[gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Walter Dnes]

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  This is happening with both python 2.7.12 and 3.4.5 on a 32-bit x86
system.  Build logs are attached, along with "emerge --info" output.  I
can't find anything relevant in bugzilla.

-- 
Walter Dnes <waltdnes@waltdnes.org>
I don't run "desktop environments"; I run useful applications

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[-- Attachment #4: info.txt.gz --]
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Re: [gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Walter Dnes]

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> \x1f‹\b\bÓ–ÝY\x02\x03info.txt
> FÃþÅL
> (£\x04)–QÂŽ@\x18J=ŽRÊ%\x16¥4ò•>#:Ó¤È\x19©½ØnuŽÎ;\x05k„ĉ\x1eÎXö;©\x1c0\x0f¿K‡

  Something failed there.  I'll attach as plain text and hopefully the
"emerge --info" output will get through



-- 
Walter Dnes <waltdnes@waltdnes.org>
I don't run "desktop environments"; I run useful applications

[-- Attachment #2: info.txt --]
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Portage 2.3.8 (python 2.7.12-final-0, default/linux/x86/13.0, gcc-6.3.0, glibc-2.23-r4, 4.9.16-gentoo i686)
=================================================================
System uname: Linux-4.9.16-gentoo-i686-Intel-R-_Core-TM-2_Duo_CPU_E4600_@_2.40GHz-with-gentoo-2.4.1
KiB Mem:     3100240 total,    391064 free
KiB Swap:    9186324 total,   6902452 free
Timestamp of repository gentoo: Tue, 10 Oct 2017 21:00:01 +0000
Head commit of repository gentoo: 7b19294d5a0188d9fa4b4e948acb2683ee3c41e8
sh bash 4.3_p48-r1
ld GNU ld (Gentoo 2.28 p1.2) 2.28
app-shells/bash:          4.3_p48-r1::gentoo
dev-lang/perl:            5.24.1-r2::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/cmake:           3.7.2::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.4.1-r2::gentoo
sys-apps/openrc:          0.28::gentoo
sys-apps/sandbox:         2.10-r3::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.28-r2::gentoo, 2.28.1::gentoo
sys-devel/gcc:            6.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.4::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r4::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

Installed sets: @dillo
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=native -mfpmath=sse -fopenmp -fomit-frame-pointer -pipe -fno-unwind-tables -fno-asynchronous-unwind-tables"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -march=native -mfpmath=sse -fopenmp -fomit-frame-pointer -pipe -fno-unwind-tables -fno-asynchronous-unwind-tables"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--autounmask=n"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=i686 -pipe"
GENTOO_MIRRORS="ftp://mirror.csclub.uwaterloo.ca/gentoo-distfiles/ http://gentoo.netnitco.net"
INSTALL_MASK="/lib/systemd/system /usr/lib/systemd/system"
LANG="en_US.iso88591"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X apng bzip2 cli cxx dri ffmpeg fortran gif jpeg modules ncurses nptl opengl openmp pcre png readline seccomp session ssl szip threads truetype webp x264 x265 x86 xattr xorg zlib" ABI_X86="32" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 ssse3" CURL_SSL="openssl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse" KERNEL="linux" L10N="en en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_US" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby22" USERLAND="GNU" VIDEO_CARDS="intel i915" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Re: [gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Mike Gilbert]

On Wed, Oct 11, 2017 at 12:16 AM, Walter Dnes <waltdnes@waltdnes.org> wrote:
>   This is happening with both python 2.7.12 and 3.4.5 on a 32-bit x86
> system.  Build logs are attached, along with "emerge --info" output.  I
> can't find anything relevant in bugzilla.

From the build log for 3.4.5:

checking whether pthreads are available without options... yes

This is clearly a lie; glibc requires that you pass "-pthread" to gcc
to enable pthreads. For some reason, configure is mis-detecting this.

I would try rebuilding with minimal CFLAGS.

Re: [gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Mike Gilbert]

On Wed, Oct 11, 2017 at 11:50 AM, Mike Gilbert <floppym@gentoo.org> wrote:
> On Wed, Oct 11, 2017 at 12:16 AM, Walter Dnes <waltdnes@waltdnes.org> wrote:
>>   This is happening with both python 2.7.12 and 3.4.5 on a 32-bit x86
>> system.  Build logs are attached, along with "emerge --info" output.  I
>> can't find anything relevant in bugzilla.
>
> From the build log for 3.4.5:
>
> checking whether pthreads are available without options... yes
>
> This is clearly a lie; glibc requires that you pass "-pthread" to gcc
> to enable pthreads. For some reason, configure is mis-detecting this.
>
> I would try rebuilding with minimal CFLAGS.

I can reproduce the issue by adding -fopenmp to my CFLAGS. You can
work around it by adding -fopenmp to LDFLAGS as well.

This is probably a bug in the Python build system; it should probably
be passing CFLAGS to gcc when linking libpython.

Re: [gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Walter Dnes]

On Wed, Oct 11, 2017 at 11:56:21AM -0400, Mike Gilbert wrote

> I can reproduce the issue by adding -fopenmp to my CFLAGS. You can
> work around it by adding -fopenmp to LDFLAGS as well.

  Thanks.  The following workaround makes python build properly.

LDFLAGS="-fopenmp" emerge =dev-lang/python-2.7.12 =dev-lang/python-3.4.5

> This is probably a bug in the Python build system; it should probably
> be passing CFLAGS to gcc when linking libpython.

  Bug https://bugs.gentoo.org/634064 filed.

-- 
Walter Dnes <waltdnes@waltdnes.org>
I don't run "desktop environments"; I run useful applications

Re: [gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Walter Dnes]

On Wed, Oct 11, 2017 at 10:15:50PM -0400, Walter Dnes wrote
> On Wed, Oct 11, 2017 at 11:56:21AM -0400, Mike Gilbert wrote
> 
> > I can reproduce the issue by adding -fopenmp to my CFLAGS. You can
> > work around it by adding -fopenmp to LDFLAGS as well.
> 
>   Thanks.  The following workaround makes python build properly.
> 
> LDFLAGS="-fopenmp" emerge =dev-lang/python-2.7.12 =dev-lang/python-3.4.5
> 
> > This is probably a bug in the Python build system; it should probably
> > be passing CFLAGS to gcc when linking libpython.
> 
>   Bug https://bugs.gentoo.org/634064 filed.

  Bump; I had to...

LDFLAGS="-fopenmp" emerge -1 =dev-lang/python-2.7.14 =dev-lang/python-3.5.4

..to get the latest pythons to build properly.

-- 
Walter Dnes <waltdnes@waltdnes.org>
I don't run "desktop environments"; I run useful applications

Re: [gentoo-user] python build fail; undefined reference to pthread_* and sem_*

[Mike Gilbert]

On Mon, Nov 27, 2017 at 11:47 AM, Walter Dnes <waltdnes@waltdnes.org> wrote:
> On Wed, Oct 11, 2017 at 10:15:50PM -0400, Walter Dnes wrote
>> On Wed, Oct 11, 2017 at 11:56:21AM -0400, Mike Gilbert wrote
>>
>> > I can reproduce the issue by adding -fopenmp to my CFLAGS. You can
>> > work around it by adding -fopenmp to LDFLAGS as well.
>>
>>   Thanks.  The following workaround makes python build properly.
>>
>> LDFLAGS="-fopenmp" emerge =dev-lang/python-2.7.12 =dev-lang/python-3.4.5
>>
>> > This is probably a bug in the Python build system; it should probably
>> > be passing CFLAGS to gcc when linking libpython.
>>
>>   Bug https://bugs.gentoo.org/634064 filed.
>
>   Bump; I had to...
>
> LDFLAGS="-fopenmp" emerge -1 =dev-lang/python-2.7.14 =dev-lang/python-3.5.4
>
> ..to get the latest pythons to build properly.

Just stick it in make.conf and call it fixed.

You can track further updates via the bug report.