[Building Sakai] sakai mysql db down

Tue Dec 17 15:19:13 PST 2013

Your problems have nothing to do with Sakai's Preferences tool. If you
continue to have issues, my first instinct would be disk corruption on the
MySQL server.

--Sam

On Tue, Dec 17, 2013 at 6:10 PM, Sanghyun Jeon <euksa99 at gmail.com> wrote:

> Oh. We successfully recovered the table already. We are just wondering
> whether SAKAI_PREFERENCES table or Preference tool might have something
> causing this problem. We are currently having a lot of db related bug
> reports such as "caused by:
> com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications
> link failure" and mysql db problem is often followed by our sakai crashes.
> Last week we have had two major crashes (four app nodes shut down) after db
> shut down and one is related with SAKAI_PREFERENCES table corruption. This
> week we have system crashes twice already (not related with
> SAKAI_PREFERENCES table, though but one is clearly related with db shut
> down -- it says mysqld normal shutdown but nobody shut down mysql at that
> time) but we don't have a clear clue why.
>
> Any advice and suggestion will be greatly appreciated.
>
> Thanks.
>
> S
>
>
> On Tue, Dec 17, 2013 at 2:28 PM, John Bush <jbush at anisakai.com> wrote:
>
>> Doesn't sound like a Sakai specific issue, try googling around for how
>> to recover mysql.  For example,
>>
>> http://rivenlinux.info/how-to-recover-innodb-corruption-for-mysql/
>>
>> On Tue, Dec 17, 2013 at 2:47 PM, Sanghyun Jeon <euksa99 at gmail.com> wrote:
>> > mysql log said so and please see the lines below highlighted on red.
>> >
>> > nnoDB: Page number (if stored to page already) 23,
>> >
>> > InnoDB: space id (if created with >= MySQL-4.1.1 and stored already) 171
>> >
>> > InnoDB: Page may be an index page where index id is 0 492
>> >
>> > InnoDB: (index "SAKAI_PREFERENCES_INDEX" of table
>> > "sakai"."SAKAI_PREFERENCES")
>> >
>> > InnoDB: Database page corruption on disk or a failed
>> >
>> > InnoDB: file read of page 187.
>> >
>> > InnoDB: You may have to recover from a backup.
>> >
>> > InnoDB: It is also possible that your operating
>> >
>> > InnoDB: system has corrupted its own file cache
>> >
>> > InnoDB: and rebooting your computer removes the
>> >
>> > InnoDB: error.
>> >
>> > InnoDB: If the corrupt page is an index page
>> >
>> > InnoDB: you can also try to fix the corruption
>> >
>> > InnoDB: by dumping, dropping, and reimporting
>> >
>> > InnoDB: the corrupt table. You can use CHECK
>> >
>> > InnoDB: TABLE to scan your table for corruption.
>> >
>> > InnoDB: See also
>> > http://dev.mysql.com/doc/refman/5.1/en/forcing-innodb-recovery.html
>> >
>> > InnoDB: about forcing recovery.
>> >
>> > InnoDB: Ending processing because of a corrupt database page.
>> >
>> > 131120 13:28:37 mysqld_safe Number of processes running now: 0
>> >
>> > 131120 13:28:37 mysqld_safe mysqld restarted
>> >
>> >
>> >
>> > On Mon, Dec 16, 2013 at 3:52 PM, Steve Swinsburg <
>> steve.swinsburg at gmail.com>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> Do you have any logs for what happened? When you say 'because of
>> >> sakai_preferences table corruption' - what do you mean?
>> >>
>> >> cheers,
>> >> Steve
>> >>
>> >>
>> >> On Tue, Dec 17, 2013 at 5:05 AM, Sanghyun Jeon <euksa99 at gmail.com>
>> wrote:
>> >>>
>> >>> Hello all,
>> >>>
>> >>> We have a system crash last week because of sakai_preferences table
>> >>> corruption and we recovered the table successfully but the sakai db
>> shut
>> >>> down again this morning without reason.
>> >>>
>> >>> Version: '5.1.69-log'  socket: '/var/lib/mysql/mysql.sock'  port: 3306
>> >>> Source distribution
>> >>> 131216  8:42:56 [Note] /usr/libexec/mysqld: Normal shutdown
>> >>>
>> >>> 131216  8:42:56 [Note] Event Scheduler: Purging the queue. 0 events
>> >>> 131216  8:42:59  InnoDB: Starting shutdown...
>> >>> 131216  8:43:23  InnoDB: Shutdown completed; log sequence number 12
>> >>> 4183647936
>> >>> 131216  8:43:23 [Note] /usr/libexec/mysqld: Shutdown complete
>> >>>
>> >>> 131216 08:43:23 mysqld_safe mysqld from pid file
>> >>> /var/run/mysqld/mysqld.pid ended
>> >>> 131216 08:55:17 mysqld_safe Starting mysqld daemon with databases from
>> >>> /opt/mysql
>> >>> 131216  8:55:17  InnoDB: Initializing buffer pool, size = 5.9G
>> >>> 131216  8:55:18  InnoDB: Completed initialization of buffer pool
>> >>> 131216  8:55:18  InnoDB: Started; log sequence number 12 4183647936
>> >>> InnoDB: !!! innodb_force_recovery is set to 4 !!!
>> >>>
>> >>>
>> >>> We are using Sakai 2.8.x and Tomcat 6 and mysql 5.1.69
>> >>> I am wondering whether any other school is having the similar
>> problem? I
>> >>> am also wondering anybody can shed some light on how I can prevent
>> this and
>> >>> we are currently at final exam period.  Any suggestion or advice will
>> be
>> >>> greatly appreciated.
>> >>>
>> >>> S
>> >>>
>> >>> _______________________________________________
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>> >>
>> >
>> >
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>>
>>
>> --
>> John Bush
>> 602-490-0470
>>
>> ** This message is neither private nor confidential in fact the US
>> government is storing it in a warehouse located in Utah for future
>> data mining use cases should they arise. **
>>
>
>
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