[GE users] ARCO database crash

Arturo Giner Gracia artginer at unizar.es
Thu Sep 18 17:09:46 BST 2008


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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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>


-- 
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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