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. 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.
I am not encountering segfaults on a 64-bit build of R 2.4.0 compiled with gcc and g77 3.4.5 and ATLAS 3.6.0 on a Red Hat Athlon64 system. -----Original Message----- From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Douglas Bates Sent: Monday, October 16, 2006 10:26 AM To: R Development Mailing List Subject: [Rd] x86_64, acml-3.5.0-gfortran64 and lme4 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. 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
I did not try the ACML but I have experienced problems both in configure and in make on my SUSE 10.0 x86_64 with gcc 4.0.2. The problem was due to a bug in gfortran so that I had to update to version 4.2 (I did not update gcc though). I do not know whether this may apply to you but updating the gfortran is highly recommended by the developers. Kind regards, Simone On 10/16/06, Douglas Bates <bates at stat.wisc.edu> 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. > > 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 >-- ______________________________________________________ Simone Giannerini Dipartimento di Scienze Statistiche "Paolo Fortunati" Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098262 Fax: +39 051 232153
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