[R-sig-Fedora] problems compiling for RHEL 5.3 x86_64

[Roger Bivand]

On Fri, 26 Jun 2009, Evan Cooch wrote:

> Well, CentOS 5.3, which amounts to the same thing.
>
> I recently decided to upgrade my main research machine from Fedora Core 8 -> 
> CentOS 5.3. Basically, I was looking to move to a distro with longer 
> 'term-of-life' than the release schedule for Fedora currently allows. The 
> machine is a multi-Opteron box, so both 32- and 64-bit apps natively 
> supported. Since I do a lot of 'linear algebra'-heavy things with R, I had 
> compiled R 2.9.0 against the ACML blas. ACML contains lapack, so I killed two 
> birds with one stone. Generally, I would do a configure with
>
> ./configure --with-tcltk --with-blas="-L/opt/acml4.3.0/gfortran64/lib -lacml"
>
> Worked perfectly. Led to 10-20x speedup in certain calculations.
>
>
> Things haven't been so good since moving to CentOS. The install of the OS 
> went fine, but I can't for the life of me figure out how to compile R against 
> blas - ACML-variety or otherwise. Moreover, putting in --with-lapack 
> explicitly causes all sorts of errors - the main one being 'hinted at' in the 
> R admin docs. The error is
>
> Error in La.svd(x, nu, nv) :
> BLAS/LAPACK routine 'DGESDD' gave error code -12
> Calls: cancor -> svd -> La.svd -> .Call
> Execution halted
>
> So, from the admin guide, I find the following
>
> Since ACML contains a full LAPACK, if selected as the BLAS it can be used as 
> the LAPACK /via/ --with-lapack.
> If you do use --with-lapack, be aware of potential problems with bugs in the 
> LAPACK 3.0 sources (or in the posted corrections to those sources). In 
> particular, bugs in |DGEEV| and |DGESDD| have resulted in error messages such 
> as
>
> DGEBRD gave error code -10
>
> Not quite the same error code, but close enough I suspect they're related.
>
> I tried different forms of blas too (atlas, acml) - made little difference.
>
> So, several quick questions:
>
> 1. anyone managed to get x86_64 R compiled under either RHEL, Fedora, or 
> CentOS? I don't mean 'installed from an RPM', but...compiled from source.

Yes, RHEL5, x86_64, no problem.

>
> 2. anyone who answers 'yes' to (1) - did you manage to get it to play nice 
> with blas and lapack?

Yes, with GoToBLAS, using the instructions in:

http://cran.r-project.org/doc/manuals/R-admin.html#Linear-algebra

especially:

"Another option to change the BLAS in use is to symlink a dynamic BLAS 
library (such as ACML or Goto's) to R_HOME/lib/libRblas.so. For example, 
just

      mv R_HOME/lib/libRblas.so R_HOME/lib/libRblas.so.keep
      ln -s /opt/acml4.0.1/gfortran64_mp/lib/libacml_mp.so \
      R_HOME/lib/libRblas.so

will change the BLAS in use to multithreaded ACML."

Note especially A.3.2. Running on a dual core box works well.

Hope this helps,

Roger

>
>
> Before I do a clean install of yet another distro, I'd really like to figure 
> out what is going on, and possibly solve the problem.
>
> Thanks in advance...
>
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-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no