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Issue with GTID enabled MySQL 5.6.10

sysadsysad EntrantCurrent User Role Beginner
Hi Folks

In order to introduce MySQL 5.6 with GTID to an existing cluster, I built a slave running a patched version of mysql Ver 14.14 Distrib 5.6.10, for Linux (x86_64) , which does not check if GTID is enabled on the master running Percona 5.5 (mysql Ver 14.14 Distrib 5.5.28, for Linux (x86_64)

The patched slave was built by taking a mysql dump of all the databases from the existing cluster.

This patched slave ran for a few days without issues, apart from a few errors in the log

============================
34551 [ERROR] Native table 'performance_schema'.'cond_instances' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_current' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_history' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_history_long' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_host_by_event_name' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_instance' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_thread_by_event_name' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_user_by_event_name' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_account_by_event_name' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_global_by_event_name' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'file_instances' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'file_summary_by_event_name' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'file_summary_by_instance' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'host_cache' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'mutex_instances' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'objects_summary_global_by_type' has the wrong structure
34551 [ERROR] Native table 'performance_schema'.'performance_timers' has the wrong structure

......

============================



and after 4-5 days, more errors were introduced into the error log


=============================
7fb3a491c700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a491c700 InnoDB: Error: Fetch of persistent statistics requested for table "xyz_ddb"."StaticPages" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using
7fb3a491c700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a491c700 InnoDB: Error: Fetch of persistent statistics requested for table "xyz_ugc"."authors" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using
7fb3a491c700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a491c700 InnoDB: Error: Fetch of persistent statistics requested for table "xyzSEO"."queries" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using
7fb3a491c700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a491c700 InnoDB: Error: Fetch of persistent statistics requested for table "xyzSEO"."stores" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "xyz_moderation"."entity_states" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "xyz_ugc"."review_summary_sources" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "xyz_ugc"."review_summary_sources" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "xyz_ugc"."review_summary" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "xyz_ugc"."review_summary_sources" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
7fb3a491c700 InnoDB: Error: Fetch of persistent statistics requested for table "xyz"."W3_CONSOLE_PRIVS" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.

..............

7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "analytics"."ORDERS" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead
7fb3a5980700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
44978 [Note] Error reading relay log event: slave SQL thread was killed
44978 [ERROR] Error reading packet from server: Lost connection to MySQL server during query ( server_errno=2013)
44978 [Note] Slave I/O thread killed while reading event

44978 [Note] Slave I/O thread exiting, read up to log 'www-db01-bin.018891', position 539176249
..........
44978 [ERROR] Error in Log_event::read_log_event(): 'Event too big', data_len: 1929577984, event_type: 32
44978 [Warning] Error reading GTIDs from binary log: -1​

..........
44978 [ERROR] Error in Log_event::read_log_event(): 'Sanity check failed', data_len: 976630074, event_type: 58

44978 [Warning] Error reading GTIDs from binary log: -1
=============================



and finally mysqld crashed over this error and I have not been able to start it up again.

=============================

7fb3a5980700 InnoDB: Recalculation of persistent statistics requested for table "analytics"."ORDERS" but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
10:20:06 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=33554432
read_buffer_size=131072
max_used_connections=2
max_threads=5000
thread_count=2
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 2020346 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.
Thread pointer: 0x5d0bf1c0
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 = 7fb3a491b9d0 thread_stack 0x30000
/usr/local/mysql/bin/mysqld(my_print_stacktrace+0x2e)[0x8a7ffe]
/usr/local/mysql/bin/mysqld(handle_fatal_signal+0x481)[0x68f801]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf030)[0x7fc21ea73030]
/usr/local/mysql/bin/mysqld[0x6a6c1d]
/usr/local/mysql/bin/mysqld(_Z11mysql_grantP3THDPKcR4ListI11st_lex_userEmbb+0x4b9)[0x6b0a09]
/usr/local/mysql/bin/mysqld(_Z21mysql_execute_commandP3THD+0x3489)[0x6fab89]
/usr/local/mysql/bin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x388)[0x6fbe58]
/usr/local/mysql/bin/mysqld(_ZN15Query_log_event14do_apply_eventEPK14Relay_log_infoPKcj+0x661)[0x84d821]
/usr/local/mysql/bin/mysqld(_ZN9Log_event11apply_eventEP14Relay_log_info+0x67)[0x84c147]
/usr/local/mysql/bin/mysqld(_Z26apply_event_and_update_posPP9Log_eventP3THDP14Relay_log_info+0x1a6)[0x877446]
/usr/local/mysql/bin/mysqld(handle_slave_sql+0x9e6)[0x879d96]
/usr/local/mysql/bin/mysqld(pfs_spawn_thread+0x16f)[0x92a06f]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x6b50)[0x7fc21ea6ab50]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fc21d7d10ed]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7fb39c03b30f): is an invalid pointer
Connection ID (thread ID): 32
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.
140620 15:50:11 mysqld_safe Number of processes running now: 0
=============================
and I have another non GTID 5.6 slave in the same cluster with the version (mysql Ver 14.14 Distrib 5.6.15, for Linux (x86_64)) running without issues.

Could someone help me here in understanding what could have been the issue with the GTID slave ?

P.S : The GTID enabled slave was built by compiling from source and commenting the lines that check whether the master is GTID enabled.

Regards
sysad

Comments

  • yogesh777yogesh777 Contributor Current User Role Beginner
    either your disk/storage is 100% utilized or system tables get corrupted, rebuilding mysql schema structure might help you.
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