Hi Nicklas,
thank you for your response.
Nicklas Nordborg ha scritto:
> Ilenia Zara wrote:
>
> [...]
> Please check Tomcat's log file if you can find any error message there.
>
From the catalina.out file:
java.sql.SQLException: Incorrect key file for table
'/tmp/#sql_6a9c_0.MYI'; try to repair it
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:946)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2934)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1616)
at
com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1230)
at
com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:740)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1428)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at
net.sf.basedb.core.QueryExecutor$FutureResultSet.call(QueryExecutor.java:180)
at
net.sf.basedb.core.QueryExecutor$FutureResultSet.call(QueryExecutor.java:168)
at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:619)
>
>> The problem doesn't occur with any of my test raw bioassays as long as I
>> use them in groups of less than 13 raw bioassays.
>>
>
> This could be some memory-related problem... but I think BASE should be
> able to handle a lot more than 12 bioassays without problems.
>
> Just some month ago we noted that the default settings of MySQL has
> changed and in order to not run into memory problems you have to set
> useServerPrepStmts=true in the db.url setting in base.config. See
> http://base.thep.lu.se/ticket/953
>
Yes, when I worked with BASE 2.5.x , I didn't have any problem with the
export of a root bioassayset with more than 12 raw bioassays on MeV.
Now with BASE 2.6.2 using the same files and base configuration I can't
export the root bioassayset even if I set useServerPrepStmts=true in the
db.url.
I tried to set useServerPrepStmts=false and modify the
'innodb_buffer_pool_size' and 'innodb_additional_mem_pool_size'
variables on mysql and it works, but it's not the solution...
Do you have any suggestions?
Thank you,
Ilenia
> /Nicklas
>
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