is not required to generate them, only view them). > Until then, you're going to need to reduce the size of your dataset > I'm afraid. 8( > > > OG message to rhelp: > > I'm sorry if the answer to my problem is buried in the archives. I > have limited experience with R and I couldn't find a solution to my > particular problem. I am running Mac OS X Aqua GUI v1.01 on a new G5 > running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just > downloaded bioconducter a week ago and I'm trying to cluster a matrix > I created with a simulation with dimensions > dim(nca35) > [1] 10481 12 > > with size >> object.size(nca352) > [1] 1426204 > > I checked my ulimits variable on the unix terminal and it says it's > unlimited as does >> mem.limits() > nsize vsize > NA NA > But I'm still getting errors like the following with funtions in the > cluster package >> daisy(nca352, metric= "euclidean", stand=FALSE)->dnca35 > Error: cannot allocate vector of size 858213 Kb > *** malloc: vm_allocate(size=878813184) failed (error code=3) > *** malloc[599]: error: Can't allocate region > if it helps i also checked >> gc() > used (Mb) gc trigger (Mb) > Ncells 448662 12.0 741108 19.8 > Vcells 847630 6.5 135357901 1032.7 > > I tried the suggested unix command in the memory help doc but that > doesn't work in the Aqua GUI. Can someone tell me how to change the > Vcells? Although to the best of my understanding (which is limited) I > shouldn't have to do that. Any suggestions would be greatly > appreciated. > thanks, > betty > > -- > Betty Gilbert > lgilbert@berkeley.edu > Taylor Lab > Plant and Microbial Biology > 321 Koshland Hall > U.C. Berkeley > Berkeley, Ca 94720 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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