From Kurt.Hornik at wu-wien.ac.at  Wed May 11 15:26:33 2005
From: Kurt.Hornik at wu-wien.ac.at (Kurt Hornik)
Date: Wed May 11 15:25:40 2005
Subject: [Rd] Implementing R on  IBM p690 cluster Jump
In-Reply-To: <A50528B3-0599-4169-8ECE-358F1C979BD6@unsw.edu.au>
References: <200505111004.j4BA31sr016854@hypatia.math.ethz.ch>
	<A50528B3-0599-4169-8ECE-358F1C979BD6@unsw.edu.au>
Message-ID: <17026.2057.639088.387478@mithrandir.hornik.net>

>>>>> Bill Northcott writes:

> On 11/05/2005, at 8:04 PM, Ralf Seppel wrote:
>> we're trying to implement R on the IBM p690 cluster "Jump" at the
>> research centre in J?lich, Germany (c.f.
>> http://www.fz-juelich.de/nic/Supercomputer/computer-e.html)
>> using the most recent version of R (2.1.0) and precisly following the
>> installation instructions.
>> 
>> .............
>> checking for cos in -lm... yes
>> checking for sin in -lm... yes
>> .............
>> checking for GNU gettext in libc... no
>> checking for GNU gettext in libintl... no
>> checking whether to use NLS... yes
>> checking where the gettext function comes from... included intl  
>> directory
>> ...............
>> gcc -Wl,-bM:SRE -Wl,-H512 -Wl,-T512 -Wl,-bnoentry -Wl,- 
>> bexpall
>> -Wl,-bI:../../../etc/R.exp -L/usr/local/lib -o R_X11.so  dataentry.lo
>> devX11.lo rotated.lo rbitmap.lo -lSM -lICE -lX11  -ljpeg -lpng -lz
>> ld: 0711-317 ERROR: Undefined symbol: .log10
>> ld: 0711-317 ERROR: Undefined symbol: .floor
>> ld: 0711-317 ERROR: Undefined symbol: .libintl_gettext
>> ld: 0711-317 ERROR: Undefined symbol: .pow
>> ld: 0711-317 ERROR: Undefined symbol: .sin
>> ld: 0711-317 ERROR: Undefined symbol: .cos
>> ld: 0711-317 ERROR: Undefined symbol: .tan
>> ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
>> information.
>> collect2: ld returned 8 exit status

> There seem to be problems in the autoconf stuff.  cos and sin are
> being located in libm but the link line you show has no '-lm' which
> accounts for 6 of the 7 missing symbols.  Also gettext seems to have
> been located by the configure script, but there is no option on the
> link line to include it in the link. Also search configure.in for
> strings like powerpc-ibm-aix to see what stuff is being done
> specifically for AIX.  It may be out of date in relation to your
> system.

> If it was my problem, I would have look at those bits of the configure
> script and the sections of configure.in that generated them.  Then I
> would compare the AC_SUBST variables with the makefile.in that
> generated the link.  It seems there is some non- communication there.

Bill:

Yes most of the undefined symbols seem to come from libm.  But they
would also be in libm on all other platforms which have such, and we do
not include it there.  On Linux I get

gcc-3.4 -shared -L/usr/local/lib -o R_X11.so  dataentry.lo devX11.lo rotated.lo rbitmap.lo  -lSM -lICE -L/usr/X11R6/lib -lX11  -ljpeg -lpng -lz -L../../../lib -lR

and this works.  As Brian already wrote, we are building a *module*
here, so I assume that we are not getting the flags for building modules
right.  Assuming that libtool can, it might be helpful to look at the
output of BUILDDIR/libtool --config.

-k


[Rd] Implementing R on IBM p690 cluster Jump
Kurt Hornik