Created attachment 313643 [details] Complete build log. When emerging openmpi, after compilation of all successfully ecompressdir gives an error trying ot compress man-files. Bug might be similar with the following fresh bugs: https://bugs.gentoo.org/show_bug.cgi?id=417025 https://bugs.gentoo.org/show_bug.cgi?id=417081 https://bugs.gentoo.org/show_bug.cgi?id=417313 usr/bin/orte-iof usr/bin/ompi-server usr/bin/ompi-probe usr/bin/orterun usr/bin/orted ecompressdir: bzip2 -9 /usr/share/man ecompressdir: bzip2 -9 /usr/share/doc * ERROR: sys-cluster/openmpi-1.6 failed: * ecompressdir failed * * If you need support, post the output of `emerge --info '=sys-cluster/openmpi-1.6'`, * the complete build log and the output of `emerge -pqv '=sys-cluster/openmpi-1.6'`. * The complete build log is located at '/var/tmp/portage/sys-cluster/openmpi-1.6/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sys-cluster/openmpi-1.6/temp/environment'. * Working directory: '/var/tmp/portage/sys-cluster/openmpi-1.6/image/usr/share/doc' * S: '/var/tmp/portage/sys-cluster/openmpi-1.6/work/openmpi-1.6' !!! post install failed; exiting. How to reproduce: emerge openmpi Reproducible: Always emerge --info '=sys-cluster/openmpi-1.6' Portage 2.1.10.63 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.15-r2, 3.4.0 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.4.0-x86_64-AMD_Opteron-TM-_Processor_6276-with-gentoo-2.1 Timestamp of tree: Wed, 30 May 2012 18:30:01 +0000 app-shells/bash: 4.2_p29 dev-lang/python: 2.7.3-r2, 3.2.3-r1 dev-util/cmake: 2.8.8-r2 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.10.2 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.69 sys-devel/automake: 1.11.5 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.3-r2 sys-devel/gcc-config: 1.7.1 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.4 (virtual/os-headers) sys-libs/glibc: 2.15-r2 Repositories: gentoo 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" 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="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="us_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j32" 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="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gpm gtk iconv ipv6 jpeg lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pppd qt3support qt4 readline sdl session spell sse sse2 sse3 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xorg xulrunner 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 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 sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON emerge -pqv '=sys-cluster/openmpi-1.6' [ebuild N ] sys-cluster/openmpi-1.6 USE="cxx fortran heterogeneous ipv6 threads -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" Build log is attached.
I met the same error. In working directory /var/tmp/portage/sys-cluster/openmpi-1.6/image/usr/share/doc every file was successfully compressed as if no error occured.
I get a similar error, but there is another line before the actual error message telling that a file already exists: usr/lib64/openmpi/mca_carto_auto_detect.so usr/lib64/libopen-pal.so.4.0.0 ln: failed to create symbolic link './man1/orteCC.1': File exists ecompressdir: bzip2 -9 /usr/share/man ecompressdir: bzip2 -9 /usr/share/doc * ERROR: sys-cluster/openmpi-1.6 failed: * ecompressdir failed
After uninstalling the old version openmpi-1.5.5 and emerging the new version, the error occurs without the file collision, but still at the same location. usr/lib64/openmpi/mca_crs_none.so usr/lib64/openmpi/mca_carto_file.so usr/lib64/openmpi/mca_carto_auto_detect.so usr/lib64/libopen-pal.so.4.0.0 ecompressdir: bzip2 -9 /usr/share/man ecompressdir: bzip2 -9 /usr/share/doc * ERROR: sys-cluster/openmpi-1.6 failed: * ecompressdir failed
Have the same problem with portage-2.2.0_alpha108, but openmpi-1.6 successfully installed after downgrading portage to 2.2.0_alpha89.
This is to confirm that the problem vanishes with portage-2.2.0_alpha108. However, the problem exists with portage-2.1.10.49 and portage-2.1.10.63.
(In reply to comment #5) > This is to confirm that the problem vanishes with portage-2.2.0_alpha108. > However, the problem exists with portage-2.1.10.49 and portage-2.1.10.63. Sorry, I was reporting wrongly: The problem vanishes with portage-2.2.0_alpha89, not with portage-2.2.0_alpha108.
It seems that reinstalling portage was resolving the issue. I have now successfully emerged openmpi with portage-2.1.10.63.
I guess it must be triggered by this commit: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=76939c46aa2817bdbcea703432c52e5aa04160f9
The "brokenlink" code inside ecompressdir's funk_up_dir function isn't safe to be run in parallel, triggering intermittent failures in the ln command like these: ln: cannot remove ‘./man1/orteCC.1’: No such file or directory ln: failed to create symbolic link ‘./man1/orteCC.1’ -> ‘’: No such file or directory
This fixes it: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=bbacf8674168cf033de0ccb161f568d0b26f032b
(In reply to comment #10) > This fixes it: > > http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit; > h=bbacf8674168cf033de0ccb161f568d0b26f032b Plus this: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=9b2e4d5a48e17ae1a637c6de7a311cd9055dd02e
This is fixed in 2.1.10.64 and 2.2.0_alpha109.
I would like to confirm, that with portage 2.1.10.64 everything works fine. Thank you for the quick fix!
*** Bug 419449 has been marked as a duplicate of this bug. ***
