/usr/bin/test -x /usr/local/cpanel/scripts/update_db_cache

[johnsap]

when this cronjob is running:
Cron <root@three> /usr/bin/test -x /usr/local/cpanel/scripts/update_db_cache && /usr/local/cpanel/scripts/update_db_cache

i see this error:

DBD::mysql::st execute failed: Lost connection to MySQL server during query at /usr/local/cpanel/Cpanel/Exception.pm line 96
Cpanel::Exception::new('Cpanel::Exception::Database::Error', 'Cpanel::ExceptionMessage::Raw=SCALAR(0x1338ea0)', 'HASH(0x243b710)') called at /usr/local/cpanel/Cpanel/Exception.pm line 47
Cpanel::Exception::create('Database::Error', 'Cpanel::ExceptionMessage::Raw=SCALAR(0x1338ea0)', 'HASH(0x243b710)') called at /usr/local/cpanel/Cpanel/Exception.pm line 55
Cpanel::Exception::create_raw('Database::Error', 'DBD::mysql::st execute failed: Lost connection to MySQL server d...', 'HASH(0x243b710)') called at /usr/local/cpanel/Cpanel/DBI.pm line 79
Cpanel::DBI::_create_exception('Cpanel::DBI::Mysql::st=HASH(0x2422810)', 'DBD::mysql::st execute failed: Lost connection to MySQL server d...', undef) called at /usr/local/cpanel/Cpanel/DBI.pm line 70
Cpanel::DBI::_error_handler('DBD::mysql::st execute failed: Lost connection to MySQL server d...', 'Cpanel::DBI::Mysql::st=HASH(0x2422810)', undef) called at bin/update_db_cache line 322
Script::Update::DB::Cache::can_get_mysql_usage('HASH(0x13128f0)', 'HASH(0x13db990)', 'Cpanel::DB::Map::Collection::Index=HASH(0x207a630)') called at bin/update_db_cache line 57
Script::Update::DB::Cache::script('Script::Update::DB::Cache') called at bin/update_db_cache line 32

there is one database that even i terminate it's cpanel account but db doesn't deleted and even i tried to drop it from ssh by below command :
DROP DATABASE dbname;
but i see this error:

ERROR 2013 (HY000): Lost connection to MySQL server during query

because update_db_cache couldn't run some databases show error after 24 hour.

Could you please help me to solve this problem?

 

[cPanelMichael]

Hello

Does /tmp/mysql.sock exist on this system? If not, please ensure you create that symbolic link via:

ln -s /var/lib/mysql/mysql.sock /tmp/mysql.sock

Also, check /var/lib/mysql/$hostname.err when restarting MySQL to see if you notice any errors.

Thank you.

 

[johnsap]

Yes i checked symlink and file exist

This is mysql error log after cronjob error:

InnoDB: Error: tried to read 16384 bytes at offset 0 49152.
InnoDB: Was only able to read 8192.
140808 17:17:27  InnoDB: Operating system error number 0 in a file operation.
InnoDB: Error number 0 means 'Success'.
InnoDB: Some operating system error numbers are described at
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/operating-system-error-codes.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.6 Operating System Error Codes[/url]
InnoDB: File operation call: 'read'.
InnoDB: Cannot continue operation.
140808 17:17:27 mysqld_safe Number of processes running now: 0
140808 17:17:27 mysqld_safe mysqld restarted
140808 17:17:27 [Warning] option 'slow_query_log': boolean value '/var/lib/mysql/slow.log' wasn't recognized. Set to OFF.
140808 17:17:27 [Note] Plugin 'FEDERATED' is disabled.
140808 17:17:27 InnoDB: The InnoDB memory heap is disabled
140808 17:17:27 InnoDB: Mutexes and rw_locks use GCC atomic builtins
140808 17:17:27 InnoDB: Compressed tables use zlib 1.2.3
140808 17:17:27 InnoDB: Using Linux native AIO
140808 17:17:27 InnoDB: Initializing buffer pool, size = 128.0M
140808 17:17:27 InnoDB: Completed initialization of buffer pool
140808 17:17:27 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 188797891627
140808 17:17:27  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 188797899922
140808 17:17:29  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78$
InnoDB: Apply batch completed
InnoDB: Last MySQL binlog file position 0 69024870, file name /var/lib/mysql/updates.000009
140808 17:17:29  InnoDB: Waiting for the background threads to start
140808 17:17:30 InnoDB: 5.5.37 started; log sequence number 188797899922
140808 17:17:30 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
140808 17:17:30 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
140808 17:17:30 [Note] Server socket created on IP: '0.0.0.0'.
140808 17:17:31 [Note] Event Scheduler: Loaded 0 events
140808 17:17:31 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.37-cll'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)

 

[cPanelMichael]

Please post the output from:

cat /etc/my.cnf

Use "CODE" tags to wrap the contents.

Thank you.

 

[johnsap]

This is My.cnf

[mysqld]
max_allowed_packet=268435456
innodb_file_per_table=1
tmpdir="/mysqltmp"
max_connections=500
local-infile=0
open_files_limit=50000
slow-query-log="/var/lib/mysql/slow.log"
query_cache_size=32M
default-storage-engine=MyISAM

- - - Updated - - -

also i don't know why max_allowed_packet is set automatically to 268435456

every time i change it to 50M but it will change automatically.

 

[cPanelMichael]

Feel free to open a support ticket using the link in my signature so we can take a closer look. You can post the ticket number here so we can update this thread with the outcome.

Thank you.