Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
Prof Brian Ripley [EMAIL PROTECTED] writes: Any clue whether there is any benefit in using the FC3 versions over the versions that ships with R? Yes: at least for earlier versions, none. (See the comments in the R-admin manual I quoted yesterday which no one else seems to have read.) I did know about them. I was being mildly sarcastic and partly curious. In principle, having lapack/blas maintained as part of the distributions would be good, especially if they could sort out the (nontrivial) processor-specific tuning issues. Currently, the RPMs of R for both SuSE and Fedora ship with minimal tuning, and you need to compile your own version to take advantage of (say) an ATLAS blas. This is not hard to do, but you lose the niceties of the RPM system with respect to upgrades, dependencies and all that. In practice, if the distributions also ship minimally tuned libs, and buggy ones too, the point gets rather moot. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
Peter Dalgaard wrote:
Prof Brian Ripley [EMAIL PROTECTED] writes:
Any clue whether there is any benefit in using the FC3 versions over
the versions that ships with R?
Yes: at least for earlier versions, none. (See the comments in the
R-admin manual I quoted yesterday which no one else seems to have
read.)
I did know about them. I was being mildly sarcastic and partly
curious.
In principle, having lapack/blas maintained as part of the
distributions would be good, especially if they could sort out the
(nontrivial) processor-specific tuning issues. Currently, the RPMs of
R for both SuSE and Fedora ship with minimal tuning, and you need to
compile your own version to take advantage of (say) an ATLAS blas.
This is not hard to do, but you lose the niceties of the RPM system
with respect to upgrades, dependencies and all that.
In practice, if the distributions also ship minimally tuned libs, and
buggy ones too, the point gets rather moot.
Just to draw this particular thread to a close - I gave the FC3 lapack a
run - as I'm stubborn and (like Peter) a little curious. The compilation
proceeded without hangs, errors or warnings, but make check failed
whilst running the examples from base. So looks like everything written
in R Admin document holds for at least the current lapack distributed
with FC3 (yes, I did read it!), so it looks like relying on
distributions for lapack is not going to work just yet...
I provide the output from make check and base-Ex.Rout.fail just for
illustration. I am quite happy with my R and the inbuilt lapack and FC3
provided blas - I was using the arrival of a new laptop as an excuse to
try out a few things I had avoided previously and have learnt quite a
lot in the process.
Thanks for everyone's input.
All the best,
Gav
Output from make check:
make[5]: Entering directory `/home/gavin/R/buildLapack/src/library'
Building/Updating help pages for package 'base'
Formats: text html latex example
make[5]: Leaving directory `/home/gavin/R/buildLapack/src/library'
running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1
make[4]: Leaving directory `/home/gavin/R/buildLapack/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/home/gavin/R/buildLapack/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/home/gavin/R/buildLapack/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home/gavin/R/buildLapack/tests'
make: *** [check-devel] Error 2
And from base-Ex.Rout.fail we have:
### Name: kappa
### Title: Estimate the Condition Number
### Aliases: kappa kappa.default kappa.lm kappa.qr kappa.tri
### Keywords: math
### ** Examples
kappa(x1 - cbind(1,1:10))# 15.71
[1] 15.70590
kappa(x1, exact = TRUE)# 13.68
[1] 13.67903
kappa(x2 - cbind(x1,2:11))# high! [x2 is singular!]
[1] 8.351867e+16
hilbert - function(n) { i - 1:n; 1 / outer(i - 1, i, +) }
sv9 - svd(h9 - hilbert(9))$ d
kappa(h9)# pretty high!
[1] 728289254735
kappa(h9, exact = TRUE) == max(sv9) / min(sv9)
Error in La.svd(x, nu, nv) : LAPACK routine 'DGEBRD' gave error code -10
Execution halted
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522
ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/
London. WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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[Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
Hi, On a new Dell laptop, with a fresh FC3 installation (with latest updates applied) I am experiencing make hanging consistently after/during building grDevices. This happens when using the configure flag --with-lapack (I have the LAPACK rpm distributed with FC3 installed). The last two lines of output are: make[5]: Leaving directory `/home/gavin/R/devel/build/src/library/grDevices/src' make[4]: Leaving directory `/home/gavin/R/devel/build/src/library/grDevices/src' hang here There are no errors or warnings printed to the console. The same thing happens with r-patched. Both source trees were checked out using subversion. If I remove the configure flag for lapack, r-patches and r devel both build fine. I'm not sure where to look for error messages or to diagnose the problem. Has anyone experienced a similar problem? Where should I look for any errors/logs? Any other suggestions? All the best, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
On Wed, 2005-05-04 at 13:56 +0100, Gavin Simpson wrote: Hi, On a new Dell laptop, with a fresh FC3 installation (with latest updates applied) I am experiencing make hanging consistently after/during building grDevices. This happens when using the configure flag --with-lapack (I have the LAPACK rpm distributed with FC3 installed). The last two lines of output are: make[5]: Leaving directory `/home/gavin/R/devel/build/src/library/grDevices/src' make[4]: Leaving directory `/home/gavin/R/devel/build/src/library/grDevices/src' hang here There are no errors or warnings printed to the console. The same thing happens with r-patched. Both source trees were checked out using subversion. If I remove the configure flag for lapack, r-patches and r devel both build fine. I'm not sure where to look for error messages or to diagnose the problem. Has anyone experienced a similar problem? Where should I look for any errors/logs? Any other suggestions? Gavin, FWIW, I can duplicate this behavior on my Dell 5150 w/ FC3 using the r- patched tarball from 2005-05-03. I thought that perhaps this might be related to the use of the nVidia proprietary driver, but temporarily going back to the 'nv' driver did not resolve the problem. Thus, I am unable to provide more information as to the etiology of the problem other than to point to some of the references in the r-admin manual starting on page 19 regarding linear algebra. Perhaps there is a problem with the FC3 LAPACK. Best regards, Marc Schwartz __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
Marc Schwartz wrote: On Wed, 2005-05-04 at 13:56 +0100, Gavin Simpson wrote: Hi, On a new Dell laptop, with a fresh FC3 installation (with latest updates applied) I am experiencing make hanging consistently after/during building grDevices. This happens when using the configure flag --with-lapack (I have the LAPACK rpm distributed with FC3 installed). The last two lines of output are: make[5]: Leaving directory `/home/gavin/R/devel/build/src/library/grDevices/src' make[4]: Leaving directory `/home/gavin/R/devel/build/src/library/grDevices/src' hang here There are no errors or warnings printed to the console. The same thing happens with r-patched. Both source trees were checked out using subversion. If I remove the configure flag for lapack, r-patches and r devel both build fine. I'm not sure where to look for error messages or to diagnose the problem. Has anyone experienced a similar problem? Where should I look for any errors/logs? Any other suggestions? Gavin, FWIW, I can duplicate this behavior on my Dell 5150 w/ FC3 using the r- patched tarball from 2005-05-03. I thought that perhaps this might be related to the use of the nVidia proprietary driver, but temporarily going back to the 'nv' driver did not resolve the problem. Thus, I am unable to provide more information as to the etiology of the problem other than to point to some of the references in the r-admin manual starting on page 19 regarding linear algebra. Perhaps there is a problem with the FC3 LAPACK. Best regards, Marc Schwartz Cheers for this Mark, I had a quick google search for this problem and found a discussion in the redhat mailing list archives that discusses the issue and points to the following bug: https://bugzilla.redhat.com/beta/show_bug.cgi?id=138447 Which describes the behaviour I am experiencing. Basically, the LAPACK in FC3 is broken because it was compiled with gcc-3.4 and that introduced errors when -O2 optimisations were used to compile the rpm. That bug was recently reopened so there may be the possibility of the FC3 rpm being updated (the underlying problem has been fixed by compiling with lower optimisation). I'll read more of the r-admin, and see about finding an alternative. Also, note that lapack has been moved to Fedora Extras from FC4 so that's one more thing to remember to add after upgrading! All the best, Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
On Wed, 4 May 2005, Marc Schwartz wrote:
On Wed, 2005-05-04 at 13:56 +0100, Gavin Simpson wrote:
Hi,
On a new Dell laptop, with a fresh FC3 installation (with latest updates
applied) I am experiencing make hanging consistently after/during
building grDevices. This happens when using the configure flag
--with-lapack (I have the LAPACK rpm distributed with FC3 installed).
The last two lines of output are:
make[5]: Leaving directory
`/home/gavin/R/devel/build/src/library/grDevices/src'
make[4]: Leaving directory
`/home/gavin/R/devel/build/src/library/grDevices/src'
hang here
There are no errors or warnings printed to the console.
The same thing happens with r-patched. Both source trees were checked
out using subversion.
If I remove the configure flag for lapack, r-patches and r devel both
build fine. I'm not sure where to look for error messages or to diagnose
the problem. Has anyone experienced a similar problem? Where should I
look for any errors/logs? Any other suggestions?
Gavin,
FWIW, I can duplicate this behavior on my Dell 5150 w/ FC3 using the r-
patched tarball from 2005-05-03.
I thought that perhaps this might be related to the use of the nVidia
proprietary driver, but temporarily going back to the 'nv' driver did
not resolve the problem.
Thus, I am unable to provide more information as to the etiology of the
problem other than to point to some of the references in the r-admin
manual starting on page 19 regarding linear algebra.
Perhaps there is a problem with the FC3 LAPACK.
In any case, we do not recommend an external LAPACK unless it is
essential. There are far too many buggy ones about, and there is no
performance gain in using someone else's compile of a nearly identical
code base. Is
Provision is made for using an external LAPACK library, principally to
cope with BLAS libraries which contain a copy of LAPACK (such as
@code{libsunperf} on Solaris and @code{vecLib} on Mac OS X).
However, the likely performance gains are thought to be small (and may
be negative), and the default is not to search for a suitable LAPACK
library.
If you do use @option{--with-lapack}, be aware of potential problems
with bugs in the LAPACK 3.0 sources (or in the posted corrections to
those sources).
not enough warning?
--
Brian D. Ripley, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
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Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
On Wed, 2005-05-04 at 16:58 +0100, Gavin Simpson wrote: snip Cheers for this Mark, I had a quick google search for this problem and found a discussion in the redhat mailing list archives that discusses the issue and points to the following bug: https://bugzilla.redhat.com/beta/show_bug.cgi?id=138447 Which describes the behaviour I am experiencing. Basically, the LAPACK in FC3 is broken because it was compiled with gcc-3.4 and that introduced errors when -O2 optimisations were used to compile the rpm. That bug was recently reopened so there may be the possibility of the FC3 rpm being updated (the underlying problem has been fixed by compiling with lower optimisation). I'll read more of the r-admin, and see about finding an alternative. Also, note that lapack has been moved to Fedora Extras from FC4 so that's one more thing to remember to add after upgrading! All the best, Gav Thanks for the update Gavin. For FC4, there are a lot of things that are either going to be new in or are moving to Extras (including R BTW). Much controversy over some of the decisions made there, but that's another topic for another thread in a different galaxy, far, far away... ;-) Best regards, Marc __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
Gavin Simpson [EMAIL PROTECTED] writes: Basically, the LAPACK in FC3 is broken because it was compiled with gcc-3.4 and that introduced errors when -O2 optimisations were used to compile the rpm. That bug was recently reopened so there may be the possibility of the FC3 rpm being updated (the underlying problem has been fixed by compiling with lower optimisation). There's a pending update on lapack/blas now, which may or may not fix the issue (no announcement in the archives). Any clue whether there is any benefit in using the FC3 versions over the versions that ships with R? -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
On Wed, 2005-05-04 at 21:15 +0200, Peter Dalgaard wrote: Gavin Simpson [EMAIL PROTECTED] writes: Basically, the LAPACK in FC3 is broken because it was compiled with gcc-3.4 and that introduced errors when -O2 optimisations were used to compile the rpm. That bug was recently reopened so there may be the possibility of the FC3 rpm being updated (the underlying problem has been fixed by compiling with lower optimisation). There's a pending update on lapack/blas now, which may or may not fix the issue (no announcement in the archives). Any clue whether there is any benefit in using the FC3 versions over the versions that ships with R? Peter, I cannot offer an authoritative response here and perhaps Gavin has other information. Recognizing the absence of evidence is not evidence of absence, I have not seen anything (benchmarks, etc.) to suggest that there is an advantage. Regards, Marc __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3
On Wed, 4 May 2005, Peter Dalgaard wrote: Gavin Simpson [EMAIL PROTECTED] writes: Basically, the LAPACK in FC3 is broken because it was compiled with gcc-3.4 and that introduced errors when -O2 optimisations were used to compile the rpm. That bug was recently reopened so there may be the possibility of the FC3 rpm being updated (the underlying problem has been fixed by compiling with lower optimisation). There's a pending update on lapack/blas now, which may or may not fix the issue (no announcement in the archives). Any clue whether there is any benefit in using the FC3 versions over the versions that ships with R? Yes: at least for earlier versions, none. (See the comments in the R-admin manual I quoted yesterday which no one else seems to have read.) -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
