Crash in InnoDB crash recovery

[Philip Muškovac]

akonadi-server keeps a session mysql database for its data storage, which became inaccessible shortly after the myslq 5.6 upgrade:

2015-03-31 00:00:14 5567 [Note] Plugin 'FEDERATED' is disabled.
2015-03-31 00:00:14 5567 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-03-31 00:00:14 5567 [Note] InnoDB: The InnoDB memory heap is disabled
2015-03-31 00:00:14 5567 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-03-31 00:00:14 5567 [Note] InnoDB: Memory barrier is not used
2015-03-31 00:00:14 5567 [Note] InnoDB: Compressed tables use zlib 1.2.8
2015-03-31 00:00:14 5567 [Note] InnoDB: Using Linux native AIO
2015-03-31 00:00:14 5567 [Note] InnoDB: Using CPU crc32 instructions
2015-03-31 00:00:14 5567 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2015-03-31 00:00:14 5567 [Note] InnoDB: Completed initialization of buffer pool
2015-03-31 00:00:14 5567 [Note] InnoDB: Highest supported file format is Barracuda.
2015-03-31 00:00:14 5567 [Note] InnoDB: The log sequence numbers 25466582202 and 25466582202 in ibdata files do not match the log sequence number 25757959127 in the ib_logfiles!
2015-03-31 00:00:14 5567 [Note] InnoDB: Database was not shutdown normally!
2015-03-31 00:00:14 5567 [Note] InnoDB: Starting crash recovery.
2015-03-31 00:00:14 5567 [Note] InnoDB: Reading tablespace information from the .ibd files...
2015-03-31 00:00:14 5567 [Note] InnoDB: Restoring possible half-written data pages
2015-03-31 00:00:14 5567 [Note] InnoDB: from the doublewrite buffer...
22:00:14 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=256
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 = 101822 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+0x3b)[0x8def1b]
/usr/sbin/mysqld(handle_fatal_signal+0x36a)[0x642cea]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10d10)[0x7ff62cba6d10]
/usr/sbin/mysqld[0xae9361]
/usr/sbin/mysqld[0xaeabb8]
/usr/sbin/mysqld[0xa5baa0]
/usr/sbin/mysqld[0x999a24]
/usr/sbin/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x48)[0x57d628]
/usr/sbin/mysqld[0x6d1fc5]
/usr/sbin/mysqld(_Z11plugin_initPiPPci+0x868)[0x6d8708]
/usr/sbin/mysqld(_Z11mysqld_mainiPPc+0x925)[0x575625]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ff62c1d5a40]
/usr/sbin/mysqld(_start+0x29)[0x569af9]
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.

ProblemType: Bug
DistroRelease: Ubuntu 15.04
Package: mysql-server-core-5.6 5.6.23-1~exp1~ubuntu4
ProcVersionSignature: Ubuntu 3.19.0-10.10-generic 3.19.2
Uname: Linux 3.19.0-10-generic x86_64
NonfreeKernelModules: nvidia
ApportVersion: 2.16.2-0ubuntu5
Architecture: amd64
CurrentDesktop: KDE
Date: Tue Mar 31 00:00:40 2015
EcryptfsInUse: Yes
InstallationDate: Installed on 2011-10-08 (1269 days ago)
InstallationMedia: Kubuntu 11.10 "Oneiric Ocelot" - Beta amd64 (20111007)
SourcePackage: mysql-5.6
UpgradeStatus: No upgrade log present (probably fresh install)

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.