From ripley at stats.ox.ac.uk  Mon Oct 16 19:18:24 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 16 Oct 2006 18:18:24 +0100 (BST)
Subject: [Rd] x86_64, acml-3.5.0-gfortran64 and lme4
In-Reply-To: <40e66e0b0610160725y1afbaa56v906ac6efc595ae26@mail.gmail.com>
References: <40e66e0b0610160725y1afbaa56v906ac6efc595ae26@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0610161758010.30837@gannet.stats.ox.ac.uk>

On Mon, 16 Oct 2006, Douglas Bates wrote:

> I am encountering segfaults when checking the lme4 package on an
> Athlon64 system if I use the acml blas.  R was built as a 64-bit
> application using the GCC 4.0.3 compiler suite including gfortran.
> The version of acml is 3.5.0 gfortran64.

gcc 4.1.1 is current, and I would suggest an update would be a good idea: 
my tests with gcc4 went a lot better with 4.1.0 than 4.0.3.

I have an FC5 dual x86_64 system (hence gcc 4.1.1) with ACML 3.5.0 and 
Goto 1.06 (I cannot get ATLAS to build on that system).  I too get a 
segfault with ACML (I used the _mp version, but also tried with it 
confined to a single thread), but not with Goto nor R's internal BLAS.

> I do not encounter the segfaults when I compile R with R's built-in
> BLAS.  The errors occur in the first example in lme4 in a call to
> lmer. It looks like they would occur in any call to lmer.  Running
> under the debugger shows that the segfault occurs in a call to dtrsm
> (a level-3 BLAS routine to solve a triangular system of equations)
> that is called from within a cholmod (sparse matrix library) routine.
>
> Has anyone succeeded in running R CMD check on the lme4 package with
> accelerated BLAS?  I'm trying to pin down is this occurs only with
> ACML or also with Atlas and/or Goto's BLAS.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at 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




[Rd] x86_64, acml-3.5.0-gfortran64 and lme4
Prof Brian Ripley