I'm only now realizing that we have severe problems with R on our
AMD 'Opteron' and 'Athlon64' clients running Redhat Enterprise
with all 64-bit libraries (AFAICS).
The Lapack problem happens for R-patched and R-devel both on
the Opteron and the Athlon64.
Here are platform details:
o "gcc -v" and "g77 -v" both end with the line
gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34)
o I've used ...../configure --without-blas
1) Opteron ("deb7", a dual-processor compute server):
- uname -a :
Linux deb7 2.4.21-9.0.3.ELsmp #1 SMP Tue Apr 20 19:44:29 EDT 2004 x86_64
x86_64 x86_64 GNU/Linux
- /proc/cpuinfo contains (among much more)
vendor_id : AuthenticAMD
cpu family : 15
model : 5
model name : AMD Opteron(tm) Processor 248
2) Athlon64 (a simple "new generation" client - to become my desktop
soon):
- uname -a :
Linux setup-12 2.4.21-15.0.2.EL #1 Wed Jun 16 22:41:44 EDT
2004 x86_64 x86_64 x86_64 GNU/Linux
- /proc/cpuinfo contains
vendor_id : AuthenticAMD
cpu family : 15
model : 14
model name : AMD Athlon(tm) 64 Processor 2800+
----------------
Now the Lapack problem, easily seen from the base eigen()
example:
> eigen(cbind(1, 3:1, 1:3))
$values
[1] 5.7015621 1.0000000 -0.7015621
$vectors
[,1] [,2] [,3]
[1,] 0.4877939 -0.7181217 -0.9576161
[2,] 0.6172751 -0.3893848 0.2036804
[3,] 0.6172751 0.5767849 0.2036804
which is simply plainly wrong and
eigen(cbind(1, 3:1, 1:3), EISPACK=TRUE)
gives the correct eigen values c(5, 1, 0) and corresponding
eigenvectors.
IIRC, we've already dealt with a Lapack problem, and that
workaround (built into R-devel's Makefiles) has been to use
-ffloat-store for the compilation of src/modules/lapack/dlamc.f
----------
Thank you for hints / suggestions.
Others with 64-bit platforms might also try to see what
eigen(cbind(1, 3:1, 1:3))
gives there.
Martin Maechler
Our `public' Opteron (dual 248, FC2 + Goto BLAS) is right, as is Solaris 64-bit. FC2 is using gcc version 3.3.3 20040412 (Red Hat Linux 3.3.3-7), quite a lot later. I would try updating your compiler (to 3.4.1?) and perhaps try a different BLAS. We do have RHEL for Opteron, but AFAIK it is not on a system at present. (There are others running SuSE 9.0/.1, I believe.) On Tue, 27 Jul 2004, Martin Maechler wrote:> I'm only now realizing that we have severe problems with R on our > AMD 'Opteron' and 'Athlon64' clients running Redhat Enterprise > with all 64-bit libraries (AFAICS). > > The Lapack problem happens for R-patched and R-devel both on > the Opteron and the Athlon64. > > Here are platform details: > > o "gcc -v" and "g77 -v" both end with the line > gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) > > o I've used ...../configure --without-blas > > 1) Opteron ("deb7", a dual-processor compute server): > > - uname -a : > Linux deb7 2.4.21-9.0.3.ELsmp #1 SMP Tue Apr 20 19:44:29 EDT 2004 x86_64 x86_64 x86_64 GNU/Linux > - /proc/cpuinfo contains (among much more) > vendor_id : AuthenticAMD > cpu family : 15 > model : 5 > model name : AMD Opteron(tm) Processor 248 > > 2) Athlon64 (a simple "new generation" client - to become my desktop soon): > > - uname -a : > Linux setup-12 2.4.21-15.0.2.EL #1 Wed Jun 16 22:41:44 EDT > 2004 x86_64 x86_64 x86_64 GNU/Linux > > - /proc/cpuinfo contains > vendor_id : AuthenticAMD > cpu family : 15 > model : 14 > model name : AMD Athlon(tm) 64 Processor 2800+ > > ---------------- > > Now the Lapack problem, easily seen from the base eigen() > example: > > > eigen(cbind(1, 3:1, 1:3)) > $values > [1] 5.7015621 1.0000000 -0.7015621 > > $vectors > [,1] [,2] [,3] > [1,] 0.4877939 -0.7181217 -0.9576161 > [2,] 0.6172751 -0.3893848 0.2036804 > [3,] 0.6172751 0.5767849 0.2036804 > > which is simply plainly wrong and > eigen(cbind(1, 3:1, 1:3), EISPACK=TRUE) > gives the correct eigen values c(5, 1, 0) and corresponding > eigenvectors. > > IIRC, we've already dealt with a Lapack problem, and that > workaround (built into R-devel's Makefiles) has been to use > -ffloat-store for the compilation of src/modules/lapack/dlamc.f > > ---------- > > Thank you for hints / suggestions. > > Others with 64-bit platforms might also try to see what > eigen(cbind(1, 3:1, 1:3)) > gives there.-- 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
Martin Maechler <maechler@stat.math.ethz.ch> writes:> I'm only now realizing that we have severe problems with R on our > AMD 'Opteron' and 'Athlon64' clients running Redhat Enterprise > with all 64-bit libraries (AFAICS). > > The Lapack problem happens for R-patched and R-devel both on > the Opteron and the Athlon64. > > Here are platform details: > > o "gcc -v" and "g77 -v" both end with the line > gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) > > o I've used ...../configure --without-blas > > 1) Opteron ("deb7", a dual-processor compute server): > > - uname -a : > Linux deb7 2.4.21-9.0.3.ELsmp #1 SMP Tue Apr 20 19:44:29 EDT 2004 x86_64 x86_64 x86_64 GNU/Linux > - /proc/cpuinfo contains (among much more) > vendor_id : AuthenticAMD > cpu family : 15 > model : 5 > model name : AMD Opteron(tm) Processor 248 > > 2) Athlon64 (a simple "new generation" client - to become my desktop soon): > > - uname -a : > Linux setup-12 2.4.21-15.0.2.EL #1 Wed Jun 16 22:41:44 EDT > 2004 x86_64 x86_64 x86_64 GNU/Linux > > - /proc/cpuinfo contains > vendor_id : AuthenticAMD > cpu family : 15 > model : 14 > model name : AMD Athlon(tm) 64 Processor 2800+ > > ---------------- > > Now the Lapack problem, easily seen from the base eigen() > example: > > > eigen(cbind(1, 3:1, 1:3)) > $values > [1] 5.7015621 1.0000000 -0.7015621 > > $vectors > [,1] [,2] [,3] > [1,] 0.4877939 -0.7181217 -0.9576161 > [2,] 0.6172751 -0.3893848 0.2036804 > [3,] 0.6172751 0.5767849 0.2036804 > > which is simply plainly wrong and > eigen(cbind(1, 3:1, 1:3), EISPACK=TRUE) > gives the correct eigen values c(5, 1, 0) and corresponding > eigenvectors. > > IIRC, we've already dealt with a Lapack problem, and that > workaround (built into R-devel's Makefiles) has been to use > -ffloat-store for the compilation of src/modules/lapack/dlamc.f > > ---------- > > Thank you for hints / suggestions. > > Others with 64-bit platforms might also try to see what > eigen(cbind(1, 3:1, 1:3)) > gives there.SuSE Linux doesn't seem to have problems, neither with a default build of 1.9.1 (as per Detlef's SPEC file), my ATLAS or GOTO builds of 1.9.0 or a 2.0.0-in-progress from May 5 (sorry: not SVN-ified yet, I *am* on vacation you know...). All give> eigen(cbind(1, 3:1, 1:3))$values [1] 5.000000e+00 1.000000e+00 -4.440892e-16 $vectors [,1] [,2] [,3] [1,] 0.5773503 -0.8451543 -0.9428090 [2,] 0.5773503 -0.1690309 0.2357023 [3,] 0.5773503 0.5070926 0.2357023 The largest and smallest eigenvectors/values are easily seen to be correct. And the middle one is basically this: pd@linux:~/r-devel/BUILD> echo 'cbind(1, 3:1, 1:3)%*%c(-5,-1,3)' | bin/R -q --vanilla> cbind(1, 3:1, 1:3)%*%c(-5,-1,3)[,1] [1,] -5 [2,] -1 [3,] 3 The g77 version info says "3.3.1 (SuSE Linux)" -- 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
On our AMD dual Opteron system running SuSE SLES 8 with
gcc version 3.2.2 (SuSE Linux)
and with R built with `./configure --without-blas' I get
> eigen(cbind(1, 3:1, 1:3))
$values
[1] 5.000000e+00 1.000000e+00 -4.440892e-16
$vectors
[,1] [,2] [,3]
[1,] 0.5773503 -0.8451543 -0.9428090
[2,] 0.5773503 -0.1690309 0.2357023
[3,] 0.5773503 0.5070926 0.2357023
-roger
Martin Maechler wrote:> I'm only now realizing that we have severe problems with R on our
> AMD 'Opteron' and 'Athlon64' clients running Redhat
Enterprise
> with all 64-bit libraries (AFAICS).
>
> The Lapack problem happens for R-patched and R-devel both on
> the Opteron and the Athlon64.
>
> Here are platform details:
>
> o "gcc -v" and "g77 -v" both end with the line
> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34)
>
> o I've used ...../configure --without-blas
>
> 1) Opteron ("deb7", a dual-processor compute server):
>
> - uname -a :
> Linux deb7 2.4.21-9.0.3.ELsmp #1 SMP Tue Apr 20 19:44:29 EDT 2004
x86_64 x86_64 x86_64 GNU/Linux
> - /proc/cpuinfo contains (among much more)
> vendor_id : AuthenticAMD
> cpu family : 15
> model : 5
> model name : AMD Opteron(tm) Processor 248
>
> 2) Athlon64 (a simple "new generation" client - to become my
desktop soon):
>
> - uname -a :
> Linux setup-12 2.4.21-15.0.2.EL #1 Wed Jun 16 22:41:44 EDT
> 2004 x86_64 x86_64 x86_64 GNU/Linux
>
> - /proc/cpuinfo contains
> vendor_id : AuthenticAMD
> cpu family : 15
> model : 14
> model name : AMD Athlon(tm) 64 Processor 2800+
>
> ----------------
>
> Now the Lapack problem, easily seen from the base eigen()
> example:
>
> > eigen(cbind(1, 3:1, 1:3))
> $values
> [1] 5.7015621 1.0000000 -0.7015621
>
> $vectors
> [,1] [,2] [,3]
> [1,] 0.4877939 -0.7181217 -0.9576161
> [2,] 0.6172751 -0.3893848 0.2036804
> [3,] 0.6172751 0.5767849 0.2036804
>
> which is simply plainly wrong and
> eigen(cbind(1, 3:1, 1:3), EISPACK=TRUE)
> gives the correct eigen values c(5, 1, 0) and corresponding
> eigenvectors.
>
> IIRC, we've already dealt with a Lapack problem, and that
> workaround (built into R-devel's Makefiles) has been to use
> -ffloat-store for the compilation of src/modules/lapack/dlamc.f
>
> ----------
>
> Thank you for hints / suggestions.
>
> Others with 64-bit platforms might also try to see what
> eigen(cbind(1, 3:1, 1:3))
> gives there.
>
> Martin Maechler
>
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
>
On our Opteron with SLES8, the GCC 3.2 is only 32-bit, and does not support the -mcpu=k8 flag. I had to install GCC33 to get them. Andy> From: Roger D. Peng > > On our AMD dual Opteron system running SuSE SLES 8 with > > gcc version 3.2.2 (SuSE Linux) > > and with R built with `./configure --without-blas' I get > > > eigen(cbind(1, 3:1, 1:3)) > $values > [1] 5.000000e+00 1.000000e+00 -4.440892e-16 > > $vectors > [,1] [,2] [,3] > [1,] 0.5773503 -0.8451543 -0.9428090 > [2,] 0.5773503 -0.1690309 0.2357023 > [3,] 0.5773503 0.5070926 0.2357023 > > -roger > > Martin Maechler wrote: > > I'm only now realizing that we have severe problems with R on our > > AMD 'Opteron' and 'Athlon64' clients running Redhat Enterprise > > with all 64-bit libraries (AFAICS). > > > > The Lapack problem happens for R-patched and R-devel both on > > the Opteron and the Athlon64. > > > > Here are platform details: > > > > o "gcc -v" and "g77 -v" both end with the line > > gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) > > > > o I've used ...../configure --without-blas > > > > 1) Opteron ("deb7", a dual-processor compute server): > > > > - uname -a : > > Linux deb7 2.4.21-9.0.3.ELsmp #1 SMP Tue Apr 20 > 19:44:29 EDT 2004 x86_64 x86_64 x86_64 GNU/Linux > > - /proc/cpuinfo contains (among much more) > > vendor_id : AuthenticAMD > > cpu family : 15 > > model : 5 > > model name : AMD Opteron(tm) Processor 248 > > > > 2) Athlon64 (a simple "new generation" client - to become > my desktop soon): > > > > - uname -a : > > Linux setup-12 2.4.21-15.0.2.EL #1 Wed Jun 16 22:41:44 EDT > > 2004 x86_64 x86_64 x86_64 GNU/Linux > > > > - /proc/cpuinfo contains > > vendor_id : AuthenticAMD > > cpu family : 15 > > model : 14 > > model name : AMD Athlon(tm) 64 Processor 2800+ > > > > ---------------- > > > > Now the Lapack problem, easily seen from the base eigen() > > example: > > > > > eigen(cbind(1, 3:1, 1:3)) > > $values > > [1] 5.7015621 1.0000000 -0.7015621 > > > > $vectors > > [,1] [,2] [,3] > > [1,] 0.4877939 -0.7181217 -0.9576161 > > [2,] 0.6172751 -0.3893848 0.2036804 > > [3,] 0.6172751 0.5767849 0.2036804 > > > > which is simply plainly wrong and > > eigen(cbind(1, 3:1, 1:3), EISPACK=TRUE) > > gives the correct eigen values c(5, 1, 0) and corresponding > > eigenvectors. > > > > IIRC, we've already dealt with a Lapack problem, and that > > workaround (built into R-devel's Makefiles) has been to use > > -ffloat-store for the compilation of src/modules/lapack/dlamc.f > > > > ---------- > > > > Thank you for hints / suggestions. > > > > Others with 64-bit platforms might also try to see what > > eigen(cbind(1, 3:1, 1:3)) > > gives there. > > > > Martin Maechler > > > > ______________________________________________ > > R-devel@stat.math.ethz.ch mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > > > > ______________________________________________ > R-devel@stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > >