Percona Server 5.5.16 crashing

All,

We are using Percona Server 5.5.16 in our production servers. When we are running below query Mysql get restarted automatically

select count(distinct entry_id) from db1.t1 where pid = xxx;

The error log is as follows that we saw during Mysql restart

Thread pointer: 0x2ab116833d90
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 = 0x533c20e0 thread_stack 0x40000
/usr/sbin/mysqld(my_print_stacktrace+0x39)[0x7ce749]
/usr/sbin/mysqld(handle_segfault+0x379)[0x500de9]
/lib64/libpthread.so.0[0x3f7220ebe0]
/lib64/libc.so.6(gsignal+0x35)[0x3f71a30285]
/lib64/libc.so.6(abort+0x110)[0x3f71a31d30]
/usr/sbin/mysqld[0x8a6ec0]
/usr/sbin/mysqld[0x8542b6]
/usr/sbin/mysqld[0x855f57]
/usr/sbin/mysqld[0x82d797]
/usr/sbin/mysqld(_ZN26QUICK_GROUP_MIN_MAX_SELECT11next_prefixEv+0x12c)[0x75c28c]
/usr/sbin/mysqld(_ZN26QUICK_GROUP_MIN_MAX_SELECT8get_nextEv+0x30)[0x75ccd0]
/usr/sbin/mysqld[0x76f2c4]
/usr/sbin/mysqld(_Z10sub_selectP4JOINP13st_join_tableb+0x66)[0x5a6dd6]
/usr/sbin/mysqld[0x5a9070]
/usr/sbin/mysqld(_ZN4JOIN4execEv+0x12a8)[0x5b8128]
/usr/sbin/mysqld(_Z12mysql_selectP3THDPPP4ItemP10TABLE_LISTjR4ListIS1_ES2_jP8st_orderSB_S2_SB_yP13select_resultP18st_select_lex_unitP13st_select_lex+0x1a9)[0x5b9589]
/usr/sbin/mysqld(_Z13handle_selectP3THDP3LEXP13select_resultm+0x1ce)[0x5b9ede]
/usr/sbin/mysqld[0x57727d]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x2505)[0x579c55]
/usr/sbin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x38c)[0x57dadc]
/usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x148e)[0x57ef8e]
/usr/sbin/mysqld(_Z10do_commandP3THD+0x106)[0x57f326]
/usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0x111)[0x61a0a1]
/usr/sbin/mysqld(handle_one_connection+0x54)[0x61a194]
/lib64/libpthread.so.0[0x3f7220677d]
/lib64/libc.so.6(clone+0x6d)[0x3f71ad325d]

130528 23:14:41 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:15:07 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:15:22 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:15:45 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:16:09 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:17:19 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:17:25 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:17:50 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:18:03 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction
130528 23:18:25 [ERROR] Failed to write to mysql.slow_log: Deadlock found when trying to get lock; try restarting transaction

@mchauhan75,

Can you post the full log starting prior to the crash and after MySQL restarted.

Here is the full log

120720 22:56:38 mysqld_safe mysqld from pid file /var/lib/mysql/db01.egnyte.com.pid ended
120720 23:30:55 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
120720 23:30:55 [Warning] The syntax ‘–log-slow-queries’ is deprecated and will be removed in a future release. Please use ‘–slow-query-log’/’–slow-query-log-file’ instead.
120720 23:30:55 [Note] Flashcache bypass: disabled
120720 23:30:55 [Note] Flashcache setup error is : ioctl failed

120720 23:30:55 [Note] Plugin ‘FEDERATED’ is disabled.
120720 23:30:55 InnoDB: The InnoDB memory heap is disabled
120720 23:30:55 InnoDB: Mutexes and rw_locks use GCC atomic builtins
120720 23:30:55 InnoDB: Compressed tables use zlib 1.2.3
120720 23:30:55 InnoDB: Using Linux native AIO
120720 23:30:55 InnoDB: Initializing buffer pool, size = 22.0G
120720 23:30:56 InnoDB: Completed initialization of buffer pool
120720 23:30:56 InnoDB: highest supported file format is Barracuda.
120720 23:30:57 InnoDB: Waiting for the background threads to start
120720 23:30:58 Percona XtraDB (http://www.percona.com) 1.1.8-20.1 started; log sequence number 33382526481
^G/usr/sbin/mysqld: File ‘/mnt/Storage/logs/mysql-bin.000259’ not found (Errcode: 2)
120720 23:30:59 [ERROR] Failed to open log (file ‘/mnt/Storage/logs/mysql-bin.000259’, errno 2)
120720 23:30:59 [ERROR] Could not open log file
120720 23:30:59 [ERROR] Can’t init tc log
120720 23:30:59 [ERROR] Aborting

120720 23:30:59 InnoDB: Starting shutdown…
120720 23:31:03 InnoDB: Shutdown completed; log sequence number 33382526481
120720 23:31:03 [Note] /usr/sbin/mysqld: Shutdown complete

120720 23:31:04 mysqld_safe mysqld from pid file /var/lib/mysql/db01.egnyte.com.pid ended
120720 23:39:43 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
120720 23:39:43 [Warning] The syntax ‘–log-slow-queries’ is deprecated and will be removed in a future release. Please use ‘–slow-query-log’/’–slow-query-log-file’ instead.
120720 23:39:43 [Note] Flashcache bypass: disabled
120720 23:39:43 [Note] Flashcache setup error is : ioctl failed

120720 23:39:43 [Note] Plugin ‘FEDERATED’ is disabled.
120720 23:39:43 InnoDB: The InnoDB memory heap is disabled
120720 23:39:43 InnoDB: Mutexes and rw_locks use GCC atomic builtins
120720 23:39:43 InnoDB: Compressed tables use zlib 1.2.3
120720 23:39:43 InnoDB: Using Linux native AIO
120720 23:39:43 InnoDB: Initializing buffer pool, size = 22.0G
120720 23:39:44 InnoDB: Completed initialization of buffer pool
120720 23:39:44 InnoDB: highest supported file format is Barracuda.
120720 23:39:46 InnoDB: Waiting for the background threads to start
120720 23:39:47 Percona XtraDB (http://www.percona.com) 1.1.8-20.1 started; log sequence number 33382526481
^G/usr/sbin/mysqld: File ‘/mnt/Storage/logs/mysql-bin.000259’ not found (Errcode: 2)
120720 23:39:47 [ERROR] Failed to open log (file ‘/mnt/Storage/logs/mysql-bin.000259’, errno 2)
120720 23:39:47 [ERROR] Could not open log file
120720 23:39:47 [ERROR] Can’t init tc log
120720 23:39:47 [ERROR] Aborting

120720 23:39:47 InnoDB: Starting shutdown…
120720 23:39:52 InnoDB: Shutdown completed; log sequence number 33382526481
120720 23:39:52 [Note] /usr/sbin/mysqld: Shutdown complete

nstead.
120720 23:41:26 [Note] Flashcache bypass: disabled
120720 23:41:26 [Note] Flashcache setup error is : ioctl failed

120720 23:41:26 [Note] Plugin ‘FEDERATED’ is disabled.
120720 23:41:26 InnoDB: The InnoDB memory heap is disabled
120720 23:41:26 InnoDB: Mutexes and rw_locks use GCC atomic builtins
120720 23:41:26 InnoDB: Compressed tables use zlib 1.2.3
120720 23:41:26 InnoDB: Using Linux native AIO
120720 23:41:26 InnoDB: Initializing buffer pool, size = 22.0G
120720 23:41:27 InnoDB: Completed initialization of buffer pool
120720 23:41:27 InnoDB: highest supported file format is Barracuda.
120720 23:41:28 InnoDB: Waiting for the background threads to start
120720 23:41:29 Percona XtraDB (http://www.percona.com) 1.1.8-20.1 started; log sequence number 33382526481
120720 23:41:29 [Note] Recovering after a crash using /logs/mysql-bin
120720 23:41:29 [Note] Starting crash recovery…
120720 23:41:29 [Note] Crash recovery finished.

Hi mchauhan75,
The second log fragment you pasted is much older one - 120720 vs 130528 you had segfault error in. So I guess it’s totally unrelated to this crash.

I would check if there is no disk space problem on this server. Also check the db1.t1 table - it may be corrupted and thus triggering the crash.

Another thing is that there has been many bug fixed since 5.5.16, I’d suggest you upgrade to latest Percona Server (5.5.31 now). Of course after you check the disk space and table I mentioned, as well as if there are another issues shown in recent error log.