Mark,
>
> To the extent that it may be helpful here and I can do more if need be, I
> built 32 bit R 2.12.0 patched on Snow Leopard (10.6.4), using the R BLAS
> rather than Apple's veclib. This is on an early 2009 17" MBP with a 2.93 Ghz
> Core 2 Duo (MacBookPro5,2) and 4Gb of RAM.
>
> Based upon Doug's comment in this thread that the issue may be related to the
> use of Apple's veclib BLAS, as opposed to R's reference BLAS, I ran some
> tests.
>
> My config includes:
>
> --without-blas --without-lapack
>
> just to be sure that the above is the correct invocation, based upon what I
> found online.
>
> Using this build, with all CRAN packages freshly installed using this build,
> I ran the example used here with lme4 0.999375-35. I get:
>
> library(lme4)
> y <- (1:20)*pi; x <- (1:20)^2;group <- gl(2,10)
> M2. <- lmer (y ~ 1 + x + (1 + x | group))
> M2 <- lmer (y ~ x + ( x | group))
>
>> identical(fixef(M2), fixef(M2.))
> [1] TRUE
>
>
>
> I then created a function so that I could use replicate() to run this test a
> "larger" number of times:
>
> testlme4 <- function()
> {
> y <- (1:20)*pi; x <- (1:20)^2;group <- gl(2,10)
> M2. <- lmer (y ~ 1 + x + (1 + x | group))
> M2 <- lmer (y ~ x + ( x | group))
> identical(fixef(M2), fixef(M2.))
> }
>
>
> RES <- replicate(1000, testlme4())
>
>> all(RES)
> [1] TRUE
>
>> table(RES)
> RES
> TRUE
> 1000
>
> Does the example need to be run a "very large" number of times to be sure
> that it does not fail, or is the above a reasonable indication that the use
> of R's BLAS is a more appropriate default option for R on OSX? If I am not
> mistaken (and somebody correct me if wrong), R's BLAS is the default on
> Windows and Linux (from my recollections on Fedora). Why should OSX be
> different in that regard?
Thanks for the very informative post. I added R-Mac in my reply to see if
someone can come up with a response to your query. It would also be interesting
to know if it were possible to switch the OSX R binary to use the R BLAS
library.
>
> Also, as an aside to Federico, I use 32 bit R on OSX largely because I have
> to interact with an Oracle server via RODBC. The only ODBC drivers available
> for Oracle on OSX are 32 bit and they are not compatible with 64 bit R. It
> would be rather cumbersome when running reports (via Sweave) to first extract
> the data in 32 bit R and then switch to 64 bit R to run the reports. I can
> run it all in a single step using 32 bit R. I also do not have a need for the
> larger memory address space afforded by 64 bit R.
I'm very primitive in any integration between R and anything else, so much so
that I abandoned Emacs (well integrated with R) for Vim (not as well
integrated). On the other hand I do need the greater memory address space of
R64. I understand my needs and habits are not universally shared, but, if the
*only* reason for using R32 vs R64 is the 20% speed difference, I'd use R64 for
running lme4.
Best,
Federico
--
Federico C. F. Calboli
Department of Epidemiology and Biostatistics
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 75941602 Fax +44 (0)20 75943193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
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