In my system I have 1 SSD and 2 HDD's that are configured in a RAID1 configuration (mdadm). My partition layout is: / on SSD /var on HDD RAID1 /tmp on tmpfs For the last few weeks I have been experiencing interruptions when performing updates. It typically happens during a long emerge routine. Tonight it happened twice. The first time it was while building Firefox. The second time it was while building wine. In both cases the trace was similar: Traceback (most recent call last): File "/usr/bin/emerge", line 50, in <module> retval = emerge_main() File "/usr/lib64/portage/pym/_emerge/main.py", line 1052, in emerge_main gc_locals=locals().clear) File "/usr/lib64/portage/pym/_emerge/actions.py", line 3950, in run_action myopts, myaction, myfiles, spinner) File "/usr/lib64/portage/pym/_emerge/actions.py", line 477, in action_build retval = mergetask.merge() File "/usr/lib64/portage/pym/_emerge/Scheduler.py", line 1010, in merge rval = self._merge() File "/usr/lib64/portage/pym/_emerge/Scheduler.py", line 1395, in _merge self._main_loop() File "/usr/lib64/portage/pym/_emerge/Scheduler.py", line 1366, in _main_loop self._event_loop.iteration() File "/usr/lib64/portage/pym/portage/util/_eventloop/EventLoop.py", line 266, in iteration if not x.callback(f, event, *x.args): File "/usr/lib64/portage/pym/portage/util/_async/PipeLogger.py", line 99, in _output_handler stdout_buf[os.write(stdout_fd, stdout_buf):] File "/usr/lib64/portage/pym/portage/__init__.py", line 246, in __call__ rval = self._func(*wrapped_args, **wrapped_kwargs) OSError: [Errno 5] Input/output error I have run fsck on the partitions and no errors were found. I ran smart tests on all drives and they all completed successfully. Here is emerge --info: Quote: # emerge --info Portage 2.1.12.2 (default/linux/amd64/13.0/desktop/kde, gcc-4.7.3, glibc-2.17, 3.9.3-gentoo x86_64) ================================================================= System uname: Linux-3.9.3-gentoo-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16394756 total, 2603156 free KiB Swap: 4194296 total, 4193860 free Timestamp of tree: Thu, 30 May 2013 05:45:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5, 3.2.5, 3.3.2 dev-util/cmake: 2.8.11::kde dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.4_p6-r1, 1.10.3, 1.11.6, 1.12.6 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.6.4, 4.7.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.9 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo dmwoodlx2_local kde sunrise gamerlay vincent 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 /usr/share/polkit-1/actions /usr/share/themes/oxygen-gtk/gtk-3.0" 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/splash /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 preserve-libs 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 ftp://gentoo.mirrors.tds.net/gentoo http://gentoo.mirrors.tds.net/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" 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 /var/lib/layman/kde /var/lib/layman/sunrise /var/lib/layman/gamerlay /var/lib/layman/vincent" SYNC="rsync://rsync.us.gentoo.org/gentoo-portage" USE="X a52 aac aacs acl acpi alsa alstream amd64 berkdb bindist bluetooth bluray branding bzip2 cairo cdda cddb cdr cli cmake consolekit cracklib crypt cuda cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fakevim fam fbcondecor ffmpeg firefox flac fortran ftp gdbm gif git gpm gtk hddtemp iconv imagemagick ipv6 java javascript joystick jpeg kde kipi lame lastfm lcms ldap libnotify lirc lm_sensors mad md5sum mercurial midi minizip mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses network nls nptl nsplugin ogg openal opengl openmp pam pango pcre pdf perl phonon plasma png policykit portmidi ppds python qt3support qt4 readline s3 samba sdl semantic-desktop session spell sqlite sse sse2 sse3 ssl startup-notification subversion svg tcpd threads tiff timidity truetype udev udisks unicode upower usb valgrind vdpau vim-syntax vorbis wxwidgets x264 xcb xcomposite xinerama xml xpm xscreensaver xv xvid zlib" ABI_X86="64" 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 author" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" LIRC_DEVICES="sb0540" NETBEANS_MODULES="*" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
This is a hardware problem not a portage issue
I am getting it too, on a raidz2 setup with six disks that are all reported online with no failures; additionally smart also reports there is no error. This also occured with me, more than once, during a long emerge run. It certainy is not a hardware issue; a zfs scrub reports there are no failures, and raidz2 allows two disks to fail. My machine has plenty of RAM and thus I suspect that the error must be caused by something in portage.
(In reply to mwoodj@knology.net from comment #0) > In my system I have 1 SSD and 2 HDD's that are configured in a RAID1 > configuration (mdadm). My partition layout is: > > / on SSD > /var on HDD RAID1 > /tmp on tmpfs What filesystem do you use on /var ?
ext4
I was also getting this error every time I tried to update Firefox to version 21. Happened twice. I then tried to use equery to find my portage version (it's 2.1.12.2) so I could comment on this bug, and it gave me an error about gentoolkit not being found. I rebuilt gentoolkit, and then Firefox I have a 16 GiB tmpfs mounted to /var/tmp, and my main hard disk is a 512 GB SSD.
(In reply to Mark W. Gabby II from comment #5) > being found. I rebuilt gentoolkit, and then Firefox That should be "Firefox built successfully" after I updated gentoolkit.
Important information is missing here. If it turns out not to be a filesystem error, then at least it is the filesystem driver that is at fault (like an -ENOENT where it should return an -EAGAIN) and there is little we can do about it unless we see more specific information. Also, I am not convinced that comment #2 and comment #5 are reports of the same issue, since "OSError: [Errno 5] Input/output error" actually doesn't tell us enough about what is going on. It could be a problem in the IPC code in sys-apps/portage or it could be something else.
It's got nothing to do with your filesystem unless you're redirecting stdout to a file like `emerge > output.log`. People in bug 459674 have been reporting this issue when stdout is a tty. *** This bug has been marked as a duplicate of bug 459674 ***
