vb543

Member
Jan 22, 2015
9
0
1
cPanel Access Level
Root Administrator
Over the past few days I've noticed my MySQL server crashes and doesn't automatically recover. I have to SSH in and restart the service. I'd appreciate any help. Here's the log. If you notice the time stamps, I restarted the service around 11:40.
Code:
150122  9:00:56  InnoDB: cannot calculate statistics for table database/wp_wfNet404s
InnoDB: because the .ibd file is missing.  For help, please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
150122  9:00:56 [ERROR] MySQL is trying to open a table handle but the .ibd file for
table database/wp_wfNet404s does not exist.
Have you deleted the .ibd file from the database directory under
the MySQL datadir, or have you used DISCARD TABLESPACE?
See [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
how you can resolve the problem.

150122  9:00:56  InnoDB: cannot calculate statistics for table database/wp_wfNet404s
InnoDB: because the .ibd file is missing.  For help, please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
150122  9:00:56 [ERROR] MySQL is trying to open a table handle but the .ibd file for
table database/wp_wfNet404s does not exist.
Have you deleted the .ibd file from the database directory under
the MySQL datadir, or have you used DISCARD TABLESPACE?
See [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
how you can resolve the problem.

150122 09:29:05 mysqld_safe Number of processes running now: 0
150122 09:29:06 mysqld_safe mysqld restarted
150122  9:29:07 [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.
150122  9:29:11 [Note] Plugin 'FEDERATED' is disabled.
150122  9:29:11 InnoDB: The InnoDB memory heap is disabled
150122  9:29:11 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150122  9:29:11 InnoDB: Compressed tables use zlib 1.2.3
150122  9:29:11 InnoDB: Using Linux native AIO
150122  9:29:15 InnoDB: Initializing buffer pool, size = 1.0G
150122  9:29:19 InnoDB: Completed initialization of buffer pool
150122  9:29:19 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 7498780996
150122  9:29:20  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 7498793437
150122  9:29:26  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
InnoDB: Apply batch completed
150122  9:29:26  InnoDB: Error: table 'database/wp_wfNet404s'
InnoDB: in InnoDB data dictionary has tablespace id 6681,
InnoDB: but a tablespace with that id does not exist. There is
InnoDB: a tablespace of name ./database/wp_wfNet404s.ibd and id 6683, though. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: Please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.3 Troubleshooting InnoDB Data Dictionary Operations[/url]
InnoDB: for how to resolve the issue.
150122  9:29:26  InnoDB: Waiting for the background threads to start
150122  9:29:27 InnoDB: 5.5.40 started; log sequence number 7498793437
150122  9:29:27 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
150122  9:29:27 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
150122  9:29:27 [Note] Server socket created on IP: '0.0.0.0'.
150122  9:29:27 [Warning] 'user' entry '[email protected]' ignored in --skip-name-resolve mode.
--snip--
150122  9:29:27 [Warning] 'db' entry 'database2\_wp [email][email protected][/email]' ignored in --skip-name-resolve mode.
150122  9:29:27 [Note] Event Scheduler: Loaded 0 events
150122  9:29:27 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.40-cll'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
150122 09:29:47 mysqld_safe Number of processes running now: 0
150122 09:29:47 mysqld_safe mysqld restarted
150122  9:29:49 [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.
150122  9:29:50 [Note] Plugin 'FEDERATED' is disabled.
150122  9:29:50 InnoDB: The InnoDB memory heap is disabled
150122  9:29:50 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150122  9:29:50 InnoDB: Compressed tables use zlib 1.2.3
150122  9:29:50 InnoDB: Using Linux native AIO
150122  9:29:51 InnoDB: Initializing buffer pool, size = 1.0G
150122  9:29:55 InnoDB: Completed initialization of buffer pool
150122  9:29:56 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 7498833010
150122  9:29:56  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 7498838727
150122  9:30:12  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
InnoDB: Apply batch completed
150122  9:30:19  InnoDB: Error: table 'database/wp_wfNet404s'
InnoDB: in InnoDB data dictionary has tablespace id 6681,
InnoDB: but a tablespace with that id does not exist. There is
InnoDB: a tablespace of name ./database/wp_wfNet404s.ibd and id 6683, though. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: Please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.3 Troubleshooting InnoDB Data Dictionary Operations[/url]
InnoDB: for how to resolve the issue.
150122  9:30:19  InnoDB: Waiting for the background threads to start
150122  9:30:20 InnoDB: 5.5.40 started; log sequence number 7498838727
150122  9:30:20 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
150122  9:30:20 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
150122  9:30:20 [Note] Server socket created on IP: '0.0.0.0'.
--same snip--
150122  9:30:20 [Note] Event Scheduler: Loaded 0 events
150122  9:30:20 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.40-cll'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
150122 09:30:47 mysqld_safe Number of processes running now: 0
150122 09:30:47 mysqld_safe mysqld restarted
150122  9:30:48 [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.
150122  9:30:49 [Note] Plugin 'FEDERATED' is disabled.
150122  9:30:49 InnoDB: The InnoDB memory heap is disabled
150122  9:30:49 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150122  9:30:49 InnoDB: Compressed tables use zlib 1.2.3
150122  9:30:49 InnoDB: Using Linux native AIO
150122  9:30:53 InnoDB: Initializing buffer pool, size = 1.0G
150122  9:30:58 InnoDB: Completed initialization of buffer pool
150122  9:30:59 InnoDB: highest supported file format is Barracuda.
InnoDB: The log sequence number in ibdata files does not match
InnoDB: the log sequence number in the ib_logfiles!
150122  9:30:59  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...
150122  9:31:07  InnoDB: Error: table 'database/wp_wfNet404s'
InnoDB: in InnoDB data dictionary has tablespace id 6681,
InnoDB: but a tablespace with that id does not exist. There is
InnoDB: a tablespace of name ./database/wp_wfNet404s.ibd and id 6683, though. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: Please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.3 Troubleshooting InnoDB Data Dictionary Operations[/url]
InnoDB: for how to resolve the issue.
150122  9:31:08  InnoDB: Waiting for the background threads to start
150122  9:31:09 InnoDB: 5.5.40 started; log sequence number 7498896732
150122  9:31:09 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
150122  9:31:09 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
150122  9:31:09 [Note] Server socket created on IP: '0.0.0.0'.
--same snip--
150122  9:31:09 [Note] Event Scheduler: Loaded 0 events
150122  9:31:09 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.40-cll'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
150122 09:31:18 mysqld_safe Number of processes running now: 0
150122 09:31:18 mysqld_safe mysqld restarted
150122  9:31:18 [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.
150122  9:31:18 [Note] Plugin 'FEDERATED' is disabled.
150122  9:31:18 InnoDB: The InnoDB memory heap is disabled
150122  9:31:18 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150122  9:31:18 InnoDB: Compressed tables use zlib 1.2.3
150122  9:31:18 InnoDB: Using Linux native AIO
150122  9:31:18 InnoDB: Initializing buffer pool, size = 1.0G
150122  9:31:21 InnoDB: Completed initialization of buffer pool
150122  9:31:21 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 7498896732
150122  9:31:21  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 7498921372
150122  9:31:27  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
InnoDB: Apply batch completed
150122  9:31:31  InnoDB: Error: table 'database/wp_wfNet404s'
InnoDB: in InnoDB data dictionary has tablespace id 6681,
InnoDB: but a tablespace with that id does not exist. There is
InnoDB: a tablespace of name ./database/wp_wfNet404s.ibd and id 6683, though. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: Please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.3 Troubleshooting InnoDB Data Dictionary Operations[/url]
InnoDB: for how to resolve the issue.
150122  9:31:31  InnoDB: Waiting for the background threads to start
150122  9:31:32 InnoDB: 5.5.40 started; log sequence number 7498921372
150122  9:31:32 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
150122  9:31:32 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
150122  9:31:32 [Note] Server socket created on IP: '0.0.0.0'.
--same snip--
150122  9:31:32 [Note] Event Scheduler: Loaded 0 events
150122  9:31:32 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.40-cll'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
150122 09:31:47 mysqld_safe Number of processes running now: 0
150122 09:31:47 mysqld_safe mysqld restarted
150122  9:31:47 [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.
150122  9:31:47 [Note] Plugin 'FEDERATED' is disabled.
150122  9:31:47 InnoDB: The InnoDB memory heap is disabled
150122  9:31:47 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150122  9:31:47 InnoDB: Compressed tables use zlib 1.2.3
150122  9:31:47 InnoDB: Using Linux native AIO
150122  9:31:48 InnoDB: Initializing buffer pool, size = 1.0G
150122  9:31:48 InnoDB: Completed initialization of buffer pool
150122  9:31:48 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 7498983550
150122  9:31:48  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
150122 09:31:49 mysqld_safe mysqld from pid file /var/lib/mysql/server5.tnahosting.net.pid ended
150122 11:40:12 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
150122 11:40:12 [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.
150122 11:40:12 [Note] Plugin 'FEDERATED' is disabled.
150122 11:40:12 InnoDB: The InnoDB memory heap is disabled
150122 11:40:12 InnoDB: Mutexes and rw_locks use GCC atomic builtins
150122 11:40:12 InnoDB: Compressed tables use zlib 1.2.3
150122 11:40:12 InnoDB: Using Linux native AIO
150122 11:40:12 InnoDB: Initializing buffer pool, size = 1.0G
150122 11:40:12 InnoDB: Completed initialization of buffer pool
150122 11:40:12 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 7498983550
150122 11:40:12  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 7498985487
150122 11:40:12  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
InnoDB: Apply batch completed
150122 11:40:13  InnoDB: Error: table 'database/wp_wfNet404s'
InnoDB: in InnoDB data dictionary has tablespace id 6681,
InnoDB: but a tablespace with that id does not exist. There is
InnoDB: a tablespace of name ./database/wp_wfNet404s.ibd and id 6683, though. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: Please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.3 Troubleshooting InnoDB Data Dictionary Operations[/url]
InnoDB: for how to resolve the issue.
150122 11:40:13  InnoDB: Waiting for the background threads to start
150122 11:40:14 InnoDB: 5.5.40 started; log sequence number 7498985487
150122 11:40:14 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
150122 11:40:14 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
150122 11:40:14 [Note] Server socket created on IP: '0.0.0.0'.
--same snip--
150122 11:40:14 [Note] Event Scheduler: Loaded 0 events
150122 11:40:14 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.40-cll'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL)
150122 11:41:39  InnoDB: error: space object of table 'database/wp_wfNet404s',
InnoDB: space id 6681 did not exist in memory. Retrying an open.
150122 11:41:39  InnoDB: Error: tablespace id and flags in file './database/wp_wfNet404s.ibd' are 6683 and 0, but in the InnoDB
InnoDB: data dictionary they are 6681 and 0.
InnoDB: Have you moved InnoDB .ibd files around without using the
InnoDB: commands DISCARD TABLESPACE and IMPORT TABLESPACE?
InnoDB: Please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting-datadict.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21.3 Troubleshooting InnoDB Data Dictionary Operations[/url]
InnoDB: for how to resolve the issue.
150122 11:41:39  InnoDB: cannot calculate statistics for table database/wp_wfNet404s
InnoDB: because the .ibd file is missing.  For help, please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
150122 11:41:39 [ERROR] MySQL is trying to open a table handle but the .ibd file for
table database/wp_wfNet404s does not exist.
Have you deleted the .ibd file from the database directory under
the MySQL datadir, or have you used DISCARD TABLESPACE?
See [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
how you can resolve the problem.

150122 11:41:39  InnoDB: cannot calculate statistics for table database/wp_wfNet404s
InnoDB: because the .ibd file is missing.  For help, please refer to
InnoDB: [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
150122 11:41:39 [ERROR] MySQL is trying to open a table handle but the .ibd file for
table database/wp_wfNet404s does not exist.
Have you deleted the .ibd file from the database directory under
the MySQL datadir, or have you used DISCARD TABLESPACE?
See [url=http://dev.mysql.com/doc/refman/5.5/en/innodb-troubleshooting.html]MySQL :: MySQL 5.5 Reference Manual :: 14.21 InnoDB Troubleshooting[/url]
how you can resolve the problem.
my.cnf
Code:
[mysqld]
skip-name-resolve
myisam_use_mmap=1
max_connections=100
max_user_connections = 50
log-slow-queries=mysql-slow.log
long_query_time = 0.1
query_cache_type = 1
query_cache_size = 128M
query_cache_limit = 2M
join_buffer_size=2M
read_rnd_buffer_size=1M
max_allowed_packet=268435456
tmp_table_size=50M
max_heap_table_size=50M
table_open_cache = 7500
thread_cache_size = 25
open_files_limit=30000
key_buffer_size = 500M
myisam_sort_buffer_size = 256M
innodb_file_per_table=1
innodb_buffer_pool_size = 1G
innodb_log_file_size = 64M
innodb_log_buffer_size = 8M
Thanks!
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,913
2,203
363
You may want to start by troubleshooting the InnoDB errors in your MySQL error log using the link referenced in my last post.

Thank you.