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Liaw, Andy

2004-Mar-16 19:37 UTC

[Rd] make check failed for R-1.9.0alpha (2004-03-16) when link against Goto's BLAS

Dear all,

Has anyone seen the same problem?  I tried compiling R-1.9.0 alpha
(2004-03-16) on our Opteron box running SUSE Linux ES8.  I ran:

./configure --enable-R-shlib --with-blas=goto

and got:

  Source directory:          .
  Installation directory:    /usr/local

  C compiler:                gcc  -m64 -O2 -g -msse2 -march=k8 -Wall
--pedantic
  C++ compiler:              g++  -m64 -O2 -g -msse2 -march=k8 -Wall
--pedantic
  Fortran compiler:          g77  -m64 -O2 -g -msse2 -march=k8

  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(generic)
  Additional capabilities:   PNG, JPEG
  Options enabled:           shared library, R profiling

  Recommended packages:      yes

(The Goto BLAS is libgoto_opt64-r0.93.so.)

"make" ran fine, but "make check" failed with tail
tests/Examples/stats-Ex.Rout.fail giving:
> ## now see the effect of the explanatory variables
> data(Seatbelts)
> X <- Seatbelts[, c("kms", "PetrolPrice",
"law")]
> X[, 1] <- log10(X[, 1]) - 4
> arima(log10(Seatbelts[, "drivers"]), c(1,0,0),+       seasonal = list(order= c(1,0,0)), xreg = X)
Error in La.svd(x, nu, nv, method) : error code 3 from Lapack routine dgesdd
Execution halted

If I do "make clean" and re-configure without the Goto BLAS, then it
passes
make check.  Does anyone know what I'm doing wrong?  Any help much
appreciated!

Best,
Andy


Andy Liaw, PhD
Biometrics Research      PO Box 2000, RY33-300     
Merck Research Labs           Rahway, NJ 07065
mailto:andy_liaw@merck.com        732-594-0820




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Peter Dalgaard

2004-Mar-16 23:03 UTC

head link

[Rd] make check failed for R-1.9.0alpha (2004-03-16) when link against Goto's BLAS

"Liaw, Andy" <andy_liaw@merck.com> writes:
> Dear all,
> 
> Has anyone seen the same problem?  I tried compiling R-1.9.0 alpha
> (2004-03-16) on our Opteron box running SUSE Linux ES8.  I ran:
> 
> ./configure --enable-R-shlib --with-blas=goto
> 
> and got:
> 
>   Source directory:          .
>   Installation directory:    /usr/local
> 
>   C compiler:                gcc  -m64 -O2 -g -msse2 -march=k8 -Wall
> --pedantic
>   C++ compiler:              g++  -m64 -O2 -g -msse2 -march=k8 -Wall
> --pedantic
>   Fortran compiler:          g77  -m64 -O2 -g -msse2 -march=k8
> 
>   Interfaces supported:      X11, tcltk
>   External libraries:        readline, BLAS(generic)
>   Additional capabilities:   PNG, JPEG
>   Options enabled:           shared library, R profiling
> 
>   Recommended packages:      yes
> 
> (The Goto BLAS is libgoto_opt64-r0.93.so.)
> 
> "make" ran fine, but "make check" failed with tail
> tests/Examples/stats-Ex.Rout.fail giving:
> 
> > ## now see the effect of the explanatory variables
> > data(Seatbelts)
> > X <- Seatbelts[, c("kms", "PetrolPrice",
"law")]
> > X[, 1] <- log10(X[, 1]) - 4
> > arima(log10(Seatbelts[, "drivers"]), c(1,0,0),
> +       seasonal = list(order= c(1,0,0)), xreg = X)
> Error in La.svd(x, nu, nv, method) : error code 3 from Lapack routine
dgesdd
> Execution halted
> 
> If I do "make clean" and re-configure without the Goto BLAS, then
it passes
> make check.  Does anyone know what I'm doing wrong?  Any help much
> appreciated!
Odd... I'm (seemingly) passing make check with 

pd@linux:~/r-devel/BUILD-GOTO> ldd bin/R.bin
        libgoto_opt64p-r0.93.so => not found
        libpthread.so.0 => /lib64/libpthread.so.0 (0x0000002a9566d000)
        libg2c.so.0 => /usr/lib64/libg2c.so.0 (0x0000002a95801000)
        libm.so.6 => /lib64/libm.so.6 (0x0000002a95923000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000002a95a7d000)
        libreadline.so.4 => /lib64/libreadline.so.4
        (0x0000002a95b88000)
        libdl.so.2 => /lib64/libdl.so.2 (0x0000002a95cc2000)
        libncurses.so.5 => /lib64/libncurses.so.5 (0x0000002a95dc5000)
        libc.so.6 => /lib64/libc.so.6 (0x0000002a95f26000)
        /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2
        (0x0000002a95556000)

(on SuSE 9) The only obvious difference is that I'm using the threaded
version of the BLAS. It is of course possible that some last-digit
difference is sending arima() out on a different branch for you.

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907

Prof Brian Ripley

2004-Mar-16 23:35 UTC

head link

[Rd] make check failed for R-1.9.0alpha (2004-03-16) when link against Goto's BLAS

I suspect you are not going wrong, but rather that the Opteron Goto BLAS 
is not accurate enough on your particular system.  Unfortunately these 
LAPACK routines can be sensitive to the buildup of rounding errors, and 
that is affected by the BLAS in use.

On Tue, 16 Mar 2004, Liaw, Andy wrote:
> Dear all,
> 
> Has anyone seen the same problem?  I tried compiling R-1.9.0 alpha
> (2004-03-16) on our Opteron box running SUSE Linux ES8.  I ran:
> 
> ./configure --enable-R-shlib --with-blas=goto
> 
> and got:
> 
>   Source directory:          .
>   Installation directory:    /usr/local
> 
>   C compiler:                gcc  -m64 -O2 -g -msse2 -march=k8 -Wall
> --pedantic
>   C++ compiler:              g++  -m64 -O2 -g -msse2 -march=k8 -Wall
> --pedantic
>   Fortran compiler:          g77  -m64 -O2 -g -msse2 -march=k8
> 
>   Interfaces supported:      X11, tcltk
>   External libraries:        readline, BLAS(generic)
>   Additional capabilities:   PNG, JPEG
>   Options enabled:           shared library, R profiling
> 
>   Recommended packages:      yes
> 
> (The Goto BLAS is libgoto_opt64-r0.93.so.)
> 
> "make" ran fine, but "make check" failed with tail
> tests/Examples/stats-Ex.Rout.fail giving:
> 
> > ## now see the effect of the explanatory variables
> > data(Seatbelts)
> > X <- Seatbelts[, c("kms", "PetrolPrice",
"law")]
> > X[, 1] <- log10(X[, 1]) - 4
> > arima(log10(Seatbelts[, "drivers"]), c(1,0,0),
> +       seasonal = list(order= c(1,0,0)), xreg = X)
> Error in La.svd(x, nu, nv, method) : error code 3 from Lapack routine
dgesdd
> Execution halted
> 
> If I do "make clean" and re-configure without the Goto BLAS, then
it passes
> make check.  Does anyone know what I'm doing wrong?  Any help much
> appreciated!
> 
> Best,
> Andy
> 
> 
> Andy Liaw, PhD
> Biometrics Research      PO Box 2000, RY33-300     
> Merck Research Labs           Rahway, NJ 07065
> mailto:andy_liaw@merck.com        732-594-0820
> 
> 
> 
> 
>
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> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
> 
> 
-- 
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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