404253 – dev-libs/boost-1.46.1-r1: cannot use boost.mpi from Python (dynamic linking error)

Bug 404253 - dev-libs/boost-1.46.1-r1: cannot use boost.mpi from Python (dynamic linking error)

Summary: dev-libs/boost-1.46.1-r1: cannot use boost.mpi from Python (dynamic linking e...

Status:	RESOLVED FIXED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	[OLD] Library (show other bugs)
Hardware:	All Linux

Importance:	Normal normal (vote)
Assignee:	Tiziano Müller (RETIRED)

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:

Reported:	2012-02-17 14:03 UTC by Igor Krivenko
Modified:	2012-04-02 01:12 UTC (History)
CC List:	5 users (show)

See Also:
Package list:
Runtime testing required:	---

Attachments
Proposed __init__.py file to solve the problem. (__init__.py,196 bytes, text/x-python) 2012-02-17 14:08 UTC, Igor Krivenko	Details
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Description Igor Krivenko 2012-02-17 14:03:13 UTC

There is a dynamic linking error while importing boost.mpi Python module.

A possible solution (workaround?) for this issue is to inject RTLD_GLOBAL dlopen flag through __init__.py of the module.

Reproducible: Always

Steps to Reproduce:
1. emerge =dev-libs/boost-1.46.1-r1
2. eselect boost set boost-1.46/default
3. python -c "import boost_1_46.mpi" (or python -c "import mpi")
Actual Results:  
/usr/bin/python2.7: symbol lookup error: /usr/lib64/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int

Expected Results:  
Successful import of the module.

$ eix openmpi
[I] sys-cluster/openmpi
     Available versions:  1.4.2!t 1.4.3!t ~1.4.4!t ~1.5.4-r3 {+cxx elibc_FreeBSD fortran heterogeneous infiniband ipv6 knem mpi-threads +numa open-mx pbs psm romio sctp slurm threads vt}
     Installed versions:  1.4.3(09:26:39 PM 02/15/2012)(cxx fortran romio threads -elibc_FreeBSD -heterogeneous -ipv6 -mpi-threads -pbs -vt)
     Homepage:            http://www.open-mpi.org
     Description:         A high-performance message passing library (MPI)

=============
emerge --info
=============

Portage 2.2.0_alpha86 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.3, glibc-2.13-r4, 3.2.1-gentoo-r2 x86_64)
=================================================================
System uname: Linux-3.2.1-gentoo-r2-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.3
Timestamp of tree: Fri, 17 Feb 2012 09:30:01 +0000
ccache version 3.1.6 [enabled]
app-shells/bash:          4.1_p9
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3
dev-util/ccache:          3.1.6
dev-util/cmake:           2.8.6-r4
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.9.8.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.5.3-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        1.3.5, 2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 3.1 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo sunrise gamerlay-stable local alps
Installed sets: @base
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -mmmx -msse -msse2 -mssse3 -msse4.1 -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /usr/share/themes/oxygen-gtk/gtk-2.0"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe -mmmx -msse -msse2 -mssse3 -msse4.1 -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--quiet-build n"
FEATURES="assume-digests binpkg-logs ccache distlocks ebuild-locks fixlafiles news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles/ ftp://mirror.yandex.ru/gentoo-distfiles/"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="ru"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/sunrise /var/lib/layman/gamerlay /usr/local/portage /home/igor/Work/Admin/alps-overlay.svn"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X \ a52 aac acpi alsa amd64 bash-completion berkdb blas bluetooth branding bzip2 cairo cdda cddb cdr chm cli consolekit crypt css cups curl cxx dbus declarative dga djvu dn dri dts dvd dvdr dvdread emboss exif expat fam ffmpeg fftw firefox flac fortran ftp gd gdu gif gimp glib gmp gnutls gpm gps gtk gtk2 hdf5 iconv icq id3tag idn ieee1394 java javascript jpeg kde kipi lame lapack latex lcms libnotify lm_sensors lzma mad mmap mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses networkmanager nls nptl nptlonly nsplugin ogg opengl openmp pam pango pch pcre pdf perl phonon plasma png policykit posix postscript ppds pppd python qt3support qt4 readline samba sdl semantic-desktop session smp sndfile spell sqlite sqlite3 sse sse2 sse3 ssl ssse3 startup-notification subversion svg sysfs threads tiff truetype udev udisks unicode upower usb v4l v4l2 vcd vim-syntax vorbis wifi wmf x264 xcb xcomposite xinerama xml xorg xscreensaver xulrunner xv xvid 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 mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="nmea" INPUT_DEVICES="synaptics evdev keyboard wacom" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" 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:  CPPFLAGS, CTARGET, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Comment 1 Igor Krivenko 2012-02-17 14:08:19 UTC

Created attachment 302263 [details]
Proposed __init__.py file to solve the problem.

This file is to put into /usr/lib/python*/site-packages/boost_*/ to resolve the issue.

Comment 2 Arfrever Frehtes Taifersar Arahesis 2012-04-02 01:10:29 UTC

Fixed in app-admin/eselect-boost-0.4 and dev-libs/boost-1.48.0-r1.