How to recover a crashed mysql server - mysql

Question

I have a Debian squeeze server that is supposed to run MySQL, but after a hard reboot it is having problems starting up. Attempting to start it using /etc/init.d/mysql start produces this snippet in syslog:
Oct 20 07:13:08 hyperion mysqld_safe: Starting mysqld daemon with databases from /var/lib/mysql
Oct 20 07:13:08 hyperion mysqld: 151020 7:13:08 [Note] Plugin 'FEDERATED' is disabled.
Oct 20 07:13:08 hyperion mysqld: 151020 7:13:08 InnoDB: Initializing buffer pool, size = 8.0M
Oct 20 07:13:08 hyperion mysqld: 151020 7:13:08 InnoDB: Completed initialization of buffer pool
Oct 20 07:13:08 hyperion mysqld: InnoDB: The log sequence number in ibdata files does not match
Oct 20 07:13:08 hyperion mysqld: InnoDB: the log sequence number in the ib_logfiles!
Oct 20 07:13:08 hyperion mysqld: 151020 7:13:08 InnoDB: Database was not shut down normally!
Oct 20 07:13:08 hyperion mysqld: InnoDB: Starting crash recovery.
Oct 20 07:13:08 hyperion mysqld: InnoDB: Reading tablespace information from the .ibd files...
Oct 20 07:13:08 hyperion mysqld: InnoDB: Restoring possible half-written data pages from the doublewrite
Oct 20 07:13:08 hyperion mysqld: InnoDB: buffer...
Oct 20 07:13:08 hyperion mysqld: 151020 7:13:08 InnoDB: Started; log sequence number 0 150617369
Oct 20 07:13:08 hyperion mysqld: 151020 7:13:08 [ERROR] Fatal error: Can't open and lock privilege tables: Incorrect file format 'user'
After googling the error I found that I had to repair a table by starting the server, then from another terminal access it and run the following:
mysql> use mysql
mysql> repair table host use_frm;
mysql> exit
However, already at the use mysql command, I get this wall of text in my mysqld terminal:
151020 7:50:03 [Note] Plugin 'FEDERATED' is disabled.
151020 7:50:03 InnoDB: Initializing buffer pool, size = 8.0M
151020 7:50:03 InnoDB: Completed initialization of buffer pool
151020 7:50:03 InnoDB: Started; log sequence number 0 150617379
151020 7:50:03 [Note] mysqld: ready for connections.
Version: '5.1.63-0+squeeze1' socket: '/var/run/mysqld/mysqld.sock' port: 3306 (Debian)
mysqld: malloc.c:3097: sYSMALLOc: Assertion `(old_top == (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long) (old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2 * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) - 1))) && ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) == 0)' failed.
05:51:07 UTC - 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=10
max_threads=151
thread_count=10
connection_count=10
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 346521 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.
Thread pointer: 0x7f98cdbcac30
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 = 7f98c59a7e88 thread_stack 0x30000
mysqld(my_print_stacktrace+0x29) [0x7f98ccc7a689]
mysqld(handle_fatal_signal+0x483) [0x7f98cca8ea53]
/lib/libpthread.so.0(+0xeff0) [0x7f98cc1e0ff0]
/lib/libc.so.6(gsignal+0x35) [0x7f98cac831b5]
/lib/libc.so.6(abort+0x180) [0x7f98cac85fc0]
/lib/libc.so.6(+0x71dda) [0x7f98cacc2dda]
/lib/libc.so.6(+0x74d2d) [0x7f98cacc5d2d]
/lib/libc.so.6(__libc_malloc+0x70) [0x7f98cacc7a30]
mysqld(my_malloc+0x32) [0x7f98ccc64372]
mysqld(alloc_root+0xd5) [0x7f98ccc64bc5]
mysqld(push_warning(THD*, MYSQL_ERROR::enum_warning_level, unsigned int, char const*)+0x194) [0x7f98cca14a84]
mysqld(my_message_sql+0x141) [0x7f98cc980c51]
mysqld(my_error+0xd8) [0x7f98ccc66118]
mysqld(open_table_def(THD*, st_table_share*, unsigned int)+0xeec) [0x7f98cc9dd95c]
mysqld(get_table_share(THD*, TABLE_LIST*, char*, unsigned int, unsigned int, int*)+0x230) [0x7f98cc9cbb00]
mysqld(+0x3c454b) [0x7f98cc9d254b]
mysqld(open_table(THD*, TABLE_LIST*, st_mem_root*, bool*, unsigned int)+0x7d5) [0x7f98cc9d3645]
mysqld(open_tables(THD*, TABLE_LIST**, unsigned int*, unsigned int)+0x6ee) [0x7f98cc9d437e]
mysqld(open_normal_and_derived_tables(THD*, TABLE_LIST*, unsigned int)+0x1e) [0x7f98cc9d451e]
mysqld(mysqld_list_fields(THD*, TABLE_LIST*, char const*)+0x20) [0x7f98ccab1f60]
mysqld(dispatch_command(enum_server_command, THD*, char*, unsigned int)+0x17f2) [0x7f98cc999a02]
mysqld(do_command(THD*)+0xea) [0x7f98cc999caa]
mysqld(handle_one_connection+0x236) [0x7f98cc98b796]
/lib/libpthread.so.0(+0x68ca) [0x7f98cc1d88ca]
/lib/libc.so.6(clone+0x6d) [0x7f98cad2092d]
Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7f98cdbd5610):
Connection ID (thread ID): 16
Status: NOT_KILLED
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.
I tried posting for help on the official forums, but it seems the moderators did not let my post through. My debugging skills are too inferior to figure out what is wrong and how to salvage data from the databases. I have been able to start up the server momentarily by skipping grant tables, but when I try to dump the databases using mysqldump --all-databases > backup.sql I hit another error:
mysqldump: Error 1194: Table 'wp_options' is marked as crashed and should be repaired when dumping table `wp_options` at row: 111
Any help is appreciated.