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Bug 530012 - dev-db/mysql-5.6.21-r1 crashes on app-office/akonadi-server-1.13.0 start
Summary: dev-db/mysql-5.6.21-r1 crashes on app-office/akonadi-server-1.13.0 start
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] KDE (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo KDE team
URL:
Whiteboard:
Keywords: PATCH
Depends on:
Blocks:
 
Reported: 2014-11-21 07:20 UTC by Pavel Volkov
Modified: 2015-06-26 22:32 UTC (History)
2 users (show)

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


Attachments
Find mysql_install_db and add required option (mysql-db-install-path-and-option.patch,1.48 KB, patch)
2015-01-08 20:20 UTC, Brian Evans (RETIRED)
Details | Diff

Note You need to log in before you can comment on or make changes to this bug.
Description Pavel Volkov 2014-11-21 07:20:49 UTC
I can't launch Akonadi anymore after update to MySQL 5.6.
I had this issue before, but I worked it around with masking MySQL 5.6.
Now Qt requires 5.6 and I'm forced to update.

$ akonadictl start
Starting Akonadi Server... 
   done. 
Connecting to deprecated signal QDBusConnectionInterface::serviceOwnerChanged(QString,QString,QString)
search paths:  ("/usr/local/bin", "/usr/bin", "/bin", "/opt/bin", "/usr/x86_64-pc-linux-gnu/gcc-bin/4.8.3", "/usr/games/bin", "/sbin", "/usr/sbin", "/usr/local/sbin", "/home/rondo/script", "/usr/sbin", "/usr/local/sbin", "/usr/local/libexec", "/usr/libexec", "/opt/mysql/libexec", "/opt/local/lib/mysql5/bin", "/opt/mysql/sbin") 
Found mysql_install_db:  "" 
Found mysqlcheck:  "/usr/bin/mysqlcheck" 
Database process exited unexpectedly during initial connection!
executable: "/usr/sbin/mysqld"
arguments: ("--defaults-file=/home/rondo/.local/share/akonadi/mysql.conf", "--datadir=/home/rondo/.local/share/akonadi/db_data/", "--socket=/tmp/akonadi-rondo.zpYhYT/mysql.socket")
stdout: ""
stderr: "2014-11-21 10:07:28 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
"
exit code: 1
process error: "Process operation timed out"
"[
0: akonadiserver(_Z11akBacktracev+0x37) [0x469757]
1: akonadiserver() [0x4699b2]
2: /lib64/libc.so.6(+0x34e90) [0x7ffcee262e90]
3: /lib64/libc.so.6(gsignal+0x37) [0x7ffcee262e17]
4: /lib64/libc.so.6(abort+0x16a) [0x7ffcee26417a]
5: /usr/lib64/qt4/libQtCore.so.4(_Z17qt_message_output9QtMsgTypePKc+0x64) [0x7ffcefd2ddd4]
6: akonadiserver(_ZN15FileDebugStream9writeDataEPKcx+0x9d) [0x46b78d]
7: /usr/lib64/qt4/libQtCore.so.4(_ZN9QIODevice5writeEPKcx+0xb0) [0x7ffcefdc9a20]
8: /usr/lib64/qt4/libQtCore.so.4(+0x11c2fd) [0x7ffcefdd92fd]
9: /usr/lib64/qt4/libQtCore.so.4(_ZN11QTextStreamD1Ev+0x31) [0x7ffcefde2011]
10: akonadiserver(_ZN6QDebugD1Ev+0x39) [0x464ab9]
11: akonadiserver(_ZN7Akonadi6Server13DbConfigMysql19startInternalServerEv+0x1e5d) [0x4d0d8d]
12: akonadiserver(_ZN7Akonadi6Server13AkonadiServer20startDatabaseProcessEv+0xd7) [0x46c2e7]
13: akonadiserver(_ZN7Akonadi6Server13AkonadiServer4initEv+0xa5) [0x46ea15]
14: akonadiserver() [0x5311c6]
15: /usr/lib64/qt4/libQtCore.so.4(_ZN7QObject5eventEP6QEvent+0x24e) [0x7ffcefe558fe]
16: /usr/lib64/qt4/libQtCore.so.4(_ZN16QCoreApplication14notifyInternalEP7QObjectP6QEvent+0x6d) [0x7ffcefe3d2ad]
17: /usr/lib64/qt4/libQtCore.so.4(_ZN23QCoreApplicationPrivate16sendPostedEventsEP7QObjectiP11QThreadData+0x1ea) [0x7ffcefe404ca]
18: /usr/lib64/qt4/libQtCore.so.4(+0x1ae1be) [0x7ffcefe6b1be]
19: /usr/lib64/libglib-2.0.so.0(g_main_context_dispatch+0x254) [0x7ffced90e984]
20: /usr/lib64/libglib-2.0.so.0(+0x48bc8) [0x7ffced90ebc8]
21: /usr/lib64/libglib-2.0.so.0(g_main_context_iteration+0x2c) [0x7ffced90ec6c]
22: /usr/lib64/qt4/libQtCore.so.4(_ZN20QEventDispatcherGlib13processEventsE6QFlagsIN10QEventLoop17ProcessEventsFlagEE+0x7e) [0x7ffcefe6a98e]
23: /usr/lib64/qt4/libQtCore.so.4(_ZN10QEventLoop13processEventsE6QFlagsINS_17ProcessEventsFlagEE+0x2f) [0x7ffcefe3be4f]
24: /usr/lib64/qt4/libQtCore.so.4(_ZN10QEventLoop4execE6QFlagsINS_17ProcessEventsFlagEE+0x175) [0x7ffcefe3c145]
25: /usr/lib64/qt4/libQtCore.so.4(_ZN16QCoreApplication4execEv+0x89) [0x7ffcefe41599]
26: akonadiserver(main+0x1ce) [0x46409e]
27: /lib64/libc.so.6(__libc_start_main+0xf5) [0x7ffcee24faa5]
28: akonadiserver() [0x4648ae]
]
ProcessControl: Application 'akonadiserver' returned with exit code 255 (Unknown error)

All the above is repeated several times and then:
"akonadiserver" crashed too often and will not be restarted!

This is app-office/akonadi-server-1.13.0 and I'm using KDE 4.14.3.

Reproducible: Always




Portage 2.2.14 (python 3.3.5-final-0, default/linux/amd64/13.0/desktop/kde/systemd, gcc-4.8.3, glibc-2.20, 3.17.3-gentoomelf x86_64)
=================================================================
System uname: Linux-3.17.3-gentoomelf-x86_64-Intel-R-_Core-TM-_i5-2400_CPU_@_3.10GHz-with-gentoo-2.2
KiB Mem:    16412532 total,   1605420 free
KiB Swap:   17825788 total,  17815020 free
Timestamp of tree: Thu, 20 Nov 2014 19:15:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.3_p30-r1
dev-java/java-config:     2.2.0
dev-lang/perl:            5.20.1-r2
dev-lang/python:          2.7.8, 3.3.5-r1, 3.4.2
dev-util/cmake:           3.0.2
dev-util/pkgconfig:       0.28-r2
sys-apps/baselayout:      2.2
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6-r1, 1.14.1
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.3-r2
sys-devel/make:           4.1-r1
sys-kernel/linux-headers: 3.17-r1 (virtual/os-headers)
sys-libs/glibc:           2.20
Repositories: gentoo custom
Installed sets: @fonts, @mkde, @python-extra, @vim
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE MPEG-4 myspell-ru_RU-ALexanderLebedev freedist vim.org unRAR BitstreamCyberbit MSttfEULA grass-ipafonts free-noncomm CC-BY-NC-ND-3.0 NVIDIA-r2 google-chrome Oracle-BCLA-JavaSE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native -mtune=native"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/ibus/component/simple.xml"
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="-O2 -pipe -march=native -mtune=native"
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.yandex.ru/gentoo-distfiles/ http://trumpetti.atm.tut.fi/gentoo/"
INSTALL_MASK="/etc/init.d/"
LANG="ru_RU.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
USE="X a52 aac acl acpi alsa amd64 anthy bluetooth branding bzip2 cairo cdda cdr cjk cli cracklib crypt cryptsetup cups cxx dbus declarative djvu dri dts dvd dvdr embedded emboss encode exif fam ffmpeg firefox flac fortran gdbm gif git glamor gpm gstreamer gtk iconv icu idn ipv6 jpeg kde kipi lame lcms libnotify lm_sensors mad mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp openvg pam pango pcre pdf phonon plasma png policykit ppds pulseaudio python qt3support qt4 raw readline samba scanner sdl session spell sse sse2 ssl startup-notification svg systemd tcpd tiff truetype udev udisks unicode upower usb vdpau vorbis wxwidgets x264 xattr xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="32 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="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 ublox ubx" GRUB_PLATFORMS="efi-64" 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 en_GB ru ja" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3 python3_4" QEMU_SOFTMMU_TARGETS="x86_64 i386" RUBY_TARGETS="ruby21" SANE_BACKENDS="genesys" USERLAND="GNU" VIDEO_CARDS="nvidia nouveau" 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 3.3"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC
Comment 1 Michael Palimaka (kensington) gentoo-dev 2014-11-24 16:22:33 UTC
Does mysql work when launched manually, and is there anything in the mysql logs? It looks like mysql is failing to start correctly.
Comment 2 Pavel Volkov 2014-11-25 15:54:23 UTC
Right, mysqld catshes SIGSEGV.

This is how I run it manually:
/usr/sbin/mysqld --debug=d:t:o,/tmp/mysql.crash --debug-check --defaults-file=/home/rondo/.local/share/akonadi/mysql.conf --datadir=/home/rondo/.local/share/akonadi/db_data/ --socket=/tmp/akonadi-rondo.EK5c6C/mysql.socket

It also exists with status 1.

And last lines from strace:
getcwd("/home/rondo/.local/share/akonadi/db_data", 4096) = 41
lseek(2, 0, SEEK_END)                   = 77599148
pread(2, "\273+\321\35\0\0\0\5\0\0\0\0\0\0\0\0\0\0\0\0004\224.\350\0\7\0\0\0\0\0\0"..., 16384, 81920) = 16384
mmap(NULL, 2117632, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fbfea834000
pread(2, "]\324\256R\0\0\n\251\0\0\0\0\0\0\0\0\0\0\0\0004\2240A\0\2\0\0\0\0\0\0"..., 1048576, 1048576) = 1048576
pread(2, "\255\202Jv\0\0\1`\0\0\0\0\0\0\0\0\0\0\0\0004\224\26\364\0\2\0\0\0\0\0\0"..., 1048576, 2097152) = 1048576
pread(2, "15:12:04 UTC - mysqld got signal"..., 16384, 0) = 16384
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0x23b5001} ---
write(2, "15:35:46 UTC - mysqld got signal"..., 38) = 38
write(2, "This could be because you hit a "..., 226) = 226
write(2, "We will try our best to scrape u"..., 177) = 177
write(2, "key_buffer_size=16777216\n", 25) = 25
write(2, "read_buffer_size=262144\n", 24) = 24
write(2, "max_used_connections=0\n", 23) = 23
write(2, "max_threads=151\n", 16)       = 16
write(2, "thread_count=0\n", 15)        = 15
write(2, "connection_count=0\n", 19)    = 19
write(2, "It is possible that mysqld could"..., 140) = 140
write(2, "Hope that's ok; if not, decrease"..., 66) = 66
write(2, "Thread pointer: 0x0\n", 20)   = 20
write(2, "Attempting backtrace. You can us"..., 159) = 159
futex(0x7fbfff0df1b0, FUTEX_WAKE_PRIVATE, 2147483647) = 0
futex(0x7fbffed4b1b0, FUTEX_WAKE_PRIVATE, 2147483647) = 0
write(2, "stack_bottom = 0 thread_stack 0x"..., 38) = 38
writev(-1, [{"/usr/sbin/mysqld", 16}, {"(", 1}, {"my_print_stacktrace", 19}, {"+0x", 3}, {"20", 2}, {")", 1}, {"[0x", 3}, {"83eab0", 6}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"(", 1}, {"handle_fatal_signal", 19}, {"+0x", 3}, {"34d", 3}, {")", 1}, {"[0x", 3}, {"62025d", 6}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/lib64/libpthread.so.0", 22}, {"(", 1}, {"+0x", 3}, {"fd30", 4}, {")", 1}, {"[0x", 3}, {"7fbfff6eed30", 12}, {"]\n", 2}], 8) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/lib64/libz.so.1", 16}, {"(", 1}, {"adler32", 7}, {"+0x", 3}, {"17c", 3}, {")", 1}, {"[0x", 3}, {"7fc0003716bc", 12}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"8a652e", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"937a73", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"977aa8", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"8f0c4a", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"851c44", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"(", 1}, {"_Z24ha_initialize_handlertonP13s"..., 44}, {"+0x", 3}, {"41", 2}, {")", 1}, {"[0x", 3}, {"57da81", 6}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"6976e0", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"(", 1}, {"_Z11plugin_initPiPPci", 21}, {"+0x", 3}, {"91c", 3}, {")", 1}, {"[0x", 3}, {"69b6ec", 6}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"(", 1}, {"_Z11mysqld_mainiPPc", 19}, {"+0x", 3}, {"83f", 3}, {")", 1}, {"[0x", 3}, {"57789f", 6}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/lib64/libc.so.6", 16}, {"(", 1}, {"__libc_start_main", 17}, {"+0x", 3}, {"f5", 2}, {")", 1}, {"[0x", 3}, {"7fbffed6daa5", 12}, {"]\n", 2}], 9) = -1 EBADF (Bad file descriptor)
writev(-1, [{"/usr/sbin/mysqld", 16}, {"[0x", 3}, {"56d055", 6}, {"]\n", 2}], 4) = -1 EBADF (Bad file descriptor)
write(2, "The manual page at http://dev.my"..., 145) = 145
exit_group(1)                           = ?
+++ exited with 1 +++
Comment 3 Brian Evans (RETIRED) gentoo-dev 2014-11-27 15:27:34 UTC
(In reply to Pavel Volkov from comment #2)
> Right, mysqld catshes SIGSEGV.
> 
> This is how I run it manually:
> /usr/sbin/mysqld --debug=d:t:o,/tmp/mysql.crash --debug-check
> --defaults-file=/home/rondo/.local/share/akonadi/mysql.conf
> --datadir=/home/rondo/.local/share/akonadi/db_data/
> --socket=/tmp/akonadi-rondo.EK5c6C/mysql.socket
> 

Please always specify --defaults-file first.  There are issues that will ignore settings if you do not.

> It also exists with status 1.
> 
> And last lines from strace:

Can you please post from the mysqld.err (or whatever log-error is set in defaults-file) file instead?  This is rather unreadable when most of the text is cut off.
Comment 4 Pavel Volkov 2014-11-27 18:02:35 UTC
This is mysql.err:

2014-11-27 21:00:05 5586 [Warning] Buffered warning: Changed limits: max_open_files: 1024 (requested 5000)

2014-11-27 21:00:05 5586 [Warning] Buffered warning: Changed limits: max_connections: 214 (requested 256)

2014-11-27 21:00:05 7f06ecce4740 InnoDB: Warning: Using innodb_additional_mem_pool_size is DEPRECATED. This option may be removed in future releases, together with the option innodb_use_sys_malloc and with the InnoDB's internal memory allocator.
2014-11-27 21:00:05 5586 [Note] InnoDB: Using atomics to ref count buffer pool pages
2014-11-27 21:00:05 5586 [Note] InnoDB: The InnoDB memory heap is disabled
2014-11-27 21:00:05 5586 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2014-11-27 21:00:05 5586 [Note] InnoDB: Memory barrier is not used
2014-11-27 21:00:05 5586 [Note] InnoDB: Compressed tables use zlib 1.2.8
2014-11-27 21:00:05 5586 [Note] InnoDB: Using Linux native AIO
2014-11-27 21:00:05 5586 [Note] InnoDB: Using CPU crc32 instructions
2014-11-27 21:00:05 5586 [Note] InnoDB: Initializing buffer pool, size = 80.0M
2014-11-27 21:00:05 5586 [Note] InnoDB: Completed initialization of buffer pool
2014-11-27 21:00:05 5586 [ERROR] InnoDB: Space id in fsp header 1416128883,but in the page header 824195850
18:00:05 UTC - mysqld got signal 11 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed, 
something is definitely wrong and this may fail.

key_buffer_size=16384
read_buffer_size=131072
max_used_connections=0
max_threads=214
thread_count=0
connection_count=0
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 85119 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0 thread_stack 0x40000
/usr/sbin/mysqld(my_print_stacktrace+0x20)[0x83eab0]
/usr/sbin/mysqld(handle_fatal_signal+0x34d)[0x62025d]
/lib64/libpthread.so.0(+0xfd30)[0x7f06eba72d30]
/lib64/libz.so.1(adler32+0x17c)[0x7f06ec6f56bc]
/usr/sbin/mysqld[0x8a652e]
/usr/sbin/mysqld[0x937a73]
/usr/sbin/mysqld[0x977aa8]
/usr/sbin/mysqld[0x8f0c4a]
/usr/sbin/mysqld[0x851c44]
/usr/sbin/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x41)[0x57da81]
/usr/sbin/mysqld[0x6976e0]
/usr/sbin/mysqld(_Z11plugin_initPiPPci+0x91c)[0x69b6ec]
/usr/sbin/mysqld(_Z11mysqld_mainiPPc+0x83f)[0x57789f]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f06eb0f1aa5]
/usr/sbin/mysqld[0x56d055]
The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
Comment 5 Michael Palimaka (kensington) gentoo-dev 2014-12-09 12:23:43 UTC
Does mysql start normally against a clean database? (ie. not passing the akonadi data dir arguments)
Comment 6 Pavel Volkov 2014-12-09 15:17:16 UTC
I tried logging into KDE with a new user — mysqld starts normally there
Comment 7 Michael Palimaka (kensington) gentoo-dev 2014-12-09 16:31:45 UTC
I guess your akonadi database is corrupted in such a way causing mysql to crash.
Comment 8 Brian Evans (RETIRED) gentoo-dev 2014-12-09 17:33:03 UTC
I agree that it looks like corrupt data.

If you want to compile mysql with debug symbols, there may be bug reports out there to search. (Example here https://wiki.gentoo.org/wiki//etc/portage/env )

If you wish to try to work around this:

1) Try using dev-db/mariadb instead.  This will use xtradb as an innodb replacement and may have better success.

2) Try https://dev.mysql.com/doc/refman/5.6/en/forcing-innodb-recovery.html to enable you to dump the data (mysqldump), delete the old files, recreate new and import from the dump.
Comment 9 Pavel Volkov 2014-12-10 20:00:14 UTC
I tried mariadb and recoveing InnoDB — it's still broken.
I think I'll wait until Plasma/Frameworks/Applications 5 are packaged and then reconfigure the entire desktop environment...
Comment 10 Andreas K. Hüttel archtester gentoo-dev 2014-12-13 10:45:11 UTC
Same behavior here. Reopening.
Comment 11 Andreas K. Hüttel archtester gentoo-dev 2014-12-13 10:59:47 UTC
http://forums.gentoo.org/viewtopic-t-967722-view-next.html
Same problem
Comment 12 Brian Evans (RETIRED) gentoo-dev 2014-12-13 16:35:29 UTC
(In reply to Andreas K. Hüttel from comment #11)
> http://forums.gentoo.org/viewtopic-t-967722-view-next.html
> Same problem

dev-db/mysql needs debug symbols for a decent backtrace in the error message.  Without this, it is pure speculation to what is causing it.

The OP is more likely to have corrupt data due to:
> 2014-11-27 21:00:05 5586 [ERROR] InnoDB: Space id in fsp header 1416128883,but in the page header 824195850

The forum post output did not list it.
Comment 13 Michael Palimaka (kensington) gentoo-dev 2014-12-18 14:09:18 UTC
I just ran into some crashing issues (independent of akonadi) and it was solved by mysql_upgrade.
Comment 14 Brian Evans (RETIRED) gentoo-dev 2015-01-05 02:01:45 UTC
Without a backtrace or a way to duplicate, I suggest closing this as NEEDINFO.

The only speculation I can think of without it is akonadi not creating the system tables which can be used for more than authentication.  Again, without more info, this is only a guess.
Comment 15 Brian Evans (RETIRED) gentoo-dev 2015-01-08 20:20:58 UTC
Created attachment 393480 [details, diff]
Find mysql_install_db and add required option

One issue I see that may be related is from akonadi-server startup:

`Found mysql_install_db: ""`

On first run, it executes an empty string and carries on its merry way without error.

The mysql system tables are critical for operations.  They contain more than just logins and permissions these days and may cause a crash if something tries to read/write to them.

Attached is a patch to fix this horrible detection.

For those already affected, you should run `/usr/share/mysql/scripts/mysql_install_db --defaults-file=~/.local/share/akonadi/mysql.conf --force --datadir=~/.local/share/akonadi/db_data/ --basedir=/usr`  while akonadi-server is stopped.

Please report if this helps.
Comment 16 Brian Evans (RETIRED) gentoo-dev 2015-01-08 20:49:59 UTC
Removing blocks as recommended by KDE team
Comment 17 Brian Evans (RETIRED) gentoo-dev 2015-02-21 21:29:00 UTC
(In reply to Brian Evans from comment #15)
> For those already affected, you should run
> `/usr/share/mysql/scripts/mysql_install_db
> --defaults-file=~/.local/share/akonadi/mysql.conf --force
> --datadir=~/.local/share/akonadi/db_data/ --basedir=/usr`  while
> akonadi-server is stopped.
> 
> Please report if this helps.

Correction on the workaround command:
`/usr/share/mysql/scripts/mysql_install_db --defaults-file=${HOME}/.local/share/akonadi/mysql.conf --datadir=${HOME}/.local/share/akonadi/db_data/ --basedir=/usr`

Seems it does not like the ~ expansion.

@kde: what's the status of patching this?
Comment 18 Michael Palimaka (kensington) gentoo-dev 2015-02-22 04:41:07 UTC
It looks OK. I'm not actively using akonadi-server so I haven't been able to test.
Comment 19 Johannes Huber (RETIRED) gentoo-dev 2015-06-26 22:32:28 UTC
Thanks all. I have added the patch to a new revision as it doesn't break my systen. 
+
+  26 Jun 2015; Johannes Huber <johu@gentoo.org>
+  +akonadi-server-1.13.0-r1.ebuild,
+  +files/akonadi-server-1.13.0-mysql56-crash.patch,
+  akonadi-server-1.13.0.ebuild:
+  Revision bump adds patch by Brian Evans <grknight@gentoo.org>, fixes a crash
+  with dev-db/mysql-5.6m bug #530012.
+