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503 error and InnoDB
Posted by: djeeem poli
Date: August 24, 2013 11:32AM

Hi,

- WordPress version : last one
- PHP/MySQL : as hosted on gandi
- Theme : customizr
- Plugins : w3 total cache, WP-DBManager, BackUpWordPress...
- Host : gandi

Problem :

I had WP DB Manager installed last night in order to optimize and repair my DB. Since this afternoon, I'm stuck with 503 error. I managed to restart the simple hosting solution from Gandi but I can't restart my wordpress website. It's still showing a 503 error.

Here are my logs :
Starting mysql
MySQL version: 5.5.31
Starting MySQL database server: mysqldshutdown
Stopping mysql
No process in pidfile '/srv/run/mysqld/mysqld.pid' found running; none
killed.
Stopping php5-fpm
No process in pidfile '/srv/run/php/fpm.pid' found running; none killed.
Stopping apache2
No process in pidfile '/srv/run/apache/apache.pid' found running; none
killed.

On www error log : [24-Aug-2013 12:48:32 UTC] Erreur de la base de données
WordPress MySQL server has gone away pour la requête insert into
wp_wfFileMods (filename, filenameMD5, knownFile, oldMD5, newMD5) values
('wp-content/cache/object/000000/c87/136/c87136335020161edbee9e1f5c5e3b83.php',
unhex(md5('wp-content/cache/object/000000/c87/136/c87136335020161edbee9e1f5c5e3b83.php')),
0, '', unhex('FCDD0E4D0780BBE3E25E5887BB8142CC')) ON DUPLICATE KEY UPDATE
newMD5=unhex('FCDD0E4D0780BBE3E25E5887BB8142CC'), knownFile=0 faite par
do_action('wp_ajax_nopriv_wordfence_doScan'), call_user_func_array,
wordfence::ajax_doScan_callback, wfScan::wfScanMain, wfScanEngine->go,
wfScanEngine->doScan, call_user_func, wfScanEngine->scan_knownFiles_main,
wordfenceHash->run, wordfenceHash->_dirHash, wordfenceHash->_dirHash,
wordfenceHash->_dirHash, wordfenceHash->_dirHash, wordfenceHash->_dirHash,
wordfenceHash->_dirHash, wordfenceHash->processFile, wfDB->queryWrite,
W3_Db->query, W3_DbCache->query, W3_DbCallUnderlying->query, W3_Db->query,
W3_DbProcessor->query, W3_Db->default_query

error log : [Sat Aug 24 14:48:32.075898 2013] [:error] [pid 2681:tid
2781754726144] (104)Connection reset by peer: [client 141.101.99.30:33433]
FastCGI: failed to read from backend server
[Sat Aug 24 14:48:32.076060 2013] [:error] [pid 2681:tid 2781746333440]
(104)Connection reset by peer: [client 173.245.49.109:34765] FastCGI: failed
to read from backend server
[Sat Aug 24 14:48:32.075934 2013] [:error] [pid 2681:tid 2782065256192]
(104)Connection reset by peer: [client 141.101.99.30:34434] FastCGI: failed
to read from backend server
[Sat Aug 24 14:48:32.147665 2013] [mpm_event:notice] [pid 161:tid
2782290229056] AH00491: caught SIGTERM, shutting down

access : [24/Aug/2013:14:48:16 +0200] "POST
/wp-admin/admin-ajax.php?action=wordfence_testAjax HTTP/1.1" 200 32
[24/Aug/2013:14:48:19 +0200] "GET
/wp-admin/admin-ajax.php?action=wordfence_logHuman&hid=7502108C308756DB77DA88598124B29E
HTTP/1.1" 500 531
[24/Aug/2013:14:48:17 +0200] "POST
/wp-admin/admin-ajax.php?action=wordfence_doScan&isFork=0&cronKey=539cf2153777863c11174d3a
HTTP/1.1" 500 531
[24/Aug/2013:14:48:09 +0200] "POST
/wp-cron.php?doing_wp_cron=1377348489.1484279632568359375000 HTTP/1.1" 500
531

DB error log : 130824 14:48:30 InnoDB: Error: Write to file ./ib_logfile0 failed at offset 0 8247296.
InnoDB: 53760 bytes should have been written, only 51200 were written.
InnoDB: Operating system error number 0.
InnoDB: Check that your OS and file system support files of this size.
InnoDB: Check also that the disk is not full or a disk quota exceeded.
InnoDB: Error number 0 means 'Success'.
InnoDB: Some operating system error numbers are described at
InnoDB: http://dev.mysql.com/doc/refman/5.5/en/ … codes.html
130824 14:48:30 InnoDB: Assertion failure in thread 3616823412480 in file fil0fil.c line 4576
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/5.5/en/ … overy.html
InnoDB: about forcing recovery.
12:48:30 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=4194304
read_buffer_size=262144
max_used_connections=4
max_threads=16
thread_count=2
connection_count=2
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 16566 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x0
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 = 0 thread_stack 0x40000
/usr/sbin/mysqld(my_print_stacktrace+0x29)[0x55c9038569]
/usr/sbin/mysqld(handle_fatal_signal+0x3d8)[0x55c8f20748]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf030)[0x34a23a61030]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35)[0x34a222f4475]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x180)[0x34a222f76f0]
/usr/sbin/mysqld(+0x5e8b4e)[0x55c90e9b4e]
/usr/sbin/mysqld(+0x6139f2)[0x55c91149f2]
/usr/sbin/mysqld(+0x613ffe)[0x55c9114ffe]
/usr/sbin/mysqld(+0x615469)[0x55c9116469]
/usr/sbin/mysqld(+0x637d1a)[0x55c9138d1a]
/usr/sbin/mysqld(+0x580e39)[0x55c9081e39]
/usr/sbin/mysqld(+0x57299c)[0x55c907399c]
/usr/sbin/mysqld(+0x5769f8)[0x55c90779f8]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x6b50)[0x34a23a58b50]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x34a2239ca7d]
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.
130824 14:48:33 [Note] Plugin 'FEDERATED' is disabled.
130824 14:48:33 InnoDB: The InnoDB memory heap is disabled
130824 14:48:33 InnoDB: Mutexes and rw_locks use GCC atomic builtins
130824 14:48:33 InnoDB: Compressed tables use zlib 1.2.7
130824 14:48:33 InnoDB: Using Linux native AIO
130824 14:48:33 InnoDB: Initializing buffer pool, size = 8.0M
130824 14:48:33 InnoDB: Completed initialization of buffer pool
InnoDB: Unable to lock ./ib_logfile0, error: 12
InnoDB: Error in opening ./ib_logfile0
130824 14:48:33 [ERROR] Plugin 'InnoDB' init function returned error.
130824 14:48:33 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
130824 14:48:33 [ERROR] Unknown/unsupported storage engine: InnoDB
130824 14:48:33 [ERROR] Aborting

130824 14:48:33 [Note] /usr/sbin/mysqld: Shutdown complete

130824 14:48:44 [Note] Plugin 'FEDERATED' is disabled.
130824 14:48:44 InnoDB: The InnoDB memory heap is disabled
130824 14:48:44 InnoDB: Mutexes and rw_locks use GCC atomic builtins
130824 14:48:44 InnoDB: Compressed tables use zlib 1.2.7
130824 14:48:44 InnoDB: Using Linux native AIO
130824 14:48:44 InnoDB: Initializing buffer pool, size = 8.0M
130824 14:48:44 InnoDB: Completed initialization of buffer pool
InnoDB: Unable to lock ./ib_logfile0, error: 12
InnoDB: Error in opening ./ib_logfile0
130824 14:48:44 [ERROR] Plugin 'InnoDB' init function returned error.
130824 14:48:44 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
130824 14:48:44 [ERROR] Unknown/unsupported storage engine: InnoDB
130824 14:48:44 [ERROR] Aborting

130824 14:48:44 [Note] /usr/sbin/mysqld: Shutdown complete

What can I do please ? Is it an error from my host Gandi or from my DB ?

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503 error and InnoDB
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