dev-db/libpq and thread failure; dup of bug 130064?

[Felig]

Trying to emerge dev-db/libpq-8.1.3-r1, I get this dump ---

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*** glibc detected *** ./conftest: free(): invalid pointer: 0x00002aaaaab00950 ***
======= Backtrace: =========
/lib/libc.so.6[0x2af2ea8b67ec]
/lib/libc.so.6(__libc_free+0x76)[0x2af2ea8b7356]
/usr/lib/libsandbox.so[0x2af2e999bcea]
/usr/lib/libsandbox.so[0x2af2e999c06f]
/usr/lib/libsandbox.so(unlink+0x139)[0x2af2e999e079]
./conftest[0x400e90]
/lib/libpthread.so.0[0x2af2ea73c41a]
/lib/libc.so.6(__clone+0x6e)[0x2af2ea9098de]
======= Memory map: ========
00400000-00402000 r-xp 00000000 08:07 18558410                           /var/tmp/portage/libpq-8.1.3-r1/work/postgresql-8.1.3/conftest
00501000-00502000 rw-p 00001000 08:07 18558410                           /var/tmp/portage/libpq-8.1.3-r1/work/postgresql-8.1.3/conftest
00502000-00523000 rw-p 00502000 00:00 0                                  [heap]
40000000-40001000 ---p 40000000 00:00 0 
40001000-40801000 rw-p 40001000 00:00 0 
40801000-40802000 ---p 40801000 00:00 0 
40802000-41002000 rw-p 40802000 00:00 0 
2aaaaab00000-2aaaaab21000 rw-p 2aaaaab00000 00:00 0 
2aaaaab21000-2aaaaac00000 ---p 2aaaaab21000 00:00 0 
2aaaaac4b000-2aaaaac56000 r-xp 00000000 08:07 17063821                   /lib64/libgcc_s.so.1
2aaaaac56000-2aaaaad55000 ---p 0000b000 08:07 17063821                   /lib64/libgcc_s.so.1
2aaaaad55000-2aaaaad56000 rw-p 0000a000 08:07 17063821                   /lib64/libgcc_s.so.1
2af2e987e000-2af2e9899000 r-xp 00000000 08:07 18531480                   /lib64/ld-2.4.so
2af2e9899000-2af2e989a000 rw-p 2af2e9899000 00:00 0 
2af2e98e5000-2af2e98e6000 rw-p 2af2e98e5000 00:00 0 
2af2e9998000-2af2e9999000 r--p 0001a000 08:07 18531480                   /lib64/ld-2.4.so
2af2e9999000-2af2e999a000 rw-p 0001b000 08:07 18531480                   /lib64/ld-2.4.so
2af2e999a000-2af2e99a1000 r-xp 00000000 fe:01 420370                     /usr/lib64/libsandbox.so.0.0.0
2af2e99a1000-2af2e9aa0000 ---p 00007000 fe:01 420370                     /usr/lib64/libsandbox.so.0.0.0
2af2e9aa0000-2af2e9aa1000 rw-p 00006000 fe:01 420370                     /usr/lib64/libsandbox.so.0.0.0
2af2e9aa1000-2af2e9aa3000 rw-p 2af2e9aa1000 00:00 0 
2af2e9aa3000-2af2e9aab000 r-xp 00000000 08:07 16730991                   /lib64/libpam.so.0.78
2af2e9aab000-2af2e9baa000 ---p 00008000 08:07 16730991                   /lib64/libpam.so.0.78
2af2e9baa000-2af2e9bab000 rw-p 00007000 08:07 16730991                   /lib64/libpam.so.0.78
2af2e9bab000-2af2e9bdd000 r-xp 00000000 fe:01 147495                     /usr/lib64/libssl.so.0.9.7
2af2e9bdd000-2af2e9cdc000 ---p 00032000 fe:01 147495                     /usr/lib64/libssl.so.0.9.7
2af2e9cdc000-2af2e9ce1000 rw-p 00031000 fe:01 147495                     /usr/lib64/libssl.so.0.9.7
2af2e9ce1000-2af2e9ce3000 rw-p 2af2e9ce1000 00:00 0 
2af2e9ce3000-2af2e9e06000 r-xp 00000000 fe:01 232659                     /usr/lib64/libcrypto.so.0.9.7
2af2e9e06000-2af2e9f05000 ---p 00123000 fe:01 232659                     /usr/lib64/libcrypto.so.0.9.7
2af2e9f05000-2af2e9f24000 rw-p 00122000 fe:01 232659                     /usr/lib64/libcrypto.so.0.9.7
2af2e9f24000-2af2e9f28000 rw-p 2af2e9f24000 00:00 0 
2af2e9f28000-2af2e9f3c000 r-xp 00000000 08:07 11783573                   /lib64/libz.so.1.2.3
2af2e9f3c000-2af2ea03c000 ---p 00014000 08:07 11783573                   /lib64/libz.so.1.2.3
2af2ea03c000-2af2ea03d000 rw-p 00014000 08:07 11783573                   /lib64/libz.so.1.2.3
2af2ea03d000-2af2ea073000 r-xp 00000000 08:07 14986004                   /lib64/libreadline.so.5.1
2af2ea073000-2af2ea172000 ---p 00036000 08:07 14986004                   /lib64/libreadline.so.5.1
2af2ea172000-2af2ea17a000 rw-p 00035000 08:07 14986004                   /lib64/libreadline.so.5.1
2af2ea17a000-2af2ea17c000 rw-p 2af2ea17a000 00:00 0 
2af2ea17c000-2af2ea181000 r-xp 00000000 08:07 18531462                   /lib64/libcrypt-2.4.so
2af2ea181000-2af2ea280000 ---p 00005000 08:07 18531462                   /lib64/libcrypt-2.4.so
2af2ea280000-2af2ea282000 rw-p 00004000 08:07 18531462                   /lib64/libcrypt-2.4.so
2af2ea282000-2af2ea2b0000 rw-p 2af2ea282000 00:00 0 
2af2ea2b0000-2af2ea2c0000 r-xp 00000000 08:07 18530207                   /lib64/libresolv-2.4.so
2af2ea2c0000-2af2ea3bf000 ---p 00010000 08:07 18530207                   /lib64/libresolv-2.4.so
2af2ea3bf000-2af2ea3c1000 rw-p 0000f000 08:07 18530207                   /lib64/libresolv-2.4.so
2af2ea3c1000-2af2ea3c3000 rw-p 2af2ea3c1000 00:00 0 
2af2ea3c3000-2af2ea3d5000 r-xp 00000000 08:07 18530659                   /lib64/libnsl-2.4.so
2af2ea3d5000-2af2ea4d5000 ---p 00012000 08:07 18530659                   /lib64/libnsl-2.4.so
2af2ea4d5000-2af2ea4d7000 rw-p 00012000 08:07 18530659                   /lib64/libnsl-2.4.so
2af2ea4d7000-2af2ea4da000 rw-p 2af2ea4d7000 00:00 0 
2af2ea4da000-2af2ea4dc000 r-xp 00000000 08:07 18531117                   /lib64/libdl-2.4.so
2af2ea4dc000-2af2ea5dc000 ---p 00002000 08:07 18531117                   /lib64/libdl-2.4.so
2af2ea5dc000-2af2ea5de000 rw-p 00002000 08:07 18531117                   /lib64/libdl-2.4.so
2af2ea5de000-2af2ea635000 r-xp 00000000 08:07 18531458                   /lib64/libm-2.4.so
2af2ea635000-2af2ea734000 ---p 00057000 08:07 18531458                   /lib64/libm-2.4.so
2af2ea734000-2af2ea736000 rw-p 00056000 08:07 18531458                   /lib64/libm-2.4.so
2af2ea736000-2af2ea747000 r-xp 00000000 08:07 18531116                   /lib64/libpthread-2.4.so
2af2ea747000-2af2ea846000 ---p 00011000 08:07 18531116                   /lib64/libpthread-2.4.so
2af2ea846000-2af2ea847000 r--p 00010000 08:07 18531116                   /lib64/libpthread-2.4.so
2af2ea847000-2af2ea848000 rw-p 00011000 08:07 18531116                   /lib64/libpthread-2.4.so
2af2ea848000-2af2ea84d000 rw-p 2af2ea848000 00:00 0 
2af2ea84d000-2af2ea96f000 r-xp 00000000 08:07 18531158                   /lib64/libc-2.4.so
2af2ea96f000-2af2eaa6f000 ---p 00122000 08:07 18531158                   /lib64/libc-2.4.so
2af2eaa6f000-2af2eaa72000 r--p 00122000 08:07 18531158                   /lib64/libc-2.4.so
2af2eaa72000-2af2eaa74000 rw-p 00125000 08:07 18531158                   /lib64/libc-2.4.so
2af2eaa74000-2af2eaa79000 rw-p 2af2eaa74000 00:00 0 
2af2eaa79000-2af2eaac9000 r-xp 00000000 08:07 16727088                   /lib64/libncurses.so.5.5
2af2eaac9000-2af2eabc8000 ---p 00050000 08:07 16727088                   /lib64/libncurses.so.5.5
2af2eabc8000-2af2eabd6000 rw-p 0004f000 08:07 16727088                   /lib64/libncurses.so.5.5
2af2eabd6000-2af2eabd9000 rw-p 2af2eabd6000 00:00 0 
7ffffffaa000-7ffffffc1000 rw-p 7ffffffaa000 00:00 0                      [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0                  [vdso]

-- and this in the log file --

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checking for DocBook V4.2... yes
checking for DocBook stylesheets... no
checking for collateindex.pl... /usr/bin/collateindex.pl
checking for sgmlspl... sgmlspl
checking thread safety of required library functions... no
configure: error:
*** Thread test program failed.  Your platform is not thread-safe.
*** Check the file 'config.log'for the exact reason.
***
*** You can use the configure option --enable-thread-safety-force
*** to force threads to be enabled.  However, you must then run
*** the program in src/tools/thread and add locking function calls
*** to your applications to guarantee thread safety.


!!! ERROR: dev-db/libpq-8.1.3-r1 failed.
Call stack:
  ebuild.sh, line 1527:   Called dyn_compile
  ebuild.sh, line 931:   Called src_compile
  libpq-8.1.3-r1.ebuild, line 74:   Called die

!!! (no error message)
!!! If you need support, post the topmost build error, and the call stack if relevant.

Emerge --info says

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Gentoo Base System version 1.12.0_pre19
Portage 2.1_rc1-r2 (default-linux/amd64/2005.1, gcc-3.4.6, glibc-2.4-r3, 2.6.16-gentoo-r7 x86_64)
=================================================================
System uname: 2.6.16-gentoo-r7 x86_64 AMD Opteron(tm) Processor 244
ccache version 2.4 [enabled]
dev-lang/python:     2.3.5, 2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r1
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.18
sys-devel/autoconf:  2.13, 2.59-r7
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r2
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r3
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O3 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/3/share/config /usr/lib/\
fax /usr/lib64/mozilla/defaults/pref /usr/share/X11/xkb /usr/share/config /var /var/qmail/alias /var/qmail/control /var/service /var/spool/fax/\
etc"
CONFIG_PROTECT_MASK="/etc/eselect/compiler /etc/gconf /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/env.d"
CXXFLAGS="-O3 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://gentoo.osuosl.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=\
180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="amd64 X a52 aac acpi aim alsa apache2 arts avi bash-completion bcmath berkdb bidi bitmap-fonts bluetooth bonobo bzlib canna cdb cdparanoia\
 cdr cjk cli crypt cups curl dba dbm dga divx4linux doc dri dv dvb dvd dvdr dvdread eds emacs emacs-w3 emboss encode esd ethereal evo examples \
exif expat fam fastcgi ffmpeg flac foomaticdb fortran freetds freewnn ftp gb gcj gd gdbm gif ginac glut gmp gnome gnustep gnutls gphoto2 gps gs\
treamer gtk gtk2 gtkhtml guile iconv icq imagemagick imap imlib innodb isdnlog ithreads jabber jack java javascript jpeg junit kde lcms ldap le\
im libg++ libgda libwww lirc lm_sensors lzw lzw-tiff mad maildir mikmod mime ming mjpeg mmap mng mono mp3 mpeg mpi mule mysql mysqli nas ncurse\
s nis nls nptl nptlonly nsplugin objc odbc offensive ofx ogg oggvorbis openal opengl pam pcre pda pdflib perl php plotutils png portaudio posix\
 postgres ppds pppd python qdbm qt quicktime readline recode reflection ruby samba sasl scanner sdl session shared sharedmem slang slp sndfile \
snmp soap sockets sox spell spl ssl sysvipc tcltk tcpd tetex theora threads tiff truetype truetype-fonts type1-fonts unicode usb v4l vcd vorbis\
 wifi wmf xine xml xml2 xmlrpc xorg xosd xpm xv xvid zlib elibc_glibc kernel_linux userland_GNU"
Unset:  ASFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS

Any takers? I have been stepping around this for a couple of weeks, simply avoiding the upgrade, but it's time to get a new version soon.

[ekutay]

You could try to change your compile flags to something less aggressive CFLAGS="-O2" or something like this.

[ekutay]

Found this bug [bug=130064]report[/bug], which is not solved yet, but shows ways to work around, in case you need the newer version

[Felig]

I'll skip the patch for the time being. I don't need the new postgresql that bad. But I will keep it in mind in case things are fixed in the next release or two.

Thanks.

[Stefan de Groot]

I just had the same error, but I get emerge libpq by:

Code: Select all

USE="-threads" emerge libpq

Oke.... it's not perfect. But, if you don't want to use threads it can be an sollution for now.

[Felig]

I added -threads to /etc/portage/package.use for both libpq and postgreql, and it seems to work so far.

What bugs me is that I didn't have to do this for a ~x86 platform. In both cases, I emerged system to start things out from scratch. So there is some remaining screwup on the ~amd64 platform. Nevertheless, this works for now.

[leifbk]

The same thing happens here on my x86 platform with libpq-8.1.4 as i run an emerge -e system after the gcc-4.1.1 upgrade. I just threw in an

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echo "dev-db/libpq -threads" >> /etc/portage/package.use

and resumed my emerge, and then both libpq and postgresql compiled just fine.

Still, I wonder why this is happening.

[Felig]

Threading changed a while back, I wonder if that is connected, and is it because of ebuild ignorance on the new threads, the new threads themselves, or what? It's been so long since I did anything with this that I have forgotten what the threads change even was. Well, postgres doesn't use threads in the backend, I believe, so it may be moot.

[leifbk]

In the second pass, emerge -e world, postgresql bombed out with the same error. So, I added -threads to postgresql as well in the /etc/portage/package.use and now everything seems to proceed fine.

This is a mainly stable x86 configuration, but with postgresql version 8.1.4 which is still in ~x86.

I should add that I have been running postgresql 8.1.4 for about three months, without any problems.

[leifbk]

After a while, compiling PHP also broke with a message that I should recompile libpq with threads enabled. I tried to add -threads to dev-lang/php as well, but that only introduced yet another conflict with apache2. So I finally gave up, removed threads from my make.conf, and started to compile world all over again.

[menion]

I just hit this after moving from gcc 3.4 to 4.1. It may be related to 8.1.4, or something, I have no idea.


I am using a P4-2.8 w/ HT. 2.6.16. I recompiled w/ -threads, but I wonder why this is happening.

This is all the tuning that I have in make.conf:
CFLAGS='-march=pentium4 -mtune=pentium4 -freorder-blocks -pipe'
CXXFLAGS='-march=pentium4 -mtune=pentium4 -freorder-blocks -pipe -fvisibility-inlines-hidden'
LDFLAGS='-Wl,-O1 -Wl,--sort-common -s'

[isolationism]

This appears to suggest a bug when compiling libpq (and postgresql) with the threads USE flag enabled.

As others have mentioned, you can get by compiling libpq and postgresql by setting them to use -threads from /etc/portage/package.use--but other apps (like php and apache) that also use threads won't work properly with a mixed threads/-threads environment.

My solution was similar to leifbk's (although perhaps a little less extreme). After removing "threads" from the USE parameter in /etc/make.conf, I did a quick look to find which installed packages were making use of threads:

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equery hasuse threads
[ Searching for USE flag threads in all categories among: ]
 * installed packages
[I--] [  ] dev-lang/tcl-8.4.9 (0)
[I--] [  ] dev-lang/php-5.1.6-r6 (5)
[I--] [  ] dev-libs/boost-1.33.1 (1)
[I--] [ ~] dev-db/libpq-8.1.4 (4)
[I--] [ ~] dev-db/postgresql-8.1.4 (0)
[I--] [  ] net-www/apache-2.0.58-r2 (2)

... Then re-emerged the affected packages only:

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emerge -vc dev-lang/tcl dev-lang/php dev-libs/boost dev-db/libpq dev-db/postgresql net-www/apache

Everything, including postgres and php, proceeded to emerge fine after that.

[menion]

This is all very facinating, but does anyone know _why_ it's happening?

[steveL]

No idea, although it has been filed on bugzilla.

[Cinquero]

Two questions:

does the bug appear on single-core systems?

Does the bug appear on multi-core systems?

[crunge]

I have an Athlon64 X2 system with my 'emerge --info' featured below. I got the same error emerging libpq but on the second try after no changes it went through without a hitch.

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igor ~ # emerge --info
Portage 2.1.2.2 (default-linux/amd64/2006.1, gcc-4.1.1, glibc-2.5-r0, 2.6.19-gentoo-r5 x86_64)
=================================================================
System uname: 2.6.19-gentoo-r5 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+
Gentoo Base System release 1.12.9
Timestamp of tree: Sun, 15 Apr 2007 18:00:01 +0000
distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled]
dev-java/java-config: 1.3.7, 2.0.31-r5
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.15-r1
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe -fomit-frame-pointer -finline-functions -ftracer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /var/bind"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/php/apache1-php5/ext-active/ /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-march=athlon64 -O2 -pipe -fomit-frame-pointer -finline-functions -ftracer"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl amd64 apache2 bash-completion berkdb bitmap-fonts bzip2 cli cracklib crypt cups curl dri fortran gdbm gnutls gpm iconv imap isdnlog jce ldap libg++ maildir midi ncurses nls no-old-linux nptl nptlonly pam parse-clocks pcre perl ppds pppd python readline reflection samba sasl session spl ssl threads truetype-fonts type1-fonts unicode xml xorg zip 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" 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="apm ark ati chips cirrus cyrix dummy fbdev glint i128 i810 mga neomagic nv rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga trident tseng v4l vesa vga via vmware voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[steveL]

Apparently this bug is fixed in 8.0.13. if it isn't holler on http://bugs.gentoo.org/show_bug.cgi?id=158509