After today's comment, we could think that there is any problem with these queries. Let's suppose that system's performance cause the DB time out. We should make more tests, increasing the time out value for the c3p0 pool.
The current exception
2013-03-22 00:20:00 GenerateSitemapJob [INFO] Daily sitemap generation cron job start
2013-03-22 00:20:00 LoggerMethodInterceptor [DEBUG] SiteMapGenerator.generate()
2013-03-22 00:20:00 NewPooledConnection [WARN] [c3p0] A PooledConnection that has already signalled a Connection error is still in use!
2013-03-22 00:20:00 NewPooledConnection [WARN] [c3p0] Another error has occurred [ com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed. ] which will not be reported to listeners!
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
at com.mysql.jdbc.Util.getInstance(Util.java:384)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:984)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:929)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1193)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1180)
at com.mysql.jdbc.ConnectionImpl.prepareStatement(ConnectionImpl.java:4137)
at com.mysql.jdbc.ConnectionImpl.prepareStatement(ConnectionImpl.java:4103)
at com.mchange.v2.c3p0.impl.NewProxyConnection.prepareStatement(NewProxyConnection.java:213)
at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.hibernate.engine.jdbc.internal.proxy.ConnectionProxyHandler.continueInvocation(ConnectionProxyHandler.java:138)
at org.hibernate.engine.jdbc.internal.proxy.AbstractProxyHandler.invoke(AbstractProxyHandler.java:81)
at $Proxy100.prepareStatement(Unknown Source)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:147)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:166)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:145)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1720)
at org.hibernate.loader.Loader.doQuery(Loader.java:828)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:289)
at org.hibernate.loader.Loader.doList(Loader.java:2447)
at org.hibernate.loader.Loader.doList(Loader.java:2433)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2263)
at org.hibernate.loader.Loader.list(Loader.java:2258)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:470)
at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:355)
at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1215)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
at org.hibernate.ejb.QueryImpl.getSingleResult(QueryImpl.java:284)
at com.google.inject.persist.jpa.JpaFinderProxy.invoke(JpaFinderProxy.java:72)
at com.google.inject.persist.jpa.JpaPersistModule$1.invoke(JpaPersistModule.java:129)
at $Proxy23.countExceptType(Unknown Source)
at cc.kune.core.server.searcheable.SiteMapGenerator.countNotClosedGroups(SiteMapGenerator.java:160)
at cc.kune.core.server.searcheable.SiteMapGenerator.generate(SiteMapGenerator.java:115)
at cc.kune.core.server.searcheable.SiteMapGenerator$$EnhancerByGuice$$26e8b0a.CGLIB$generate$0(<generated>)
at cc.kune.core.server.searcheable.SiteMapGenerator$$EnhancerByGuice$$26e8b0a$$FastClassByGuice$$a56540aa.invoke(<generated>)