Bug 119479 – lam-mpi 7.1.2 fails (it wants PIC libpbs.a)

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Eric Thibodeau 2006-01-18 13:06:28 UTC]

First, the environment: 

headless portage # emerge --info
Portage 2.0.53 (default-linux/amd64/2005.1, gcc-3.4.4, glibc-2.3.5-r2, 2.6.14-gentoo-r5 x86_64)
=================================================================
System uname: 2.6.14-gentoo-r5 x86_64 AMD Opteron(tm) Processor 244
Gentoo Base System version 1.6.14
dev-lang/python:     2.3.5, 2.4.2
sys-apps/sandbox:    1.2.12
sys-devel/autoconf:  2.13, 2.59-r6
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1
sys-devel/binutils:  2.16.1
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=opteron -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/X11/xkb /usr/share/config /usr/spool/PBS /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-march=opteron -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig buildpkg ccache distlocks fixpackages sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.datapipe.net/gentoo http://ftp.romnet.org/gentoo/ ftp://gentoo.mirrors.tds.net/gentoo"
LINGUAS="fr en"
MAKEOPTS="-j6"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 berkdb bitmap-fonts blas bzip2 cups emboss expat foomaticdb fortran gif glut gpm imlib lcms lzw lzw-tiff mng mpi ncurses nls opengl openssh pam pdflib perl png python qt readline sdl slang spell ssl tcpd truetype truetype-fonts type1-fonts udev unicode usb userlocales xml2 xpm xv zlib linguas_fr linguas_en userland_GNU kernel_linux elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS

The error message I get:
x86_64-pc-linux-gnu-gcc -shared  -Wl,--whole-archive ../../share/args/.libs/liblamargs.a ../../share/boot/.libs/liblamboot.a ../../share/etc/.libs/liblametc.a ../../share/freq/.libs/liblamfreq.a ../../share/kreq/.libs/liblamkreq.a ../../share/libltdl/.libs/libltdlc.a ../../share/mpi/.libs/liblamextra.a ../../share/nreq/.libs/liblamnreq.a ../../share/rreq/.libs/liblamrreq.a ../../share/ssi/.libs/libssi_lam.a ../../share/threads/.libs/liblamthreads.a ../../share/trillium/.libs/liblamtrillium.a ../../share/tstdio/.libs/liblamtstdio.a -Wl,--no-whole-archive  -pthread -ldl -lpbs -lnsl  -march=opteron -Wl,-soname -Wl,liblam.so.0 -o .libs/liblam.so.0.0.0
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.4/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.4/../../../../lib64/libpbs.a(tm.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.4/../../../../lib64/libpbs.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [liblam.la] Error 1
make[2]: Leaving directory `/var/tmp/portage/lam-mpi-7.1.1-r3/work/lam-7.1.1/share/liblam'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/var/tmp/portage/lam-mpi-7.1.1-r3/work/lam-7.1.1/share'
make: *** [all-recursive] Error 1

What is especially weird is that, according to my logs, this version of lam-mpi _did_ compile correctly once. I must have rebuilt the system with slightly different USE flags in between but, unfortuntalely, portage doesn't log the basic info in the log files (which I will attach for differentiation)

[Comment 1 Eric Thibodeau 2006-01-18 13:13:54 UTC]

Created attachment 77461 [details]
Portage logs for one good and bad merge case

The file contains 2 logs, on working merge, the other fails, hoping that the config information might help.

[Comment 2 Donnie Berkholz (RETIRED) 2006-07-19 22:41:51 UTC]

Do your changes in bug #140725 take care of this?

[Comment 3 Donnie Berkholz (RETIRED) 2006-07-19 23:19:48 UTC]

Nevermind, they wouldn't.

[Comment 4 Donnie Berkholz (RETIRED) 2006-09-25 00:54:09 UTC]

Is this an issue with torque? It provides the shared lib, so I'd guess it's only an openpbs problem.

[Comment 5 Donnie Berkholz (RETIRED) 2006-09-25 10:06:40 UTC]

eh, lam can't even link against torque.

[Comment 6 Donnie Berkholz (RETIRED) 2006-09-26 00:21:16 UTC]

Fixed in openpbs 2.3.16-r4 in CVS.