On Oct 21, 2010, at 9:47 AM, Federico Calboli wrote:
> 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.
Yes, see R for Mac FAQ 12.5.
Cheers,
Simon
>>
>> 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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