[R-SIG-Mac] [R] lmer2 error under Mac OS X on PowerPC G5 but not on Dual-Core Intel Xeon
Benilton Carvalho
bcarvalh at jhsph.edu
Mon Jan 29 17:40:13 CET 2007
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/
>>>
>>
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