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256GB RAM, 64 Core , AMD running Ubuntu 12.04 with Percona MySQL 5.5.28.

Below is the assertion failure. We just had a second assertion failure (different "in file", position, etc) while running a large set of inserts.

After the first failure, MySQL restarted after a reboot only - after continuously looping on the same error after trying to recover.

I decided to do a mysqlcheck with -o for optimize. Since these are all Innodb tables (very large tables, 60+GB) this would do an alter table on all tables.

In the middle of this , the below assertion failure happened again:

121115 22:30:31  InnoDB: Assertion failure in thread 140086589445888 in file btr0pcur.c line 452
InnoDB: Failing assertion: btr_page_get_prev(next_page, mtr) == buf_block_get_page_no(btr_pcur_get_block(cursor))
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/5.5/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
03:30:31 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.
Please help us make Percona Server better by reporting any
bugs at http://bugs.percona.com/

key_buffer_size=536870912
read_buffer_size=131072
max_used_connections=404
max_threads=500
thread_count=90
connection_count=90
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 1618416 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x14edeb710
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 = 7f687366ce80 thread_stack 0x30000
/usr/sbin/mysqld(my_print_stacktrace+0x2e)[0x7b52ee]
/usr/sbin/mysqld(handle_fatal_signal+0x484)[0x68f024]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)[0x7f9cbb23fcb0]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)[0x7f9cbaea6425]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x17b)[0x7f9cbaea9b8b]
/usr/sbin/mysqld[0x858463]
/usr/sbin/mysqld[0x804513]
/usr/sbin/mysqld[0x808432]
/usr/sbin/mysqld[0x7db8bf]
/usr/sbin/mysqld(_Z13rr_sequentialP11READ_RECORD+0x1d)[0x755aed]
/usr/sbin/mysqld(_Z17mysql_alter_tableP3THDPcS1_P24st_ha_create_informationP10TABLE_LISTP10Alter_infojP8st_orderb+0x216b)[0x60399b]
/usr/sbin/mysqld(_Z20mysql_recreate_tableP3THDP10TABLE_LIST+0x166)[0x604bd6]
/usr/sbin/mysqld[0x647da1]
/usr/sbin/mysqld(_ZN24Optimize_table_statement7executeEP3THD+0xde)[0x64891e]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x1168)[0x59b558]
/usr/sbin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x30c)[0x5a132c]
/usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x1620)[0x5a2a00]
/usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0x14f)[0x63ce6f]
/usr/sbin/mysqld(handle_one_connection+0x51)[0x63cf31]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a)[0x7f9cbb237e9a]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f9cbaf63cbd]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7f6300004b60): is an invalid pointer
Connection ID (thread ID): 876
Status: NOT_KILLED

You may download the Percona Server operations manual by visiting
http://www.percona.com/software/percona-server/. You may find information
in the manual which will help you identify the cause of the crash.
121115 22:31:07 [Note] Plugin 'FEDERATED' is disabled.
121115 22:31:07 InnoDB: The InnoDB memory heap is disabled
121115 22:31:07 InnoDB: Mutexes and rw_locks use GCC atomic builtins

.. Then it recovered , without a reboot this time. from the log, what would cause this?

I am currently running a dump to see if the problem resurfaces. - mysqldump completed fine. I am now trying to restore the entire database from the dump.

edit: data partition is all in / since this is a hosted, defaulted file system unfortunately:

Filesystem      Size  Used Avail Use% Mounted on
/dev/vda3       742G  445G  260G  64% /
udev            121G  4.0K  121G   1% /dev
tmpfs            49G  248K   49G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none            121G     0  121G   0% /run/shm
/dev/vda1        99M   54M   40M  58% /boot

my.cnf:

[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock


[mysqld_safe]
socket          = /var/run/mysqld/mysqld.sock
nice            = 0

[mysqld]
skip-name-resolve
innodb_file_per_table
default_storage_engine=InnoDB

user            = mysql
socket          = /var/run/mysqld/mysqld.sock
port            = 3306
basedir         = /usr
datadir         = /data/mysql
tmpdir          = /tmp
skip-external-locking

key_buffer              = 512M
max_allowed_packet      = 128M
thread_stack            = 192K
thread_cache_size       = 64

myisam-recover         = BACKUP
max_connections        = 500
table_cache            = 812
table_definition_cache = 812

#query_cache_limit       = 4M
#query_cache_size        = 512M
join_buffer_size        = 512K


innodb_additional_mem_pool_size = 20M
innodb_buffer_pool_size = 196G
#innodb_file_io_threads = 4
#innodb_thread_concurrency = 12
innodb_flush_log_at_trx_commit = 1
innodb_log_buffer_size = 8M
innodb_log_file_size = 1024M
innodb_log_files_in_group = 2
innodb_max_dirty_pages_pct = 90
innodb_lock_wait_timeout = 120

log_error                = /var/log/mysql/error.log

long_query_time =       5
slow_query_log  =       1
slow_query_log_file     =       /var/log/mysql/slowlog.log

[mysqldump]
quick
quote-names
max_allowed_packet      = 16M

[mysql]

[isamchk]
key_buffer              = 16M

EDIT: the mysqldump completed without issues. Why would these crashes occur on an alter table?

share|improve this question
    
posting your my.cnf and data partition details may help –  thinice Nov 16 '12 at 4:03
    
done. I have posted the my.cnf and partition table. –  Tom Geee Nov 16 '12 at 5:28
    
As the error would suggest, table space corruption, since an alter is going to touch the whole table space. It smells like a possible hardware issue, have you run diagnostics on the array/each disk and the controller? –  thinice Nov 16 '12 at 13:54
    
I will have to get my host to do that. This is on a dedicated hosted system. thanks for the input. –  Tom Geee Nov 16 '12 at 17:15
    
The output from dmesg or /var/log/messages would likely be helpful as well –  kormoc Jan 22 '13 at 21:33

1 Answer 1

I had a similar crash in the same line of code, with little explanation as to why.

Opened this bug with Percona: https://bugs.launchpad.net/percona-server/+bug/1252792

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