sys-cluster/openmpi failed when trying to update from 1.10.3 to 1.10.3-r1 The error message: ================== Making install in util * Header files have changed between ABIs. * --- /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/temp/.multilib_header_cksum 2016-09-04 14:07:57.746478296 +1000 * +++ /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/temp/.multilib_header_cksum.new 2016-09-04 14:08:24.815621188 +1000 * @@ -35,6 +35,7 @@ * 1336871310 4940 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/cxx/functions_inln.h * 2263507481 5119 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/cxx/topology_inln.h * 2601013270 5177 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/cxx/intracomm.h * +342196233 6053 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/java/mpiJava.h * 4258384839 6256 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/cxx/request.h * 1362969192 6572 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/cxx/intracomm_inln.h * 374817209 6746 /var/tmp/portage/sys-cluster/openmpi-1.10.3-r1/image/usr/include/openmpi/ompi/mpi/cxx/win.h * ERROR: sys-cluster/openmpi-1.10.3-r1::gentoo failed (install phase): * Header checksum mismatch, aborting. * * Call stack: * ebuild.sh, line 115: Called src_install * environment, line 4964: Called multilib-minimal_src_install * environment, line 4115: Called multilib_foreach_abi 'multilib-minimal_abi_src_install' * environment, line 4309: Called multibuild_foreach_variant '_multilib_multibuild_wrapper' 'multilib-minimal_abi_src_install' * environment, line 4002: Called _multibuild_run '_multilib_multibuild_wrapper' 'multilib-minimal_abi_src_install' * environment, line 4000: Called _multilib_multibuild_wrapper 'multilib-minimal_abi_src_install' * environment, line 685: Called multilib-minimal_abi_src_install * environment, line 4112: Called multilib_check_headers * environment, line 4171: Called die * The specific snippet of code: * die "Header checksum mismatch, aborting."; emerge info: ============== # emerge --info '=sys-cluster/openmpi-1.10.3-r1::gentoo' Portage 2.3.0 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.4.0, glibc-2.23-r2, 4.7.2-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.7.2-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_950_@_3.07GHz-with-gentoo-2.3 KiB Mem: 6098956 total, 927536 free KiB Swap: 4194300 total, 3751504 free Timestamp of repository gentoo: Sun, 04 Sep 2016 01:00:01 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] ccache version 3.2.7 [disabled] app-shells/bash: 4.3_p46::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo dev-util/ccache: 3.2.7::gentoo dev-util/cmake: 3.6.1-r1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.21.7::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 5.4.0::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 x-portage location: /usr/local/portage masters: gentoo priority: 0 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* PUEL" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -mtune=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/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="-O2 -pipe -march=native -mtune=native" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n --with-bdeps=y --verbose-conflicts --buildpkg --buildpkg-exclude='virtual/* sys-kernel/*-sources */*-bin x11-drivers/nvidia-drivers'" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_AU.UTF-8" LC_ALL="en_AU.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5 -s " 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 a52 aac aacs aalib acl acpi alsa amd64 asf berkdb bidi bluetooth bluray branding bzip2 cairo cdda cdio cdr cli consolekit cracklib crypt cups cxx dbus declarative directfb dri dts dv dvb dvd dvdr dvi emboss enca encode exif extensions extras faac faad fam fbcon ffmpeg firefox flac fontconfig fortran gcj gd gdbm gif glamor gpm graphviz gstreamer gtk gtk2 httpd iconv icu ilbc imagemagick imlib ipod java jpeg jpeg2k kde kipi lcms ldap legacy-systray libcaca libmpeg2 libnotify live lua lzo mad matroska mjpeg mmx mmxext mng modplug modules mp3 mp4 mpeg multilib multislot mysql ncurses nls nptl ogg opengl openmp pam pango pcre pdf phonon plasma png policykit postproc ppds profile qml qt3support qt5 quicktime readline rtc rtmp scanner script sddm sdl seccomp semantic-desktop session speex spell sql sqlite sse sse2 ssl startup-notification subversion svg tcpd theora threads tiff toolame truetype twolame udev udisks unicode upower usb v4l vcd vlm vorbis webkit widgets wxwidgets x264 xanim xattr xcb xcomposite xine xinerama xml xscreensaver xv xvid xvmc zlib" ABI_X86="32 64" ALSA_CARDS="intel8x0" 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" DVB_CARDS="tda10046" 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 ublox ubx" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" L10N="en_AU.UTF8" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en ar" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="x86_64 arm" QEMU_USER_TARGETS="arm armeb" RUBY_TARGETS="ruby20 ruby21" 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" USE_PYTHON="2.7" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS JAVA: ======= GENTOO_VM=oracle-jdk-bin-1.8 CLASSPATH="" JAVA_HOME="/opt/oracle-jdk-bin-1.8.0.102" JAVACFLAGS="-source 1.6 -target 1.6" COMPILER=""
I cannot add the build.log. Everytime, I try I get error: the attachment site is down.
(In reply to email200202 from comment #1) > I cannot add the build.log. Everytime, I try I get error: the attachment > site is down.
Same here WRT openmpi. No point in attaching my log file, since it is practically identical. Only thing differing is that I compiled my entiry system with gcc-6.2.0.
(In reply to Jeroen Roovers from comment #2) > (In reply to email200202 from comment #1) > > I cannot add the build.log. Everytime, I try I get error: the attachment > > site is down. Inaccurate error description, no idea what an "attachment site" is. Follow-up to bugzilla@gentoo.org if need be.
This is the error message I got where trying to upload the build.log as attachment. ------------------------------------------------------------------ This site can’t be reached The webpage at https://bugs.gentoo.org/attachment.cgi might be temporarily down or it may have moved permanently to a new web address. ERR_ACCESS_DENIED ------------------------------------------------------------------
Created attachment 444988 [details] build.log 1
Created attachment 444990 [details] build.log The problem was the size of the attachment is greater than the limit. Ignore my previous attachment post, it was a test. Here is the build.log file:
I can confirm the exact same error message above. emerge --info: Portage 2.3.0 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.4.0, glibc-2.23-r2, 4.7.1-gentoo x86_64) ================================================================= System uname: Linux-4.7.1-gentoo-x86_64-AMD_FX-tm-8350_Eight-Core_Processor-with-gentoo-2.3 KiB Mem: 16381156 total, 8593860 free KiB Swap: 7807576 total, 7807576 free Timestamp of repository gentoo: Tue, 06 Sep 2016 04:45:01 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 app-shells/bash: 4.3_p46::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.3.5-r8::gentoo, 3.4.5::gentoo, 3.5.2::gentoo dev-util/cmake: 3.6.1-r1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.21.7::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 4.9.3::gentoo, 5.4.0::gentoo, 6.1.0::musl sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.us.gentoo.org/gentoo-portage/ priority: -1000 sync-rsync-vcs-ignore: true x-portage location: /usr/local/portage masters: gentoo priority: 0 steam-overlay location: /var/lib/layman/steam-overlay sync-type: laymansync sync-uri: git://github.com/anyc/steam-overlay.git masters: gentoo priority: 50 Installed sets: @system ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O3 -march=native -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/lib64/libreoffice/program/sofficerc /usr/lib64/mozilla/defaults/pref /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O3 -march=native -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 preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://gentoo.mirrors.easynews.com/linux/gentoo/ ftp://mirror.leaseweb.com/gentoo/ http://gentoo.osuosl.org/ http://mirrors.rit.edu/gentoo/" LANG="en_US" LDFLAGS="-Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -O3 -march=native -pipe" MAKEOPTS="-j8" 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="3dnow 3dnowext 3ds X a52 aac acl acpi aes-ni alsa amd64 assistant audacious audiofile avahi avx bash-completion berkdb boost branding bzip2 cairo caps cdda cddb cdr cdrom cg cli conntrack consolekit cracklib crypt css cups cursors cvs cvsgraph cxx d dbus declarative dhclient disable-watermark dri dts dv dvd dvdr emboss enca encode exif extensions fam fat fftw firefox flac fma fortran ftp fuse gcj gd gdbm gdbui gif glamor gmp gnutls gphoto2 gpm graphite gtk guile hbci hddtemp hpn icons iconv icq ieee1394 image imagemagick imap imlib jack jack-tmpfs java javascript joystick jpeg jpeg2k kde kipi lame lash lcms libnotify live lm_sensors lua lz4 lzma lzo lzw mad mdnsresponder-compat mixer mmap mmx mmxext mng modules mp3 mp4 mpeg mpi multilib multislot mysql ncurses net netlink network networkmanager nfs nftables nls npp nptl nsplugin ntfs odbc ode offensive ofx ogg openal openexr opengl openmp openssh openssl orc pam pango pcre pda pdf phonon physfs pkcs11 plasma pmu png policykit pop portage portaudio ppds private-headers pulseaudio python-bindings qml qt3support qt4 qt5 quicktime rar readline realmedia realtime redland reiser4 reiserfs romio rtc samba scanner sdl sdl-image seccomp sensord session sharedmem slang smp smtp sockets socks5 sox spell sse sse2 ssl startup-notification subversion svg sysvipc tao tcl tcpd teamd theora threads threadsonly thunar tiff tk tools transcode truetype udev udisks unicode upower usb vorbis wav wext widgets wifi wma wmp wxwidgets x264 xattr xcb xcomposite xine xinerama xml xscreensaver xv xvid yahoo zlib" ABI_X86="64 32" ALSA_CARDS="usb_audio" 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx fma3 fma4 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3 xop" 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 ublox ubx" INPUT_DEVICES="evdev" KERNEL="linux" L10N="en pt-BR" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en pt_BR" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php_5-2+" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" SANE_BACKENDS="xerox_mfp" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
commit 516a3286cdbf24653e83d91580115e0fd424f0e6 Author: Christoph Junghans <ottxor@gentoo.org> Date: Thu Sep 8 14:18:00 2016 -0600 sys-cluster/openmpi: fix build for java (bug #592834) Package-Manager: portage-2.2.28
