Re: [Rd] unable to load lapack.so

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri 29 Sep 2006 - 07:55:25 GMT

On Fri, 29 Sep 2006, Hiroyuki Kawakatsu wrote:

> On 9/28/06, Prof Brian Ripley <ripley@stats.ox.ac.uk> wrote:
>
>>> I'm having problems using ACML with R. I made two changes in
>>> config.site by setting
>>> LDFLAGS="-L/opt/acml3.1.0/gnu64/lib"
>>> BLAS_LIBS="-lacml"
>>
>> That's not how the R-admin manual describes how to do this.
>> Please try the way it does describe

There is a specific section on using ACML, via command-line flags. One point is that you want the path as part of BLAS_LIBS, not for all compilation.

> After re-reading appendix A2.2, I still don't see what I am doing
> wrong. The comments in config.site say
> ## Use LAPACK_LIBS for all '-L' and '-l' options needed for linking
> ## against an external LAPACK implementation.
> ## Note that (see R-admin) that our main intention is to allow a
> ## LAPACK-containing BLAS to be used, so this is rarely needed, and
> ## it is not used if the BLAS already contains LAPACK.
> so I don't need to set LAPACK_LIBS as the acml BLAS already contains LAPACK?
>
>> I am a bit puzzled: currently ACML is only available for Linux, Solaris
>> and Windows, so where did you find a FreeBSD version?
>
> I didn't; but see
> http://lists.freebsd.org/pipermail/freebsd-amd64/2005-September/006043.html

Well, you failed to mention that you were using a Linux version ....

>> Apparently libRlapack.so. Is it there (in R_HOME/lib)?
>
> yes:
> erdos# ls -l /usr/local/R-patched/lib
> total 1808
> -rwxr-xr-x 1 root 30 1832001 Sep 29 07:08 libRlapack.so*
>
>> (and please try 2.4.0 RC rather than an old patched version of 2.3.1).
>
> Ah, when I tried R-rc, I found what I was doing wrong: the copy of R
> in /usr/local/bin/R was not updated from R_HOME/bin/R
>
> For R-rc with the same two changes in config.site, the build passes
> make check (except for internet.R as I am behind a firewall and set
> http_proxy in .Renviron which appears to be ignored by make check).

Yes, all tests are run with --vanilla. You need to set variables in the global environment.

> But in lib/ I now have
>
> erdos# ls -l /usr/local/R-rc/lib/
> total 2112
> -rwxr-xr-x 1 root 506 289732 Sep 29 07:52 libRblas.so*
> -rwxr-xr-x 1 root 506 1831697 Sep 29 07:57 libRlapack.so*
>
> Does this mean that the acml BLAS is not being used?

What does libRblas.so link to?
You really do need to study the manual section on BLASes, as that suggests a different (and more efficient) way of doing this.

>
>> version
> _
> platform x86_64-unknown-freebsd6.1
> arch x86_64
> os freebsd6.1
> system x86_64, freebsd6.1
> status RC
> major 2
> minor 4.0
> year 2006
> month 09
> day 27
> svn rev 39543
> language R
> version.string R version 2.4.0 RC (2006-09-27 r39543)
>
> h.
> --
> ----------------------------------
> Hiroyuki Kawakatsu
> Business School
> Dublin City University
> Dublin 9, Ireland
> Tel +353 (0)1 700 7496
>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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