Bug 442542 – dev-libs/boost-1.51.0-r1 Fails looking for mpi libs

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description Chris Woods 2012-11-10 04:17:21 UTC]

Created attachment 329060 [details]
build.log for dev-libs/boost-1.51.0-r1

Attempt to build dev-libs/boost-1.51.0-r1 fails with

Renaming of 'stage/lib/mpi.so' to 'stage/lib/mpi.so-2.7' failed

$ emerge -pqv '=dev-libs/boost-1.51.0-r1'
[ebuild   R   ] dev-libs/boost-1.51.0-r1  USE="doc icu mpi python -debug -static-libs -tools"


$ emerge --info '=dev-libs/boost-1.51.0-r1'
Portage 2.1.11.31 (default/linux/amd64/10.0, gcc-4.6.3, glibc-2.16.0, 3.6.2-gentoo-bitspace-custom x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.6.2-gentoo-bitspace-custom-x86_64-AMD_FX-tm-6100_Six-Core_Processor-with-gentoo-2.2
Timestamp of tree: Fri, 09 Nov 2012 09:45:01 +0000
ld GNU ld (GNU Binutils) 2.23
app-shells/bash:          4.2_p39
dev-java/java-config:     2.1.12
dev-lang/python:          2.7.3-r2, 3.2.3-r1
dev-util/cmake:           2.8.9-r1
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.4
sys-apps/sandbox:         2.6
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.4
sys-devel/binutils:       2.23
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.6 (virtual/os-headers)
sys-libs/glibc:           2.16.0
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /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"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://www.gtlib.gatech.edu/pub/gentoo ftp://ftp.gtlib.gatech.edu/pub/gentoo http://gentoo.osuosl.org/ http://gentoo.mirrors.pair.com/"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j7"
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="/usr/local/portage"
SYNC="rsync://rsync.us.gentoo.org/gentoo-portage"
USE="X a52 aac aalib acl alsa amd64 avahi bash-completion berkdb bluetooth bzip2 cairo cdda cddb cdparanoia cdr cjk cli consolekit cracklib crypt cscope cups curl cxx dbi dbus dga directfb djvu doc dri dts dv dvb dvd eds emacs encode examples exif fam fbcon ffmpeg flac fontconfig fortran freetds ftp gd gdbm geoip ggi gif gnome gnome-keyring gnuplot gphoto2 gpm gps graphviz gsm gstreamer gtk guile hscolour iconv icu idn imlib ios ipv6 jack java jbig jingle jpeg jpeg2k kde kontact ladspa lame lapack lash latex lcms ldap libass libnl libnotify libsamplerate lm_sensors lua lzma lzo mad matroska mms mmx mmxext mng modplug modules mono mozilla mp3 mpeg mpi mplayer msn mtp mudflap multilib musepack musicbrainz nas ncurses networkmanager nls nptl nsplugin nss oci8 odbc offensive ogg openal openexr opengl openmp oscar oss pam pcre pdf perl plasma plotutils png policykit portaudio postgres postscript pppd pulseaudio python qt4 quicktime raw rdesktop readline rss ruby samba sasl scanner sdl semantic-desktop session slang slp sndfile soap sound source speex sqlite sse sse2 ssl startup-notification subversion svg symlink syslog taglib tcl tcpd theora threads tidy tiff tk truetype udev unicode upnp usb v4l vcd vim-syntax vnc vorbis wavpack webkit wifi wmf x264 xcb xemacs xface xft xine xinetd xml xmp xosd xpm xscreensaver xv xvid yahoo zeroconf zlib zsh-completion" 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="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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver pdfimport scripting-beanshell scripting-javascript wiki-publisher presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="radeon" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

dev-libs/boost-1.51.0-r1 was built with the following:
USE="doc icu mpi python -debug -static-libs -tools"

[Comment 1 Diego Elio Pettenò (RETIRED) 2012-11-10 22:57:17 UTC]

Can you please try with 1.52.0-r1? Thanks.

[Comment 2 Chris Woods 2012-11-11 18:36:35 UTC]

Tried again with 1.52.0-r2, still failing. It looks like the build might have completed successfully but some post-build cleanup failed. Attaching latest build.log for review.

[Comment 3 Chris Woods 2012-11-11 18:37:36 UTC]

Created attachment 329258 [details]
build.log for dev-libs/boost-1.52.0-r2

[Comment 4 Diego Elio Pettenò (RETIRED) 2012-11-11 18:58:09 UTC]

On it

[Comment 5 Arfrever Frehtes Taifersar Arahesis 2012-11-13 00:28:42 UTC]

(In reply to comment #3)
> MPI auto-detection failed: unknown wrapper compiler mpic++
> Please report this error to the Boost mailing list: http://www.boost.org
> You will need to manually configure MPI support.

Do you use sys-cluster/openmpi or sys-cluster/mpich2?

[Comment 6 Chris Woods 2012-11-13 11:10:48 UTC]

(In reply to comment #5)
> (In reply to comment #3)
> > MPI auto-detection failed: unknown wrapper compiler mpic++
> > Please report this error to the Boost mailing list: http://www.boost.org
> > You will need to manually configure MPI support.
> 
> Do you use sys-cluster/openmpi or sys-cluster/mpich2?

sys-cluster/openmpi-1.6.2  USE="cxx fortran ipv6 threads -heterogeneous -mpi-threads -romio -vt" OPENMPI_FABRICS="-dapl -knem -ofed -open-mx -psm -sctp" OPENMPI_OFED_FEATURES="-connectx-xrc -control-hdr-padding -dynamic-sl -failover -rdmacm" OPENMPI_RM="-pbs -slurm"

Unsurprisingly, removing 'mpi' from my global USE flags gets by this issue. I don't honestly even recall why I had it to begin with.

[Comment 7 Arfrever Frehtes Taifersar Arahesis 2012-11-13 19:44:39 UTC]

Show output of:
mpic++ -showme:compile
mpic++ -showme:link
mpic++ -show
mpic++ -showme

[Comment 8 Chris Woods 2012-11-14 11:05:50 UTC]

(In reply to comment #7)
> Show output of:
> mpic++ -showme:compile
> mpic++ -showme:link
> mpic++ -show
> mpic++ -showme

# mpic++ -showme:compile
-pthread

# mpic++ -showme:link
-pthread -L/usr/lib64 -lmpi_cxx -lmpi -ldl -lhwloc -Wl,--export-dynamic -lrt -lnsl -lutil -lm -lhwloc -ldl

# mpic++ -show
x86_64-pc-linux-gnu-g++ -pthread -L/usr/lib64 -lmpi_cxx -lmpi -ldl -lhwloc -Wl,--export-dynamic -lrt -lnsl -lutil -lm -lhwloc -ldl

# mpic++ -showme
x86_64-pc-linux-gnu-g++ -pthread -L/usr/lib64 -lmpi_cxx -lmpi -ldl -lhwloc -Wl,--export-dynamic -lrt -lnsl -lutil -lm -lhwloc -ldl

[Comment 9 Sergey Popov (RETIRED) 2014-12-11 07:55:23 UTC]

Not reproduceable with current stable version of Boost. Please reopen if it's still an issue