search for: vm_allocate

...lyis on the whole dataset without even considering to partition it. So I was really wondering if you could give me a clue about how to handle this problem. model6 <-lm(logintens~ factor (slide) + factor(ind) + factor(dye) + factor(id)*factor(l6) + factor(rep)-1, data=sample_data2) *** malloc: vm_allocate(size=381886464) failed (error code=3) *** malloc[387]: error: Can't allocate region *** malloc: vm_allocate(size=381886464) failed (error code=3) *** malloc[387]: error: Can't allocate region *** malloc: vm_allocate(size=381886464) failed (error code=3) *** malloc[387]: error: Can't all...

Hi All, I want to print a square matrix of 7000 x 7000 into a text file. But I got a error after few hours of computation... -------- > write.table(MyDistMxDF, file = "temp.csv", sep=",", quote=F) *** malloc: vm_allocate(size=8421376) failed (error code=3) *** malloc[2889]: error: Can't allocate region Error: vector memory exhausted (limit reached?) *** malloc: vm_allocate(size=8421376) failed (error code=3) *** malloc[2889]: error: Can't allocate region > q() *** malloc: vm_allocate(size=8421376) fail...

I''m using acts_as_ferret and when I call Object.find_by_contents("A & B"), Ruby dies with the following message: ^Cruby(5014,0xa000cf60) malloc: *** vm_allocate(size=1069056) failed (error code=3) ruby(5014,0xa000cf60) malloc: *** error: can''t allocate region ruby(5014,0xa000cf60) malloc: *** set a breakpoint in szone_error to debug ruby(5014,0xa000cf60) malloc: *** vm_allocate(size=1069056) failed (error code=3) ruby(5014,0xa000cf60) malloc: *...

...rary(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some sort of memory error that crashes the R program. Specifically it states: R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3) R(1763) malloc: *** error: can't allocate region R(1763) malloc: *** set a breakpoint in szone_error to debug R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3) R(1763) malloc: *** error: can't allocate region R(1763) malloc: *** set...

Full_Name: Hans Kestler Version: 2.2.0 OS: 10.4.3 Submission from: (NULL) (84.156.184.101) > sam1.out<-sam(raw1[,2:23],raw1.cl,B=0,rand=124) We're doing 319770 complete permutations Error: cannot allocate vector of size 575586 Kb R(572,0xa000ed68) malloc: *** vm_allocate(size=589402112) failed (error code=3) R(572,0xa000ed68) malloc: *** error: can't allocate region R(572,0xa000ed68) malloc: *** set a breakpoint in szone_error to debug R(572,0xa000ed68) malloc: *** vm_allocate(size=589402112) failed (error code=3) R(572,0xa000ed68) malloc: *** error: can't...

...r neuroimage analysis, so I am loading in some large image files. I get the following error in the middle of my script: > source("3dLME.R") Read 1 record Read 1 record Read 1 record Read 1 record Read 1 record Error: cannot allocate vector of size 3.1 Gb R(2081,0xa000d000) malloc: *** vm_allocate(size=3321675776) failed (error code=3) R(2081,0xa000d000) malloc: *** error: can't allocate region R(2081,0xa000d000) malloc: *** set a breakpoint in szone_error to debug R(2081,0xa000d000) malloc: *** vm_allocate(size=3321675776) failed (error code=3) R(2081,0xa000d000) malloc: *** error: can&...

...unbalanced anova on 272,992 observations with 405 factors including 2-way interactions between 1 of these factors and the other 404. After fitting only 11 factors and their interactions I get error messages like: Error: cannot allocate vector of size 1433066 Kb R(365,0xa000ed68) malloc: *** vm_allocate(size=1467461632) failed (error code=3) R(365,0xa000ed68) malloc: *** error: can't allocate region R(365,0xa000ed68) malloc: *** set a breakpoint in szone_error to debug I think that the anova involves a matrix of 272,992 rows by 29025 columns (using dummy variables)=7,900 million elements....

...> >> I want to print a square matrix of 7000 x 7000 into a text > file. But I > >> got a error after few hours of computation... > >> -------- > >>> write.table(MyDistMxDF, file = "temp.csv", sep=",", quote=F) > >> *** malloc: vm_allocate(size=8421376) failed (error code=3) > >> *** malloc[2889]: error: Can't allocate region > >> Error: vector memory exhausted (limit reached?) > >> *** malloc: vm_allocate(size=8421376) failed (error code=3) > >> *** malloc[2889]: error: Can't allocate regi...

...<- round(rnorm(dims*dims),rnd) x[((abs(x) - p) < 0)] <- 0 y <- matrix(x,nrow=dims,ncol=dims) proc.time() - ptm } When trying to generate the matrix around 20,000 rows/cols on a machine with 32G of memory, the error message I receive is: R(335) malloc: *** vm_allocate(size=3200004096) failed (error code=3) R(335) malloc: *** error: can't allocate region R(335) malloc: *** set a breakpoint in szone_error to debug R(335) malloc: *** vm_allocate(size=3200004096) failed (error code=3) R(335) malloc: *** error: can't allocate region R(335) malloc: *** set a b...

...in R. The model is of the form X~A*B*(C/D/F) A,B,C,D,F being the independent variables some of which are nested. The problem occurs when using aov but also when using glm or lme. In particular I get the following response, Error: cannot allocate vector of size 1.6 Gb R(311,0xa000d000) malloc: *** vm_allocate(size=1733365760) failed (error code=3) R(311,0xa000d000) malloc: *** error: can't allocate region R(311,0xa000d000) malloc: *** set a breakpoint in szone_error to debug R(311,0xa000d000) malloc: *** vm_allocate(size=1733365760) failed (error code=3) R(311,0xa000d000) malloc: *** error: can'...

I am using the Openbase adapter and have had a similar glitch here and there, but after I go into production I consistently get an error on one page. ActionView::TemplateError (NoMemoryError: failed to allocate memory: SELECT * FROM ... I cannot track down the exact location of the error, but the production log says it was around:

...work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was trying to write this file out using the command: write.table(all,file="~/Desktop/alex.lgen",sep=" ",row.names=F,na="0",quote=F,col.names=F) I got the error message: R(319,0xa000d000) malloc: *** vm_allocate(size=88764416) failed (error code=3) R(319,0xa000d000) malloc: *** error: can't allocate region R(319,0xa000d000) malloc: *** set a breakpoint in szone_error to debug I then confirmed in Windows (Windows XP, 1G RAM) R by trying it again. It seems that it has to do with my R memory limit alloc...

...y ~ trt + (trt-1|group), d) VarCorr(lme1)@reSumry$group[2,1] #just as an example } > off.boot <- boot(data=data.sim, statistic=off.fun, R=100) If I choose small values of R (<10) then I get very reasonable results but for large R I get the following error massage: *** malloc: vm_allocate(size=1069056) failed (error code=3) *** malloc[682]: error: Can't allocate region Error in .local(x, ...) : Calloc could not allocate (48 of 8) memory Can anyone tell me why I get this error massage and what I can do to avoid this problem? Thank you very much for your help! T...

...oaded into R a very large matrix, around 600,000 X 30 integers. My machine has 2G ram. After trying to write.table a modification of this matrix, R generated some sort of malloc error. Then, Error: vector memory exhausted (limit reached?) > q() Save workspace image? [y/n/c]: n *** malloc: vm_allocate(size=8421376) failed (error code=3) *** malloc[14681]: error: Can't allocate region Error: vector memory exhausted (limit reached?) > Eventually I just killed the R session directly. Michael

...ide your own malloc/free. :) One of the existing malloc replacements should provide hints for how to go about that. www.hoard.org for one. The details on Windows are especially complicated. Be aware that even doing this won't reliably intercept all allocations. With Mac OS X, Mach's vm_allocate call is accessible. With Unix, mmap with flags = MAP_ANON allocates memory. And even still, the implementations of these aren't magic; it's possible to make the syscalls without linking to these symbols per se. There are likely further facilities to distrust on any given platform, a...

On Tue, 10 Jul 2007, Sandro Magi wrote: >> used. Your choices are to either override malloc/free for both the JIT >> and the program or for neither of them. > > I want to 'intercept' ALL allocations actually, including the stack if > possible, so the above suits me just fine. Ok, just provide your own malloc/free. :) -Chris -- http://nondot.org/sabre/

From: Mihai Don?u <mdontu at bitdefender.com> This is needed to filter #PF introspection events. Signed-off-by: Mihai Don?u <mdontu at bitdefender.com> Co-developed-by: Nicu?or C??u <ncitu at bitdefender.com> Signed-off-by: Nicu?or C??u <ncitu at bitdefender.com> Signed-off-by: Adalbert Laz?r <alazar at bitdefender.com> --- arch/x86/include/asm/kvm_host.h | 4 ++++

...you have better performance. This is a problem for people doing performance measurements on Mac OS X and iOS, because exotic memory allocation schemes seem to be becoming more common (I hope not because they dodge reporting!). In particular, may image buffers are allocated directly from mmap and vm_allocate, within CoreGraphics and elsewhere. -Ken Cocoa Frameworks > > I thought I dug into the register allocation code, and found the > VNInfo::Allocator typedef. I assumed that was getting the traffic we > saw in Instruments, but I don't have the data to back that up. > > >&g...

Dear list, I am using R.2.0.1 on a G5 biprocessor 2.5GHz with 2Go RAM (Mac OS X 10.3.8). I'm trying to calculate an object of type "dist". I am getting the following memory error : *** malloc: vm_allocate(size=1295929344) failed (error code=3) *** malloc[25960]: error: Can't allocate region Error: cannot allocate vector of size 1265554 Kb When I do a top on the terminal, I can see that this size has already been allocated... It seems that R tries to allocate the memory twice. Does anybody have...

...ys 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 bu...