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Issue with GTID enabled MySQL 5.6.10

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  • Issue with GTID enabled MySQL 5.6.10

    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_inst ance' has the wrong structure
    34551 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_thre ad_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_acco unt_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_ty pe' 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_user Embb+0x4b9)[0x6b0a09]
    /usr/local/mysql/bin/mysqld(_Z21mysql_execute_commandP3THD+0x3489)[0x6fab89]
    /usr/local/mysql/bin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x38 8)[0x6fbe58]
    /usr/local/mysql/bin/mysqld(_ZN15Query_log_event14do_apply_eventEPK14Re lay_log_infoPKcj+0x661)[0x84d821]
    /usr/local/mysql/bin/mysqld(_ZN9Log_event11apply_eventEP14Relay_log_inf o+0x67)[0x84c147]
    /usr/local/mysql/bin/mysqld(_Z26apply_event_and_update_posPP9Log_eventP 3THDP14Relay_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

  • #2
    either your disk/storage is 100% utilized or system tables get corrupted, rebuilding mysql schema structure might help you.

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