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Bug 544726 - fsck on every boot because of "time" problem
Summary: fsck on every boot because of "time" problem
Status: RESOLVED INVALID
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Core system (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo's Team for Core System packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2015-03-28 08:48 UTC by Thomas Capricelli
Modified: 2015-04-19 11:50 UTC (History)
4 users (show)

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


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Description Thomas Capricelli 2015-03-28 08:48:47 UTC
For the last few weeks (maybe months), my main desktop computer does fsck on all (but one) partitions on every reboot.

The message displayed translate to "Superblock last write time is in the future (by less than a day, probably due to th hardware clock being incorrectly set)"

My setup regarding this is standard and hasn't changed for years : i use ntpd and my hardware clock is set to UTC

All my partitions are ext4, i have /dev/sda1 (ssd, i dont think it matters) mounted as root and /dev/sdb{1,2,3,4} mounted on other stuff.

On boot, /dev/sda1 is reported 'clean', and every other partition has the problem. The boot time usually very fast (ssd!) now takes ages, and i'm worried about the state of those partitions.

Each time the fsck reports no problem. The system is a typical ~amd64 often updated.


Reproducible: Always

Steps to Reproduce:
1. Turn off computer on evening
2. Bring it on next morning
3.
Comment 1 Andrew Savchenko gentoo-dev 2015-03-29 07:48:52 UTC
Is your CMOS battery alive? Please go to the BIOS/EFI prior to the boot and check that hardware time there is correct. If it is reset, please replace your battery.

ntp can't fix your time before on-boot fsck by design.

Anyway please post your emerge --info.
Comment 2 Thomas Capricelli 2015-03-29 11:11:12 UTC
I don't think a dead CMOS battery would set the time in future. Especially with such precision as "less than a day", could it ?

emerge --info :

Portage 2.2.18 (python 2.7.9-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.8.4, glibc-2.20-r2, 3.19.3 x86_64)
=================================================================
System uname: Linux-3.19.3-x86_64-AMD_Athlon-tm-_II_X4_620_Processor-with-gentoo-2.2
KiB Mem:    11766984 total,   9721736 free
KiB Swap:    5242876 total,   5242876 free
Timestamp of repository gentoo: Thu, 26 Mar 2015 21:15:01 +0000
sh bash 4.3_p33-r2
ld GNU ld (Gentoo 2.25 p1.0) 2.25
app-shells/bash:          4.3_p33-r2::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.9-r2::gentoo
dev-util/cmake:           3.1.0::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.13.11::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.13::<unknown repository>, 2.69-r1::gentoo
sys-devel/automake:       1.11.6-r1::gentoo, 1.12.6::gentoo, 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25::gentoo
sys-devel/gcc:            4.8.4::gentoo, 4.9.2::gentoo
sys-devel/gcc-config:     1.8::gentoo
sys-devel/libtool:        2.4.6-r1::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 3.19::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://freehackers.org/gentoo-portage
    priority: -1000

freehackers
    location: /usr/portage-overlay
    masters: gentoo
    priority: 0

qt                                                                                                                                                            
    location: /var/lib/layman/qt                                                                                                                              
    masters: gentoo                                                                                                                                           
    priority: 1                                                                                                                                               
                                                                                                                                                              
kde                                                                                                                                                           
    location: /var/lib/layman/kde                                                                                                                             
    masters: gentoo                                                                                                                                           
    priority: 2                                                                                                                                               
                                                                                                                                                              
Installed sets: @kde-frameworks, @kde-plasma                                                                                                                  
ABI="amd64"                                                                                                                                                   
ABI_X86="64"                                                                                                                                                  
ACCEPT_KEYWORDS="amd64 ~amd64"                                                                                                                                
ACCEPT_LICENSE="*"                                                                                                                                            
ACCEPT_PROPERTIES="*"                                                                                                                                         
ACCEPT_RESTRICT="*"
ANT_HOME="/usr/share/ant"
ARCH="amd64"
AUTOCLEAN="yes"
BASH_ENV="$HOME/.profile"
BOOTSTRAP_USE="cxx unicode internal-glib python_targets_python3_3 python_targets_python2_7 multilib"
CAMERAS="canon ptp2"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -pipe -O3"
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CHOST_x86="i686-pc-linux-gnu"
CLEAN_DELAY="5"
COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog"
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LC_MESSAGES="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LDFLAGS_amd64="-m elf_x86_64"
LDFLAGS_x32="-m elf32_x86_64"
LDFLAGS_x86="-m elf_i386"
LESS="-R -M --shift 5"
LESSOPEN="|lesspipe %s"
LINGUAS="en fr it fr_FR it_IT"
LOGNAME="root"
MAIL="/var/mail/root"
MAKEOPTS="-j 5 -l 4"
MANPATH="/usr/local/share/man:/usr/share/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.8.4/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.25/man:/etc/java-config-2/current-system-vm/man/"
MULTILIB_ABIS="amd64 x86"
MULTILIB_STRICT_DENY="64-bit.*shared object"
MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib"
MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage|udev|systemd|clang|python-exec)"
NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml"
NOCOLOR="false"
OFFICE_IMPLEMENTATION="libreoffice"
OPENGL_PROFILE="xorg-x11"
PAGER="/usr/bin/less"
PATH="/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/opt/bin"
PHP_TARGETS="php5-5"
PKGDIR="/usr/portage/packages"
PORTAGE_BIN_PATH="/usr/lib/portage/python2.7"
PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png"
PORTAGE_CONFIGROOT="/"
PORTAGE_DEBUG="0"
PORTAGE_DEPCACHEDIR="/var/cache/edb/dep"
PORTAGE_ECLASS_WARNING_ENABLE="0"
PORTAGE_ELOG_CLASSES="log warn error"
PORTAGE_ELOG_MAILFROM="portage@localhost"
PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}"
PORTAGE_ELOG_MAILURI="root"
PORTAGE_ELOG_SYSTEM="save_summary:log,warn,error,qa echo"
PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5"
PORTAGE_FETCH_RESUME_MIN_SIZE="350K"
PORTAGE_GID="250"
PORTAGE_GPG_SIGNING_COMMAND="gpg --sign --digest-algo SHA256 --clearsign --yes --default-key "${PORTAGE_GPG_KEY}" --homedir "${PORTAGE_GPG_DIR}" "${FILE}""
PORTAGE_INST_GID="0"
PORTAGE_INST_UID="0"
PORTAGE_INTERNAL_CALLER="1"
PORTAGE_NICENESS="15"
PORTAGE_OVERRIDE_EPREFIX=""
PORTAGE_PYM_PATH="/usr/lib64/python2.7/site-packages"
PORTAGE_PYTHONPATH="/usr/lib64/python2.7/site-packages"
PORTAGE_QUIET="1"
PORTAGE_RSYNC_EXTRA_OPTS="--exclude ChangeLog"
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"
PORTAGE_RSYNC_RETRIES="-1"
PORTAGE_SYNC_STALE="30"
PORTAGE_TMPDIR="/var/tmp"
PORTAGE_TMPFS="/dev/shm"
PORTAGE_VERBOSE="1"
PORTAGE_WORKDIR_MODE="0700"
PYTHONDONTWRITEBYTECODE="1"
PYTHON_SINGLE_TARGET="python2_7"
PYTHON_TARGETS="python2_7"
QEMU_SOFTMMU_TARGETS="i386 x86_64"
QEMU_USER_TARGETS="i386 x86_64"
QT_GRAPHICSSYSTEM="native"
ROOT="/"
ROOTPATH="/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.8.4:/usr/x86_64-pc-linux-gnu/avr/gcc-bin/4.8.3:/usr/x86_64-pc-linux-gnu/mingw32/gcc-bin/4.8.3"
RPMDIR="/usr/portage/rpm"
RUBY_TARGETS="ruby21"
SHELL="/bin/tcsh"
SUDO_COMMAND="/usr/bin/emerge -qvta --keep-going -j 4 --load-average=7 --info"
SUDO_GID="100"
SUDO_UID="501"
SUDO_USER="orzel"
SYMLINK_LIB="yes"
TERM="xterm"
UNINSTALL_IGNORE="/lib/modules/* /var/run /var/lock"
USE="3dnow 3dnowext X a52 aac acl acpi additions alsa amd64 amr amrnb amrr amrwb apng apulse artworkextra autoipd avahi berkdb bidi bluetooth branding browserplugin bzip2 cairo cdda cdio cdr chm cli cmake community compositor consolekit cracklib crypt css cups cxx dbus debugger declarative designer-plugin device-mapper dirac divx4linux djvu dri dts dv dvd dvdnav dvdr dvdread edl egl eigen emboss encode evdev exif faac fam farstream ffmpeg fftw firefox flac fluidsynth font-server fontconfig freebox freetype fts3 g3dvl gallium gbm gd gdbm geoip gif git glamor glitz glut gnutls gpg gphoto2 gps graphite gsm gstreamer hpcups hpijs ical iconv icu ilbc imap innodb inotify int64 ipv6 ipython irc irda jabber jack java jingle jit joystick jpeg jpeg2k kde kdevelop kdevplatform kipi kompare kpathsea kqemu ladspa lame lash latex lcms libkms libnotify libsamplerate lightdm live llvm llvm-shared-libs lm_sensors lua lv2 lzma lzo mad matroska melt mercurial midi mikmod minizip mjpeg mmap mmx mmxext mng mod modules mozilla mp3 mp4 mpeg mtp multilib multimedia mutouch ncurses network nls nodrm npp nptl nsplugin obex ofx ogg oggvorbis okular openexr opengl openmp opus osgapps pam pango pch pcre pcre16 pdf pep8 perlsuid phonon pic pipechan plasma png policykit popcnt ppds printsupport projectm pyqt4 python qhull qmake qml qt-bundled qt3support qt4 qt5 quicktime qwt rdp readline real realmedia reports rss rtc rtsp scanner schroedinger scripttools sddm sdl secure-delete session sip sipim slp smp sndfile social-desktop solver soundtouch sox spatialite speex spell sphinx spice sql sqlite sqlite3 sse sse2 sse3 sse4a ssl startup-notification static-libs stream svg system-cairo system-icu system-jpeg system-libvpx system-sqlite szip tb4 tcpd theora threads thumbnail thuna tiff truetype udev udisks unicode upower usb usbredir v4l v4l2 vcd vdpau vga vhook video vim-syntax vlm vnc vorbis vpx vst wav wavpack wayland wayland-compositor webkit webp wicd widgets wifi win32codecs wma wma-fixed wmf wpd x264 xcb xcomposite xetex xinerama xkb xml xpm xrandr xscreensaver xv xvfb xvid xwayland zeroconf zlib zrtp" 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" 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="author braindump flow karbon kexi krita sheets stage words" CAMERAS="canon ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext popcnt sse sse2 sse3 sse4a" 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" GRUB_PLATFORMS="pc" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en fr it fr_FR it_IT" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="r600 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"
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VBOX_APP_HOME="/opt/VirtualBox"
VIDEO_CARDS="r600 radeon"
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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"
Comment 3 Thomas Capricelli 2015-03-29 11:36:51 UTC
I was mentionning ntp to give details on the setup. I've been using it for 20 or more years probably. I did not install it hoping to fix the bug.
Comment 4 Andrew Savchenko gentoo-dev 2015-03-29 12:20:15 UTC
(In reply to Thomas Capricelli from comment #3)
> I was mentionning ntp to give details on the setup.

You are misunderstanding error message. "Superblock last write time is in the future" means that at the moment of file system mount attempt superblock is updated later than current system time. This is perfectly valid in case when CMOS drops your time to manufacturer default value which is less than real time. So your system end up booting "in the past" and thus correct superblock write time becomes "in future" for that system.

I had exactly the same problem a while ago. Just replace your battery. To check for this problem, turn off your system for at least 24 hours and go straight to BIOS afterwards.
Comment 5 Thomas Capricelli 2015-03-29 23:03:53 UTC
I (respectfully) disagree. I think I understand the message well.

I insisted, and i keep insisting on the fact that the messages also says "less than a day". So a reset to the CMOS default date (1970/1/1) is not the problem heree
Comment 6 Thomas Capricelli 2015-03-29 23:05:23 UTC
(In reply to Andrew Savchenko from comment #4)
> I had exactly the same problem a while ago. Just replace your battery. To
> check for this problem, turn off your system for at least 24 hours and go
> straight to BIOS afterwards.

I understand very well. But you might consider that my problem is not the same as the one you had. I've just checked and all my (non-default) cmos settings are still there.
Comment 7 Mike Gilbert gentoo-dev 2015-03-30 13:31:56 UTC
Are you booting using openrc or systemd?

What does /etc/conf.d/hwclock contain?

What does /etc/adjtime contain (if anything)?
Comment 8 Thomas Capricelli 2015-03-30 15:25:32 UTC
I'm using openrc (emerge --info doesn't report such a useful information !?).
/etc/conf.d/hwclock contains
    clock="UTC"
    clock_args=""
(everything else commented).


berlioz ~ # cat /etc/adjtime 
-13.368038 1254180250 0.000000
1254180250
UTC
Comment 9 Thomas Capricelli 2015-03-30 15:26:35 UTC
If that matters "ntptrace localhost" reports :

localhost: stratum 4, offset -0.000418, synch distance 0.108768
Comment 10 Mike Gilbert gentoo-dev 2015-03-30 16:07:24 UTC
Does the output of "date" and "hwclock" show the same time?

If you boot your system with init=/bin/sh, do "date" and "hwclock" match? This will test if your kernel is setting the clock on boot before init starts.
Comment 11 Thomas Capricelli 2015-03-30 17:51:23 UTC
They do:

berlioz ~ # hwclock ; date
lun 30 mar 2015 19:49:30 CEST  .921546 seconds
lun 30 mar 2015, 19.49.30, CEST

Will try with init=/bin/sh on next reboot and report.

I got this option in kernel : CONFIG_GENERIC_CMOS_UPDATE=y, you think it could interfere, right .. ?
Comment 12 Mike Gilbert gentoo-dev 2015-03-30 17:58:35 UTC
Well, I'm thinking of two possibilities:

1. CONFIG_RTC_HCTOSYS is not set, so the kernel does not set your system clock on boot. The system clock would then default to Jan 1 1970. This seems unlikely, given the "less than a day" message, but maybe fsck is lying about that due to some bug.

2. Some init script(s) are messing up your system clock before fsck, and fixing it afterwards. I'm not sure how this could happen.
Comment 13 Thomas Capricelli 2015-03-31 01:01:06 UTC
(for the record) CONFIG_RTC_HCTOSYS seems ok.

orzel@berlioz /home/orzel% zgrep RTC_HCTOSYS /proc/config.gz
CONFIG_RTC_HCTOSYS=y
CONFIG_RTC_HCTOSYS_DEVICE="rtc0"
Comment 14 Andrew Savchenko gentoo-dev 2015-04-01 22:18:22 UTC
Still, please check your BIOS date before booting Linux and compare it to the real time. At least this will help to understand when your time is messed up: during OS boot or before/at shutdown.

Also please disable your NTP client/server (if any) for testing and post the following:

1. BIOS time
2. Time reported by fsck
3. Time just after your system is booted.

And compare them with some external clock for that exact moments.

P.S.
I still have no idea even whom to assign this issue...
Comment 15 Mike Gilbert gentoo-dev 2015-04-01 22:35:38 UTC
(In reply to Andrew Savchenko from comment #14)
> I still have no idea even whom to assign this issue...

Thus far, no "bug" has been identified, so there's really nobody to assign it. If a bug is not identified, we close it as NEEDINFO.
Comment 16 Andrew Savchenko gentoo-dev 2015-04-01 23:06:38 UTC
Some more thoughts...

(In reply to Thomas Capricelli from comment #0)
> For the last few weeks (maybe months), my main desktop computer does fsck on
> all (but one) partitions on every reboot.

Can you find in logs after what action this had happened? Maybe some package was updated or kernel.

Could you please update kernel, e2fsprogs and openrc to the latest versions available and see if bug is still here?
Comment 17 Andrew Savchenko gentoo-dev 2015-04-03 08:01:44 UTC
Well, we have the problem: fsck is being run after each reboot. Though we don't know where this problem originates from. My guess is that one of the following components may be responsible:
- fsck (e2fsprogs);
- base init scripts (openrc);
- kernel.

So I'm assigning/CC'ing relevant teams. Maybe they have some new ideas.

Thomas, please provide information requested in comment 16.
This should help to rule out some reasons.
Comment 18 Thomas Capricelli 2015-04-03 23:24:12 UTC
(In reply to Andrew Savchenko from comment #16)
> Can you find in logs after what action this had happened? Maybe some package
> was updated or kernel.

I update both system (gentoo) and kernel very regularly, wont teach us much.

> Could you please update kernel, e2fsprogs and openrc to the latest versions
> available and see if bug is still here?

Already at last versions (as i update often). Anyway, i dont think the bug is in one of those packages.

Regarding your comment #14, i dont know how what is the "time reported by fsck". The date/time in bios is correct afaics (usual UTC time, as it has always been).

I've noticed that the CONFIG_RTC_DRV_CMOS kernel stuff was configured as module, and I'm investigating if having it compile-in could solve the problem.

I set "in progress" as anyway i'm more and more convinced that this is a configuration problem of my own and not a bug in some gentoo package.
Comment 19 Andrew Savchenko gentoo-dev 2015-04-04 09:11:56 UTC
(In reply to Thomas Capricelli from comment #18)
> (In reply to Andrew Savchenko from comment #16)
> > Can you find in logs after what action this had happened? Maybe some package
> > was updated or kernel.
> 
> I update both system (gentoo) and kernel very regularly, wont teach us much.

/var/log/emerge.log should contain all emerge history from the initial install of the system (if you don't clear this log using logrotate or similar approach). So if you know when this bug appeared for the first time, you can find in a log after update of what package(s) this happened. This may help to find what triggered the issue.

> Regarding your comment #14, i dont know how what is the "time reported by
> fsck". 

When fsck is complaining:
"Superblock last write time is in the future (by less than a day, probably due to th hardware clock being incorrectly set)"
Does it show exact timestamp for what time is in future?

> I've noticed that the CONFIG_RTC_DRV_CMOS kernel stuff was configured as
> module, and I'm investigating if having it compile-in could solve the
> problem.

Modules are loading after fsck, so this maybe indeed the reason.
Comment 20 Thomas Capricelli 2015-04-07 22:03:17 UTC
The problem is still there with RTC driver built-in. The problem is also here after the computer is several hours down, so it's not utc-related (i'm at utc+2 hours here).

I don't know precisely when the bug appeared, genlop wont help. I'm not even sure it's a installed/updated gentoo package that triggered this.
Comment 21 Thomas Capricelli 2015-04-07 22:06:34 UTC
(In reply to Andrew Savchenko from comment #19)
> When fsck is complaining:
> "Superblock last write time is in the future (by less than a day, probably
> due to th hardware clock being incorrectly set)"
> Does it show exact timestamp for what time is in future?

Of course not, that would have helped a LOT for sure ..

I tested again and everything seems fine
* when booting into bios, the date/time is the right utc one (here minus 2 hours)
* booting with init=/bin/bash, I confirm hwclock/date give the same time, which is the right time (utc+2)
* still in this session, "dumpe2fs -h" gives totally normal information. The "Last write time" is when i shut the computer down. 

The error message by e2fsck mentions "Superblock last write time" but i dont know how to get this exact date. dumpe2fs only reports "Last write time"
Comment 22 Thomas Capricelli 2015-04-19 11:50:10 UTC
Fixed, was rather a configuration problem.

For the record, the default gentoo settings give this behaviour when using ntpd. If so, you need to change /etc/conf.d/hwclock with:

clock_hctosys="no"
clock_systohc="no"