Bug 233764

Summary:	python 2.5.2-r7 (and r6) emerge fails with threads
Product:	Gentoo Linux	Reporter:	ivo welch <ivo.welch>
Component:	[OLD] Core system	Assignee:	Python Gentoo Team <python>
Status:	RESOLVED TEST-REQUEST
Severity:	minor
Priority:	Lowest
Version:	2008.0
Hardware:	AMD64
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	environment and build log

Description ivo welch 2008-08-03 01:45:29 UTC

something or another emerge required pulling in a newer version of python...so I ran into the following:

# emerge python
...
x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -L. -fno-strict-aliasing -DNDEBUG -march=nocona -pipe -O2 -fwrapv -I. -IInclude -I./Include build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/cache.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/connection.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/cursor.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/microprotocols.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/module.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/prepare_protocol.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/row.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/statement.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/util.o -L/usr/lib64 -L/usr/local/lib -L. -Wl,-R/usr/lib64 -lsqlite3 -lpython2.5 -o build/lib.linux-x86_64-2.5/_sqlite3.so
/bin/sh: line 1:  6133 Segmentation fault      LD_LIBRARY_PATH=/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2: CC='x86_64-pc-linux-gnu-gcc -pthread' LDSHARED='x86_64-pc-linux-gnu-gcc -pthread -shared' OPT='-DNDEBUG -march=nocona -pipe -O2 -fwrapv' ./python -E ./setup.py build
make: *** [sharedmods] Error 139

SOLUTION: USE="-threads" emerge -u python .  In my case, I had to switch from a python 2.4 solution with threads to a 2.5 solution without them.   unfortunately,  I then run into multiple versions in single package slots.




# emerge --info
Portage 2.1.4.4 (default/linux/amd64/2008.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.26 x86_64)
=================================================================
System uname: 2.6.26 x86_64 Intel(R) Core(TM)2 CPU 6600 @ 2.40GHz
Timestamp of tree: Thu, 31 Jul 2008 23:04:01 +0000
app-shells/bash:     3.2_p33
dev-java/java-config: 1.3.7, 2.1.6
dev-lang/python:     2.5.2-r7
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r2
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1
sys-devel/binutils:  2.18-r3
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.23-r3
ACCEPT_KEYWORDS="amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -pipe -O2"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-march=nocona -pipe -O2"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer noinfo parallel-fetch sandbox sfperms splitdebug strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://www.gtlib.gatech.edu/pub/gentoo http://gentoo.mirrors.pair.com/ http://adelie.polymtl.ca/ http://distro.ibiblio.org/pub/linux/distributions/gentoo/"
LC_ALL="POSIX"
LDFLAGS="-Wl,-O1"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="# #mysql 3dnow X aac aalib acl acpi alsa amd64 apache2 arts asf atlas audio berkdb bitmap-fonts blas bluetooth bonobo branding bzip2 bzlib cairo calendar cddb cdr cli cracklib crypt cups curl dbus directfb dri dv dvd dvdr dvdread eds emacs emboss encode esd evo examples f77 fam fbcon ffmpeg firefox fortran freetype ftp g77 gcj gdbm ggi gif gnome gphoto2 gpm gstreamer gtk gtk2 gtkhtml guile hal hdhomerun iconv ieee1394 imagemagick imlib ipv6 isdnlog java javascript jpeg kde kdeenablefinal kerberos ldap libedit libnotify libwww lm_sensors mad mbox midi mikmod mime mmx mmx2 mono motif mozilla mp3 mpeg mpeg-4 mudflap multilib mval nas ncurses networking nls nptl nptlonly nsplugin ogg opengl openmp pam pcm pcre pdf perl png postgres ppds pppd python qt qt3 qt3support qt4 quicktime readline reflection ruby samba scanner sdl server session slang snmp soap spell spl sse sse2 ssl startup-notification svg symlink sysfs t1lib tcltk tcpd tidy tiff tightvnc truetype type1 unicode usb utempter vnc vorbis wma xinerama xml xml2 xorg xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="video_cards_nv"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Comment 1 Carsten Lohrke (RETIRED) gentoo-dev

2008-08-03 12:11:49 UTC

Works fine here. Sure that this isn't a hardware issue?

Comment 2 ivo welch 2008-08-03 13:11:07 UTC

Created attachment 162085 [details]
environment and build log

 environment and build log

Comment 3 ivo welch 2008-08-03 13:12:16 UTC

positive.  it occurs on two virtually identical machines (hardware, software, etc.)

the complete emerge is

[ebuild  NS   ] dev-lang/python-2.5.2-r6  USE="berkdb examples gdbm ipv6 ncurses readline ssl threads -bootstrap -build -doc -sqlite -tk -ucs2 -wininst"

hope it helps.

/iaw

Comment 4 Tiziano Müller (RETIRED) gentoo-dev

2008-08-03 19:28:40 UTC

Did you try without "-Wl,-01"?

Comment 5 ivo welch 2008-08-03 21:18:45 UTC

(In reply to comment #4)
> Did you try without "-Wl,-01"?
> 

really dumb question: how?  I tried CFLAGS="-W0" for example, but it does not seem to have an effect.  I have even tried taking out -O2 from my make.conf file.  I also have no idea even what -Wl means/does, nor how to take it out.

(It also looks like this is more serious for me than I thought, because gnome and some other packages depend on python.  So, help appreciated.)

/iaw

Comment 6 Tiziano Müller (RETIRED) gentoo-dev

2008-08-04 06:16:00 UTC

Well, it seems you have this in your make.conf:
  LDFLAGS="-Wl,-O1"
So, just comment it out and try again. Atm it seems that the compiler is segfaulting, therefore I'm asking you to try without...

Comment 7 Ingo Dageförde 2008-08-04 13:02:34 UTC

(In reply to comment #6)
> Well, it seems you have this in your make.conf:
>   LDFLAGS="-Wl,-O1"
> So, just comment it out and try again. Atm it seems that the compiler is
> segfaulting, therefore I'm asking you to try without...
> 
for me it worked when I commented "-O2" out of CFLAGS in my make.conf

Comment 8 ivo welch 2008-08-04 13:09:22 UTC

unfortunately, not for me.  I do not have these flags in my make.conf .  I used to have -O2 in my make.conf, but I have removed it like Ingo, too.  the invoke is still

x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -L. -fno-strict-aliasing -DNDEBUG -march=nocona -pipe -fwrapv -I. -IInclude -I./Include build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/cache.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/connection.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/cursor.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/microprotocols.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/module.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/prepare_protocol.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/row.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/statement.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2/Modules/_sqlite/util.o -L/usr/lib64 -L/usr/local/lib -L. -Wl,-R/usr/lib64 -lsqlite3 -lpython2.5 -o build/lib.linux-x86_64-2.5/_sqlite3.so
/bin/sh: line 1: 22313 Segmentation fault      LD_LIBRARY_PATH=/var/tmp/portage/dev-lang/python-2.5.2-r6/work/Python-2.5.2: CC='x86_64-pc-linux-gnu-gcc -pthread' LDSHARED='x86_64-pc-linux-gnu-gcc -pthread -shared' OPT='-DNDEBUG -march=nocona -pipe -fwrapv' ./python -E ./setup.py build

"-O1" seems to come from the ebuild itself.  "-Wl" is a mystery to me.  It is explicitly mentioned in earlier python ebuilds, but not in the current one.

so, if this is a gcc compiler bug, maybe I should move onto a later gcc and try again...

Comment 9 Tiziano Müller (RETIRED) gentoo-dev

2008-08-04 14:13:08 UTC

ivo: sorry, it seems that LDFLAGS="-Wl,-O1" comes from the profile. Could you please add LDFLAGS="" to your make.conf and try again please?

Comment 10 ivo welch 2008-08-05 01:45:06 UTC

sorry, no:

...
x86_64-pc-linux-gnu-gcc -pthread -fPIC -fno-strict-aliasing -DNDEBUG -march=nocona -pipe -fwrapv -DMODULE_NAME="sqlite3" -IModules/_sqlite -I/usr/include -I. -I/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/./Include -I. -IInclude -I./Include -I/usr/local/include -I/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Include -I/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2 -c -DMODULE_NAME="sqlite3" -IModules/_sqlite -I/usr/include -I. -I/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/./Include -I. -IInclude -I./Include -I/usr/local/include -I/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Include -I/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2 -c /var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/util.c -o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/util.o
x86_64-pc-linux-gnu-gcc -pthread -shared -L. -fno-strict-aliasing -DNDEBUG -march=nocona -pipe -fwrapv -I. -IInclude -I./Include build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/cache.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/connection.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/cursor.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/microprotocols.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/module.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/prepare_protocol.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/row.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/statement.o build/temp.linux-x86_64-2.5/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2/Modules/_sqlite/util.o -L/usr/lib64 -L/usr/local/lib -L. -Wl,-R/usr/lib64 -lsqlite3 -lpython2.5 -o build/lib.linux-x86_64-2.5/_sqlite3.so
/bin/sh: line 1:  9181 Segmentation fault      LD_LIBRARY_PATH=/var/tmp/portage/dev-lang/python-2.5.2-r7/work/Python-2.5.2: CC='x86_64-pc-linux-gnu-gcc -pthread' LDSHARED='x86_64-pc-linux-gnu-gcc -pthread -shared' OPT='-DNDEBUG -march=nocona -pipe -fwrapv' ./python -E ./setup.py build
make: *** [sharedmods] Error 139

Comment 11 Arfrever Frehtes Taifersar Arahesis (RETIRED) gentoo-dev

2010-04-03 21:04:18 UTC

Please test with newer versions.