innodb - Mysql crashed and won't start up

Our production mysql server just crashed and won't come back up. It's giving a segfault error. I tried a reboot, and just don't know what else to try. Here is the stacktrace:

140502 14:13:05 [Note] Plugin 'FEDERATED' is disabled.
InnoDB: Log scan progressed past the checkpoint lsn 108 1057948207
140502 14:13:06  InnoDB: Database was not shut down normally!

InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 108 1058059648
InnoDB: 1 transaction(s) which must be rolled back or cleaned up
InnoDB: in total 15 row operations to undo
InnoDB: Trx id counter is 0 562485504
140502 14:13:06  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 

InnoDB: Apply batch completed
InnoDB: Starting in background the rollback of uncommitted transactions
140502 14:13:06  InnoDB: Rolling back trx with id 0 562485192, 15 rows to undo
140502 14:13:06  InnoDB: Started; log sequence number 108 1058059648
140502 14:13:06  InnoDB: Assertion failure in thread 1873206128 in file ../../../storage/innobase/fsp/fsp0fsp.c line 1593
InnoDB: Failing assertion: frag_n_used > 0
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be

InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.1/en/forcing-recovery.html
InnoDB: about forcing recovery.
140502 14:13:06 - mysqld got signal 6 ;
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=16777216
read_buffer_size=131072
max_used_connections=0
max_threads=151
threads_connected=0
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 345919 K
bytes of memory
Hope that's ok; if not, decrease some variables in the equation.


thd: 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 = (nil) thread_stack 0x30000
140502 14:13:06 [Note] Event Scheduler: Loaded 0 events
140502 14:13:06 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.1.41-3ubuntu12.10'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  (Ubuntu)
/usr/sbin/mysqld(my_print_stacktrace+0x2d) [0xb7579cbd]

/usr/sbin/mysqld(handle_segfault+0x494) [0xb7245854]
[0xb6fc0400]
/lib/tls/i686/cmov/libc.so.6(abort+0x182) [0xb6cc5a82]
/usr/sbin/mysqld(+0x4867e9) [0xb74647e9]
/usr/sbin/mysqld(btr_page_free_low+0x122) [0xb74f1622]
/usr/sbin/mysqld(btr_compress+0x684) [0xb74f4ca4]
/usr/sbin/mysqld(btr_cur_compress_if_useful+0xe7) [0xb74284e7]
/usr/sbin/mysqld(btr_cur_pessimistic_delete+0x332) [0xb7429e72]
/usr/sbin/mysqld(btr_node_ptr_delete+0x82) [0xb74f4012]
/usr/sbin/mysqld(btr_discard_page+0x175) [0xb74f41e5]

/usr/sbin/mysqld(btr_cur_pessimistic_delete+0x3e8) [0xb7429f28]
/usr/sbin/mysqld(+0x526197) [0xb7504197]
/usr/sbin/mysqld(row_undo_ins+0x1b1) [0xb7504771]
/usr/sbin/mysqld(row_undo_step+0x25f) [0xb74c210f]
/usr/sbin/mysqld(que_run_threads+0x58a) [0xb74a31da]
/usr/sbin/mysqld(trx_rollback_or_clean_all_without_sess+0x3e3) [0xb74ded43]
/lib/tls/i686/cmov/libpthread.so.0(+0x596e) [0xb6f9f96e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e) [0xb6d65a4e]
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.

Any recommendations?

Answer

Ouch.

InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.1/en/forcing-recovery.html
InnoDB: about forcing recovery.

Check the suggested webpage: http://dev.mysql.com/doc/refman/5.1/en/forcing-recovery.html.

Basically, try to start the MySQL server in a recovery mode and make a backup of your crashed tables.

Edit your /etc/my.cnf and add:

 innodb_force_recovery = 1

...to see if you can get into your database and get your data / find the corrupted table.

Usually, when this happens it's a re-build (at least of a corrupted table or two).

From http://chepri.com/mysql-innodb-corruption-and-recovery/:

1. Stop mysqld (service mysql stop).


2. Backup /var/lib/mysql/ib*




3. Add the following line into /etc/my.cnf:

   
   
   

   innodb_force_recovery = 1
   

   
   
   

   (they suggest 4, but its best to start with 1 and increment if it won't start)




4. Restart mysqld (service mysql start).



5. Dump all tables: mysqldump -A > dump.sql


6. Drop all databases which need recovery.


7. Stop mysqld (service mysql stop).



8. Remove /var/lib/mysql/ib*


9. Comment out innodb_force_recovery in /etc/my.cnf


10. Restart mysqld. Look at mysql error log. By default it should be /var/lib/mysql/server/hostname.com.err to see how it creates new ib* files.


11. Restore databases from the dump: mysql < dump.sql