[R-SIG-Mac] [R] lmer2 error under Mac OS X on PowerPC G5 but not on Dual-Core Intel Xeon
Douglas Bates
bates at stat.wisc.edu
Fri Feb 2 19:18:36 CET 2007
There was a bug in lme4_0.9975-11 that I tracked down with help from
Andrew Robinson and this bug caused the reported symptoms. Please try
again with lme4_0.9975-12
On 1/29/07, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> Michael has a PPC G5 with 2GB of RAM and can't get that example to
> run. It can't allocate enough memory (or at least it's what I
> understand from the error he reported).
>
> Given that the example doesn't require much RAM (and I could get it
> to run on a G4, Mac OS X 10.4.8), I failed to have a plausible
> explanation for the problem.
>
> b
>
> On Jan 29, 2007, at 11:28 AM, Simon Urbanek wrote:
>
> > I'm not sure - what is the question here? It works for me on a both
> > PowerPC G5 and Mac Pro (R 2.4.1 CRAN binary):
> >
> > > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> > > fm1
> > Linear mixed-effects model fit by REML
> > Formula: Reaction ~ Days + (Days | Subject)
> > Data: sleepstudy
> > AIC BIC logLik MLdeviance REMLdeviance
> > 1754 1770 -871.8 1752 1744
> > Random effects:
> > Groups Name Variance Std.Dev. Corr
> > Subject (Intercept) 610.835 24.7151
> > Days 35.056 5.9208 0.067
> > Residual 655.066 25.5943
> > number of obs: 180, groups: Subject, 18
> >
> > Fixed effects:
> > Estimate Std. Error t value
> > (Intercept) 251.405 6.820 36.86
> > Days 10.467 1.546 6.77
> >
> > Correlation of Fixed Effects:
> > (Intr)
> > Days -0.137
> > > gc()
> > used (Mb) gc trigger (Mb) max used (Mb)
> > Ncells 966960 25.9 1368491 36.6 1265230 33.8
> > Vcells 523595 4.0 1031040 7.9 755843 5.8
> > > sessionInfo()
> > R version 2.4.1 (2006-12-18)
> > i386-apple-darwin8.8.1
> >
> > locale:
> > C
> >
> > attached base packages:
> > [1] "stats" "graphics" "grDevices" "utils" "datasets"
> > "methods"
> > [7] "base"
> >
> > other attached packages:
> > lme4 Matrix lattice
> > "0.9975-11" "0.9975-8" "0.14-16"
> >
> > Cheers,
> > Simon
> >
> > On Jan 29, 2007, at 10:40 AM, Benilton Carvalho wrote:
> >
> >> So, I decided to give it a try (and just now noticed that this is the
> >> example in lmer2)
> >>
> >> I just gave it a try on a PPC G4 and it worked as expected. I'm
> >> copying R-sig-mac (sorry for the crosspost) as the experts there
> >> might give you a better suggestion.
> >>
> >>> fm1 <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)
> >>> fm1
> >> Linear mixed-effects model fit by REML
> >> Formula: Reaction ~ Days + (Days | Subject)
> >> Data: sleepstudy
> >> AIC BIC logLik MLdeviance REMLdeviance
> >> 1754 1770 -871.8 1752 1744
> >> Random effects:
> >> Groups Name Variance Std.Dev. Corr
> >> Subject (Intercept) 612.128 24.7412
> >> Days 35.049 5.9202 0.066
> >> Residual 654.970 25.5924
> >> Number of obs: 180, groups: Subject, 18
> >>
> >> Fixed effects:
> >> Estimate Std. Error t value
> >> (Intercept) 251.405 6.825 36.84
> >> Days 10.467 1.545 6.77
> >>
> >> Correlation of Fixed Effects:
> >> (Intr)
> >> Days -0.137
> >>> sessionInfo()
> >> R version 2.5.0 Under development (unstable) (2007-01-03 r40349)
> >> powerpc-apple-darwin8.8.0
> >>
> >> locale:
> >> C
> >>
> >> attached base packages:
> >> [1] "stats" "graphics" "grDevices" "utils" "datasets"
> >> "methods"
> >> [7] "base"
> >>
> >> other attached packages:
> >> lme4 Matrix lattice
> >> "0.9975-11" "0.9975-8" "0.14-16"
> >>
> >>
> >> On Jan 29, 2007, at 7:40 AM, Michael Kubovy wrote:
> >>
> >>> On Jan 28, 2007, at 9:39 PM, Benilton Carvalho wrote:
> >>>
> >>>> This seems to be due to the fact that you didn't have enough
> >>>> memory when running lmer2.
> >>>>
> >>>> I might be wrong, but I think Calloc tries to get contiguous
> >>>> memory, so this might the problem.
> >>>>
> >>>> If you are positive that you have enough memory, a gc() might help.
> >>>
> >>> I have 2 GB memory on this machine. Should be enough, no?
> >>>
> >>>> gc()
> >>> used (Mb) gc trigger (Mb) max used (Mb)
> >>> Ncells 1008175 27.0 1476915 39.5 1368491 36.6
> >>> Vcells 540055 4.2 1031040 7.9 1031026 7.9
> >>>> (fm1 <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy))
> >>> Error in as.double(start) : Calloc could not allocate (903190944 of
> >>> 4) memory
> >>>
> >>>
> >>>> On Jan 28, 2007, at 8:35 PM, Michael Kubovy wrote:
> >>>>
> >>>>>> (fm1 <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy))
> >>>>> Error in as.double(start) : Calloc could not allocate
> >>>>> (888475968 of
> >>>>> 4) memory
> >>>>> *************************
> >>>>>> sessionInfo()
> >>>>> R version 2.4.1 (2006-12-18)
> >>>>> powerpc-apple-darwin8.8.0
> >>>>>
> >>>>> locale:
> >>>>> C
> >>>>>
> >>>>> attached base packages:
> >>>>> [1] "grid" "datasets" "stats" "graphics" "grDevices"
> >>>>> "utils" "methods"
> >>>>> [8] "base"
> >>>>>
> >>>>> other attached packages:
> >>>>> lme4 Matrix xtable latticeExtra lattice
> >>>>> gridBase MASS
> >>>>> "0.9975-11" "0.9975-8" "1.4-3" "0.1-4" "0.14-16"
> >>>>> "0.4-3" "7.2-31"
> >>>>> JGR iplots JavaGD rJava
> >>>>> "1.4-15" "1.0-5" "0.3-5" "0.4-13"
> >>>>> *************************
> >>>>> lmer runs the example w/o a problem
> >>>>>
> >>>>> I just tried to run it on on Intel-based MacPro, and lmer2 ran
> >>>>> without a hitch.
> >>> _____________________________
> >>> Professor Michael Kubovy
> >>> University of Virginia
> >>> Department of Psychology
> >>> USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
> >>> Parcels: Room 102 Gilmer Hall
> >>> McCormick Road Charlottesville, VA 22903
> >>> Office: B011 +1-434-982-4729
> >>> Lab: B019 +1-434-982-4751
> >>> Fax: +1-434-982-4766
> >>> WWW: http://www.people.virginia.edu/~mk9y/
> >>>
> >>
> >> _______________________________________________
> >> R-SIG-Mac mailing list
> >> R-SIG-Mac at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >>
>
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