[Rd] problem building R-patched on x86-64 with PGI 6.1
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Mar 11 09:02:11 CET 2006
On Fri, 10 Mar 2006, Liaw, Andy wrote:
> Dear R-devel,
>
> [I'm not sure if this is appropriate for R-devel. If not, I'm more than
> happy to move it to R-help.]
It is certainly not appropriate to R-help: see the posting guide.
> As those of you who saw my post on R-help know, I've been trying to build
> R-patched on a dual Opteron box running Scyld Beowulf, using the PGI 6.1
> compilers. The build went fine, but I couldn't get it to pass make
> check-all. Jennifer Lai, who reported success with PGI 6.0 previously,
> seems to have the same problem with 6.1. Here are the particulars:
>
> Since R requires IEEE754 conformance, the flag to use for PGI is -Kieee.
> (BTW, configure still insist on sticking in -mieee-fp, which generates a
> warning.) With that flag, the build runs into trouble with the first
> example in ?optim. Running it by hand gives me:
Well, configure insists on doing so because we were told it was correct.
(Will change.) Is -Kieee always correct for PG?
Looking at
http://www.amd.com/us-en/assets/content_type/DownloadableAssets/dwamd_PGI_nov603.pdf
suggests you might want to try -pc64 -Kieee.
>> optim(c(-1.2,1), fr, control=list(trace=6))
> Nelder-Mead direct search function minimizer
> function value for initial parameters = 24.200000
> Scaled convergence tolerance is 3.60608e-07
> Stepsize computed as 0.120000
> BUILD 3 24.200000 7.095296
> REFLECTION 5 15.080000 4.541696
> REFLECTION 7 7.095296 4.456256
> [...]
> HI-REDUCTION 191 0.000002 0.000000
> LO-REDUCTION 193 0.000001 0.000000
>
> and the process just hangs (until ctrl-z and kill -9).
This could well be a problem with extended precision: I'll see if I can
spot anything.
> If I build R without the -Kieee flag, make check-all fails at arith-true.R,
> in particular, the following:
>
>> pretty(pi, n = 10) - 2:5
> [1] -2.220446e-16 -4.440892e-16 -8.881784e-16 -8.881784e-16
>
> whereas the build with the -Kieee flag gives:
>
>> pretty(pi, n = 10) - 2:5
> [1] 0 0 0 0
>
> and can pass the arith-true.R test.
>
> The configuration is as follows:
>
> export PG_HOME=/usr/pgi/linux86-64/6.1
> ~/Rbuild/R-patched/configure \
> CC=pgcc \
> CFLAGS="-g -Kieee" \
> CPPFLAGS="-I$PG_HOME/include -I$PG_HOME/include/CC" \
> CPICFLAGS=-fpic \
> F77=pgf95 \
> FFLAGS="-g -Kieee"\
> FPICFLAGS=-fpic \
> CXX=pgCC \
> CXXFLAGS="-g -Kieee" \
> CXXPICFLAGS=-fpic \
> SHLIB_CXXLDFLAGS=-shared \
> SHLIB_LDFLAGS=-shared \
> LDFLAGS="-L$PG_HOME/libso -L/usr/lib64 -L/usr/X11R6/lib64" \
> --without-tcltk \
> --with-blas="-L/usr/pgi/linux86-64/6.1/libso -lacml"
>
> [The pgf95 (or pgf90) is needed for linking against ACML to work. This
> should be unrelated as optim is in C.]
>
> I'd very much appreciate any pointers.
>
> Best,
> Andy
>
>
> Andy Liaw, PhD
> Biometrics Research PO Box 2000 RY33-300
> Merck Research Labs Rahway, NJ 07065
> andy_liaw(a)merck.com 732-594-0820
>
> ______________________________________________
> 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
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