[GE users] ARCO database crash

Arturo Giner Gracia artginer at unizar.es
Wed Sep 24 15:11:41 BST 2008


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Yes, thanks. The problem was solved changing the storage engine to innodb.
Besides changing the file my.cnf, I had to regenerate all the database, 
because each table contains the info about what engine to use 
(type=innodb).

Arturo


Jana Olivova escribió:
> Hi Arturo,
>
> Has the issue been solved?
>
> Jana
>
> On 09/18/08 18:43, alena plestilova wrote:
>> Hi Arturo,
>> can you try to check/repair the ARCo tables, they seem to be 
>> corrupted. see 
>> http://www.karakas-online.de/EN-Book/repair-corrupt-table.html
>> Did you restart MySQL database server after reconfiguring it? I guess 
>> you did, just to be sure..;-)
>> aja
>>
>>
>> Arturo Giner Gracia wrote:
>>> More info about the problem. This is the first error in the 
>>> dbwriter.log
>>>
>>> 18/09/2008 17:58:01|lxsrv2|bwriter.ReportingException.log|E|Commit 
>>> failed
>>>                              
>>> com.sun.grid.reporting.dbwriter.ReportingException: Commit failed
>>>                                
>>> com.sun.grid.reporting.dbwriter.db.Database.createSQLError(Database.java:359) 
>>>
>>>                                
>>> com.sun.grid.reporting.dbwriter.db.Database.commit(Database.java:614)
>>>                                
>>> com.sun.grid.reporting.dbwriter.db.Database.commit(Database.java:600)
>>>                                
>>> com.sun.grid.reporting.dbwriter.ReportingDBWriter.processMySQLDeletes(ReportingDBWriter.java:1108) 
>>>
>>>                                
>>> com.sun.grid.reporting.dbwriter.ReportingDBWriter.deleteData(ReportingDBWriter.java:1011) 
>>>
>>>                                
>>> com.sun.grid.reporting.dbwriter.ReportingDBWriter$DerivedValueThread.run(ReportingDBWriter.java:899) 
>>>
>>>                              Caused by java.sql.SQLException: No 
>>> operations allowed after connection closed.
>>>                                
>>> com.mysql.jdbc.Connection.checkClosed(Connection.java:1842)
>>>                                
>>> com.mysql.jdbc.Connection.commit(Connection.java:2154)
>>>                                
>>> com.sun.grid.reporting.dbwriter.db.Database$ConnectionProxy.commit(Database.java:725) 
>>>
>>>                                
>>> com.sun.grid.reporting.dbwriter.db.Database.commit(Database.java:608)
>>>                                
>>> com.sun.grid.reporting.dbwriter.db.Database.commit(Database.java:600)
>>>                                
>>> com.sun.grid.reporting.dbwriter.ReportingDBWriter.processMySQLDeletes(ReportingDBWriter.java:1108) 
>>>
>>>                                
>>> com.sun.grid.reporting.dbwriter.ReportingDBWriter.deleteData(ReportingDBWriter.java:1011) 
>>>
>>>                                
>>> com.sun.grid.reporting.dbwriter.ReportingDBWriter$DerivedValueThread.run(ReportingDBWriter.java:899) 
>>>
>>>
>>> Why the connection is closed?
>>>
>>> Regards
>>> Arturo
>>>
>>>
>>> Arturo Giner Gracia escribió:
>>>> Hello again,
>>>>
>>>> After 1 hour working with InnoDB, the error is here again. In the 
>>>> mysql log file:
>>>>
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> 080918 16:54:53 [ERROR] /usr/sbin/mysqld: Incorrect key file for 
>>>> table './ARCO/sge_host_values.MYI'; try to repair it
>>>> ...........
>>>>
>>>> Any other idea?
>>>>
>>>>
>>>>
>>>> alena plestilova escribió:
>>>>> I think so. Please refer to 
>>>>> http://gridengine.sunsource.net/howto/arco/arco_mysql.txt, step 5
>>>>> ARCo requires the use of transaction-safe tables. The default 
>>>>> MySQL table type, MyISAM, does not support transactions.
>>>>> Hope this helps,
>>>>> aja
>>>>>
>>>>>
>>>>> Arturo Giner Gracia wrote:
>>>>>> Sometimes it happens with sge_job_usage.
>>>>>>
>>>>>> MyISAM is the engine I'm using. Do you think the errors can 
>>>>>> dissapear if I change the database to InnoDB?
>>>>>> There are no errors in the log file.
>>>>>>
>>>>>> Thanks a lot.
>>>>>> Arturo
>>>>>>
>>>>>>
>>>>>> alena plestilova escribió:
>>>>>>> No other idea... Just that the DB is somehow corrupted..
>>>>>>>
>>>>>>> Does this happen with other ARCo tables?
>>>>>>>
>>>>>>> What storage engine in MySQL do you use?InnoDB? Haven't you 
>>>>>>> checked MySQL database log, there might be some useful 
>>>>>>> information in the logfile...
>>>>>>>
>>>>>>> Regards,
>>>>>>> aja
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Arturo Giner Gracia wrote:
>>>>>>>> Yes, there is enough space in the disk. Any other idea?
>>>>>>>>
>>>>>>>> Regards
>>>>>>>>
>>>>>>>> Arturo Giner Gracia escribió:
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> Almost every day I find in the dbwriter.log file errors like 
>>>>>>>>> this:
>>>>>>>>>
>>>>>>>>> 18/09/2008 
>>>>>>>>> 12:20:31|lxsrv2|cordManager.batchErrorHandling|W|Error in SQL 
>>>>>>>>> Statement: INSERT INTO sge_host_values (hv_id, hv_parent, 
>>>>>>>>> hv_time_start, hv_time_end, hv_variable, hv_svalue, hv_dvalue, 
>>>>>>>>> hv_dconfig) VALUES (94801413, 5, {ts '2008-09-18 12:20:07.0'}, 
>>>>>>>>> {ts '2008-09-18 12:20:07.0'}, 'cpu', '100.000000', 100.0, 0.0) 
>>>>>>>>> java.sql.BatchUpdateException: Incorrect key file for table 
>>>>>>>>> './ARCO/sge_host_values.MYI'; try to repair it
>>>>>>>>>
>>>>>>>>> How can I fix this? Do you think the table is too big?
>>>>>>>>>
>>>>>>>>> I'm using SGE 6.1u4 & mysql-5.0.26-16.
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> Arturo
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
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-- 
Arturo Giner Gracia
System Administrator
Instituto de Biocomputación y Física de Sistemas Complejos
de la Universidad de Zaragoza (BIFI)
e-mail: artginer at bifi.es    artginer at unizar.es
phone: (+34)976562212 ext.224 


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