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Issue with MySQL

Discussion in 'Database Discussions' started by david.cocos, Sep 24, 2014.

  1. david.cocos

    david.cocos Member

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    I run a vps with:
    CPU: Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz 15360 KB cache 8 cores
    RAM: 32 GB
    SSD drive
    CentOS 6.5
    MySQL 5.6.17
    The server runs about 100 domains.
    A problem with it is that it uses very little ram (like 10%at most).
    MySQL uses both myisam and innodb tables.
    Mysql crashes once or twice a day, and the errors have roughly a difference of almost 5 minutes between them, in the error log.
    This is one of the many errors from the error log, and the basically say the same thing, that innodb has ran out of locks.
    Code:
    2014-09-15 02:12:21 13973 [ERROR] InnoDB: Unable to lock ./"something"/ps_tax.ibd, error: 37
    2014-09-15 02:12:21 7f22c8ac6700  InnoDB: Assertion failure in thread 139787372357376 in file fil0fil.cc line 875
    InnoDB: Failing assertion: ret
    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/5.6/en/forcing-innodb-recovery.html
    InnoDB: about forcing recovery.
    00:12:21 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=134217728
    read_buffer_size=131072
    max_used_connections=19
    max_threads=1000
    thread_count=5
    connection_count=4
    It is possible that mysqld could use up to 
    key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 528775 K  bytes of memory
    Hope that's ok; if not, decrease some variables in the equation.
    
    Thread pointer: 0x32b2880
    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 = 7f22c8ac5e18 thread_stack 0x40000
    /usr/sbin/mysqld(my_print_stacktrace+0x35)[0x8c8af5]
    /usr/sbin/mysqld(handle_fatal_signal+0x4a4)[0x65ffb4]
    /lib64/libpthread.so.0(+0xf710)[0x7f25459bb710]
    /lib64/libc.so.6(gsignal+0x35)[0x7f2544666635]
    /lib64/libc.so.6(abort+0x175)[0x7f2544667e15]
    /usr/sbin/mysqld[0xaafc78]
    /usr/sbin/mysqld[0xaaff19]
    /usr/sbin/mysqld[0xab02cb]
    /usr/sbin/mysqld[0xa815ad]
    /usr/sbin/mysqld[0xa81d1b]
    /usr/sbin/mysqld[0xa6f0b3]
    /usr/sbin/mysqld[0xa5b7e0]
    /usr/sbin/mysqld[0xa038d9]
    /usr/sbin/mysqld[0x9732e5]
    /usr/sbin/mysqld[0x9743b1]
    /usr/sbin/mysqld(_ZN7handler7ha_openEP5TABLEPKcii+0x3e)[0x5a68ce]
    /usr/sbin/mysqld(_Z21open_table_from_shareP3THDP11TABLE_SHAREPKcjjjP5TABLEb+0x624)[0x763724]
    /usr/sbin/mysqld(_Z10open_tableP3THDP10TABLE_LISTP18Open_table_context+0x1c8)[0x695b08]
    /usr/sbin/mysqld(_Z11open_tablesP3THDPP10TABLE_LISTPjjP19Prelocking_strategy+0xcaa)[0x69834a]
    /usr/sbin/mysqld(_Z30open_normal_and_derived_tablesP3THDP10TABLE_LISTj+0x4f)[0x69846f]
    /usr/sbin/mysqld[0x710a5c]
    /usr/sbin/mysqld(_Z14get_all_tablesP3THDP10TABLE_LISTP4Item+0x670)[0x717510]
    /usr/sbin/mysqld(_Z24get_schema_tables_resultP4JOIN23enum_schema_table_state+0x2f1)[0x705111]
    /usr/sbin/mysqld(_ZN4JOIN14prepare_resultEPP4ListI4ItemE+0x9d)[0x6f956d]
    /usr/sbin/mysqld(_ZN4JOIN4execEv+0xdf)[0x6b9caf]
    /usr/sbin/mysqld(_Z12mysql_selectP3THDP10TABLE_LISTjR4ListI4ItemEPS4_P10SQL_I_ListI8st_orderESB_S7_yP13select_resultP18st_select_lex_unitP13st_select_lex+0x250)[0x6fa5e0]
    /usr/sbin/mysqld(_Z13handle_selectP3THDP13select_resultm+0x187)[0x6fae67]
    /usr/sbin/mysqld[0x6d782d]
    /usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x2138)[0x6dad78]
    /usr/sbin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x32f)[0x6dd9ff]
    /usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x145f)[0x6def4f]
    /usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0xcf)[0x6ac46f]
    /usr/sbin/mysqld(handle_one_connection+0x47)[0x6ac597]
    /usr/sbin/mysqld(pfs_spawn_thread+0x12a)[0x9452aa]
    /lib64/libpthread.so.0(+0x79d1)[0x7f25459b39d1]
    /lib64/libc.so.6(clone+0x6d)[0x7f254471c86d]
    
    Trying to get some variables.
    Some pointers may be invalid and cause the dump to abort.
    Query (7f224c01af60): is an invalid pointer
    Connection ID (thread ID): 13900
    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.
    140915 02:12:21 mysqld_safe Number of processes running now: 0
    140915 02:12:21 mysqld_safe mysqld restarted
    2014-09-15 02:12:22 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
    2014-09-15 02:12:22 23461 [Note] Plugin 'FEDERATED' is disabled.
    2014-09-15 02:12:22 23461 [Note] InnoDB: Using atomics to ref count buffer pool pages
    2014-09-15 02:12:22 23461 [Note] InnoDB: The InnoDB memory heap is disabled
    2014-09-15 02:12:22 23461 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
    2014-09-15 02:12:22 23461 [Note] InnoDB: Compressed tables use zlib 1.2.3
    2014-09-15 02:12:22 23461 [Note] InnoDB: Using Linux native AIO
    2014-09-15 02:12:22 23461 [Note] InnoDB: Using CPU crc32 instructions
    2014-09-15 02:12:22 23461 [Note] InnoDB: Initializing buffer pool, size = 8.0G
    2014-09-15 02:12:23 23461 [Note] InnoDB: Completed initialization of buffer pool
    2014-09-15 02:12:23 23461 [Note] InnoDB: Highest supported file format is Barracuda.
    2014-09-15 02:12:23 23461 [Note] InnoDB: Log scan progressed past the checkpoint lsn 152091627747
    2014-09-15 02:12:23 23461 [Note] InnoDB: Database was not shutdown normally!
    2014-09-15 02:12:23 23461 [Note] InnoDB: Starting crash recovery.
    2014-09-15 02:12:23 23461 [Note] InnoDB: Reading tablespace information from the .ibd files...
    2014-09-15 02:12:23 23461 [Note] InnoDB: Restoring possible half-written data pages 
    2014-09-15 02:12:23 23461 [Note] InnoDB: from the doublewrite buffer...
    InnoDB: Doing recovery: scanned up to log sequence number 152091627757
    2014-09-15 02:12:24 23461 [Note] InnoDB: 128 rollback segment(s) are active.
    2014-09-15 02:12:24 23461 [Note] InnoDB: Waiting for purge to start
    2014-09-15 02:12:24 23461 [Note] InnoDB: 5.6.17 started; log sequence number 152091627757
    2014-09-15 02:12:24 23461 [Note] Server hostname (bind-address): '*'; port: 3306
    2014-09-15 02:12:24 23461 [Note] IPv6 is available.
    2014-09-15 02:12:24 23461 [Note]   - '::' resolves to '::';
    2014-09-15 02:12:24 23461 [Note] Server socket created on IP: '::'.
    2014-09-15 02:12:24 23461 [Note] Event Scheduler: Loaded 0 events
    2014-09-15 02:12:24 23461 [Note] /usr/sbin/mysqld: ready for connections.
    Version: '5.6.17'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
    140915 02:12:32 mysqld_safe Number of processes running now: 0
    140915 02:12:32 mysqld_safe mysqld restarted
    2014-09-15 02:12:33 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
    2014-09-15 02:12:33 23766 [Note] Plugin 'FEDERATED' is disabled.
    2014-09-15 02:12:33 23766 [Note] InnoDB: Using atomics to ref count buffer pool pages
    2014-09-15 02:12:33 23766 [Note] InnoDB: The InnoDB memory heap is disabled
    2014-09-15 02:12:33 23766 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
    2014-09-15 02:12:33 23766 [Note] InnoDB: Compressed tables use zlib 1.2.3
    2014-09-15 02:12:33 23766 [Note] InnoDB: Using Linux native AIO
    2014-09-15 02:12:33 23766 [Note] InnoDB: Using CPU crc32 instructions
    2014-09-15 02:12:33 23766 [Note] InnoDB: Initializing buffer pool, size = 8.0G
    2014-09-15 02:12:33 23766 [Note] InnoDB: Completed initialization of buffer pool
    2014-09-15 02:12:33 23766 [Note] InnoDB: Highest supported file format is Barracuda.
    2014-09-15 02:12:33 23766 [Note] InnoDB: The log sequence numbers 99802598776 and 99802598776 in ibdata files do not match the log sequence number 152091752069 in the ib_logfiles!
    2014-09-15 02:12:33 23766 [Note] InnoDB: Database was not shutdown normally!
    2014-09-15 02:12:33 23766 [Note] InnoDB: Starting crash recovery.
    2014-09-15 02:12:33 23766 [Note] InnoDB: Reading tablespace information from the .ibd files...
    2014-09-15 02:12:34 23766 [Note] InnoDB: Restoring possible half-written data pages 
    2014-09-15 02:12:34 23766 [Note] InnoDB: from the doublewrite buffer...
    2014-09-15 02:12:34 23766 [Note] InnoDB: 128 rollback segment(s) are active.
    2014-09-15 02:12:34 23766 [Note] InnoDB: Waiting for purge to start
    2014-09-15 02:12:34 23766 [Note] InnoDB: 5.6.17 started; log sequence number 152091752069
    2014-09-15 02:12:34 23766 [Note] Server hostname (bind-address): '*'; port: 3306
    2014-09-15 02:12:34 23766 [Note] IPv6 is available.
    2014-09-15 02:12:34 23766 [Note]   - '::' resolves to '::';
    2014-09-15 02:12:34 23766 [Note] Server socket created on IP: '::'.
    2014-09-15 02:12:34 23766 [Note] Event Scheduler: Loaded 0 events
    2014-09-15 02:12:34 23766 [Note] /usr/sbin/mysqld: ready for connections.
    Version: '5.6.17'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
    2014-09-15 02:17:21 23766 [Note] /usr/sbin/mysqld: Normal shutdown
    
    2014-09-15 02:17:21 23766 [Note] Giving 0 client threads a chance to die gracefully
    2014-09-15 02:17:21 23766 [Note] Event Scheduler: Purging the queue. 0 events
    2014-09-15 02:17:21 23766 [Note] Shutting down slave threads
    2014-09-15 02:17:21 23766 [Note] Forcefully disconnecting 0 remaining clients
    2014-09-15 02:17:21 23766 [Note] Binlog end
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'partition'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'ARCHIVE'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_FT_DELETED'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_METRICS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_CMPMEM'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_CMP_RESET'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_CMP'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_LOCKS'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'INNODB_TRX'
    2014-09-15 02:17:21 23766 [Note] Shutting down plugin 'InnoDB'
    2014-09-15 02:17:21 23766 [Note] InnoDB: FTS optimize thread exiting.
    2014-09-15 02:17:21 23766 [Note] InnoDB: Starting shutdown...
    2014-09-15 02:17:23 23766 [Note] InnoDB: Shutdown completed; log sequence number 152091879169
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'BLACKHOLE'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'MRG_MYISAM'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'CSV'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'MEMORY'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'MyISAM'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'sha256_password'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'mysql_old_password'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'mysql_native_password'
    2014-09-15 02:17:23 23766 [Note] Shutting down plugin 'binlog'
    2014-09-15 02:17:23 23766 [Note] /usr/sbin/mysqld: Shutdown complete
    
    And this is my.cnf:
    Code:
    [mysqld]
    thread_cache_size=16K
    query_cache_size=512M
    tmp_table_size=512M
    query_cache_limit=8M
    max_heap_table_size=256M
    max_connections=1000
    key_buffer_size=128M
    join_buffer_size=12M
    innodb_buffer_pool_size=8G
    query_cache_type=1
    max_allowed_packet=536870912
    open_files_limit=50000
    
    I would be very grateful if you could post a solution to my problem.
    Thanks in advance!
     
  2. cPanelMichael

    cPanelMichael Forums Analyst
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  3. david.cocos

    david.cocos Member

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    I don't think that it is a corruption issue, because the server never failed to go back on, after crashing, and the error log doesn't show the same file that can't be locked. Also, the errors mention a file named "fil0fil.cc" which I am unable to find on the server (I used the "find" command via SSH). Can it be something regarding the maximum number of open files? It is set to 50000, is that enough?
    Regarding the RAM issue, what values should I increase in my.cnf? Would this be any good?
    Code:
    Global
    
    key_buffer_size=128M->4G 
    innodb_buffer_pool_size=8->11G 
    query_cache_limit=8M->1G 
    
    Thread
    
    sort_buffer_size=256K->1M 
    read_buffer_size=128K->512K 
    join_buffer_size=12M->512K
    read_rnd_buffer_size=256k->1M
    thread_stack=256K->1M
    
     
  4. cPanelMichael

    cPanelMichael Forums Analyst
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    You may want to run the MySQL tuner and make changes based on it's recommendations. We have a "Workarounds and Optimization" forum that you can open a thread in to get input from others on how to best configure MySQL.

    Thank you.
     
  5. david.cocos

    david.cocos Member

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    Can you give me any information about the "fil0fil.cc" file? This file is called on every error that appears in the error log "Assertion failure in thread in file fil0fil.cc line 875", and it always says that it is unable to lock a ibd file, giving the error 37.
     
  6. cPanelMichael

    cPanelMichael Forums Analyst
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    It's simply part of the InnoDB corruption error message. Please see this part of the output:

    The fact that MySQL starts does not mean there is not InnoDB corruption. You may need to consult with a qualified system administrator if the guide linked earlier is not helpful.

    Thank you.
     
  7. david.cocos

    david.cocos Member

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    Hello,
    I have decoded this with stack trace.
    Code:
    fil_node_open_file(fil_node_t*, fil_system_t*, fil_space_t*) + 1624
    fil_node_prepare_for_io(fil_node_t*, fil_system_t*, fil_space_t*) + 89
    fil_io(unsigned long, bool, unsigned long, unsigned long, unsigned long, unsigned long, unsigned long, void*, void*) + 299
    buf_read_page_low(dberr_t*, bool, unsigned long, unsigned long, unsigned long, unsigned long, long, unsigned long) + 285
    buf_read_page(unsigned long, unsigned long, unsigned long) + 75
    buf_page_get_gen(unsigned long, unsigned long, unsigned long, unsigned long, buf_block_t*, unsigned long, char const*, unsigned + 659
    btr_cur_open_at_index_side_func(bool, dict_index_t*, unsigned long, btr_cur_t*, unsigned long, char const*, unsigned long, mtr_ + 864
    row_search_max_autoinc(dict_index_t*, char const*, unsigned long*) + 281
    ha_innobase::innobase_initialize_autoinc() + 373
    ha_innobase::open(char const*, int, unsigned int) + 2801
    handler::ha_open(TABLE*, char const*, int, int) + 62
    open_table_from_share(THD*, TABLE_SHARE*, char const*, unsigned int, unsigned int, unsigned int, TABLE*, bool) + 1572
    open_table(THD*, TABLE_LIST*, Open_table_context*) + 456
    open_tables(THD*, TABLE_LIST**, unsigned int*, unsigned int, Prelocking_strategy*) + 3242
    open_normal_and_derived_tables(THD*, TABLE_LIST*, unsigned int) + 79
    fill_schema_table_by_open(THD*, bool, TABLE*, st_schema_table*, st_mysql_lex_string*, st_mysql_lex_string*, Open_tables_backup* + 524
    get_all_tables(THD*, TABLE_LIST*, Item*) + 1648
    get_schema_tables_result(JOIN*, enum_schema_table_state) + 753
    JOIN::prepare_result(List<Item>**) + 157
    JOIN::exec() + 223
    mysql_select(THD*, TABLE_LIST*, unsigned int, List<Item>&, Item*, SQL_I_List<st_order>*, SQL_I_List<st_order>*, Item*, unsigned + 592
    handle_select(THD*, select_result*, unsigned long) + 391
    execute_sqlcom_select(THD*, TABLE_LIST*) + 621
    mysql_execute_command(THD*) + 8504
    mysql_parse(THD*, char*, unsigned int, Parser_state*) + 815
    dispatch_command(enum_server_command, THD*, char*, unsigned int) + 5215
    do_handle_one_connection(THD*) + 207
    handle_one_connection + 71
    pfs_spawn_thread + 298
     _end + 110703905
    _end + 91210685
    
    Can you please tell me what it does and if there is anything wrong with it.
     
    #7 david.cocos, Oct 15, 2014
    Last edited: Oct 15, 2014
  8. cPanelMichael

    cPanelMichael Forums Analyst
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    I'm not seeing much information there to help determine the cause of the issue. Have you reviewed the InnoDB repair guide linked in the earlier post?

    Thank you.
     
  9. david.cocos

    david.cocos Member

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    Yes I've done that. I have checked all the ibd files with innochecksum and they all appeared to be ok. What happens is: every 5 minutes innodb finds a corrupted tablespace, and it crashes, and when it gets back up it repairs the broken file. And like once a day I receive a like 5 e-mails saying that mysql has failed, and after that it recovers. My problem is that I can't figure out what is causing these crashes.
    Also I tried to install mysqlmymonlite, and when I try to use ./mysqlmymonlite mysqltuner " The --forcemem option is required for remote connections". How can I run past this?
     
    #9 david.cocos, Oct 16, 2014
    Last edited: Oct 16, 2014
  10. cPanelMichael

    cPanelMichael Forums Analyst
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    You may need to consult with a database specialist or a qualified system administrator if you are unable to determine why MySQL is crashing. I don't believe a MySQL tuner would help very much, but you can post to the following thread if you are having trouble with that application:

    mysqlmymonlite.sh server stats gathering tool for cPanel Server

    Thank you.
     
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