[ome-users] OMERO 5 postgres 9.1 configuration for file deletion
Yanling Liu
vrnova at gmail.com
Wed Jun 4 13:31:56 BST 2014
Hello, I'd like to have some suggestion on configuring OMERO 5.0.2 +
postgres 9.1 on Ubuntu 12.04 for file deletion.
Basically when I tried to delete a set of 910 images in OMERO 5, I am
getting follow error in Blitz-0.log file:
2014-06-03 08:43:19,924 WARN [ o.h.h.ast.exec.
MultiTableDeleteExecutor] (2-thread-3) unable to drop temporary id table
after use [ERROR: current transaction is aborted, commands ignored until
end of transaction block]
2014-06-03 08:43:19,927 ERROR [ ome.services.delete.Deletion]
(2-thread-3) Failure during DeleteHandle.steps :
org.hibernate.exception.GenericJDBCException: could not insert/select ids
for bulk delete
at
org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140)
~[hibernate-core.jar:na]
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128)
~[hibernate-core.jar:na]
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
~[hibernate-core.jar:na]
at
org.hibernate.hql.ast.exec.MultiTableDeleteExecutor.execute(MultiTableDeleteExecutor.java:125)
~[hibernate-core.jar:na]
at
org.hibernate.hql.ast.QueryTranslatorImpl.executeUpdate(QueryTranslatorImpl.java:421)
~[hibernate-core.jar:na]
at
org.hibernate.engine.query.HQLQueryPlan.performExecuteUpdate(HQLQueryPlan.java:283)
~[hibernate-core.jar:na]
at org.hibernate.impl.SessionImpl.executeUpdate(SessionImpl.java:1280)
~[hibernate-core.jar:na]
at org.hibernate.impl.QueryImpl.executeUpdate(QueryImpl.java:117)
~[hibernate-core.jar:na]
at ome.services.delete.DeleteStep.action(DeleteStep.java:97)
~[server.jar:na]
at ome.services.graphs.GraphState.perform(GraphState.java:410)
~[server.jar:na]
at ome.services.graphs.GraphState.execute(GraphState.java:334)
~[server.jar:na]
at ome.services.delete.Deletion.execute(Deletion.java:304)
~[server.jar:na]
at omero.cmd.graphs.DeleteI.step(DeleteI.java:120) ~[blitz.jar:na]
at omero.cmd.basic.DoAllI$X.step(DoAllI.java:107) ~[blitz.jar:na]
at omero.cmd.basic.DoAllI.step(DoAllI.java:319) ~[blitz.jar:na]
at omero.cmd.HandleI.steps(HandleI.java:435) ~[blitz.jar:na]
at omero.cmd.HandleI$1.doWork(HandleI.java:365) ~[blitz.jar:na]
at omero.cmd.HandleI$1.doWork(HandleI.java:361) ~[blitz.jar:na]
at sun.reflect.GeneratedMethodAccessor272.invoke(Unknown Source)
~[na:na]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
~[na:1.6.0_30]
at java.lang.reflect.Method.invoke(Method.java:622) ~[na:1.6.0_30]
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
~[server.jar:na]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
~[server.jar:na]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
~[org.springframework.orm.jar:3.0.1.RELEASE-A]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
~[org.springframework.transaction.jar:3.0.1.RELEASE-A]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
~[server.jar:na]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
~[server.jar:na]
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
~[org.springframework.aop.jar:3.0.1.RELEASE-A]
at com.sun.proxy.$Proxy66.doWork(Unknown Source) ~[na:na]
at ome.services.util.Executor$Impl.execute(Executor.java:457)
~[server.jar:na]
at omero.cmd.HandleI.run(HandleI.java:359) ~[blitz.jar:na]
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
~[na:1.6.0_30]
at ome.services.util.Executor$Impl$1.call(Executor.java:498)
~[server.jar:na]
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
~[na:1.6.0_30]
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
~[na:1.6.0_30]
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
~[na:1.6.0_30]
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
~[na:1.6.0_30]
at java.lang.Thread.run(Thread.java:701) ~[na:1.6.0_30]
Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is
aborted, commands ignored until end of transaction block
at
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2103)
~[postgresql.jar:na]
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1836)
~[postgresql.jar:na]
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
~[postgresql.jar:na]
at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:512)
~[postgresql.jar:na]
at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:388)
~[postgresql.jar:na]
at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:334)
~[postgresql.jar:na]
at sun.reflect.GeneratedMethodAccessor256.invoke(Unknown Source)
~[na:na]
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
~[na:1.6.0_30]
at java.lang.reflect.Method.invoke(Method.java:622) ~[na:1.6.0_30]
at
bitronix.tm.resource.jdbc.BaseProxyHandlerClass.invoke(BaseProxyHandlerClass.java:64)
~[btm.jar:2.1.3]
at com.sun.proxy.$Proxy9.executeUpdate(Unknown Source) ~[na:na]
at
org.hibernate.hql.ast.exec.MultiTableDeleteExecutor.execute(MultiTableDeleteExecutor.java:116)
~[hibernate-core.jar:na]
... 43 common frames omitted
Plus there's error message in postgres log file:
2014-06-03 08:43:19 EDT WARNING: out of shared memory
2014-06-03 08:43:19 EDT ERROR: out of shared memory
2014-06-03 08:43:19 EDT HINT: You might need to increase
max_locks_per_transaction.
2014-06-03 08:43:19 EDT STATEMENT: create temporary table HT_job (id int8
not null) on commit drop
2014-06-03 08:43:19 EDT ERROR: current transaction is aborted, commands
ignored until end of transaction block
2014-06-03 08:43:19 EDT STATEMENT: insert into HT_job select job0_.id as
id from job job0_ where
(
1 = $1 OR
1 = $2 OR
(group_id in ($3)) OR
(owner_id = $4 AND (select (__g.permissions & 1024) = 1024 from
experimentergroup __g where __g.id = group_id)) OR
(group_id in ($5,$6) AND (select (__g.permissions & 64) = 64 from
experimentergroup __g where __g.id = group_id)) OR
((select (__g.permissions & 4) = 4 from experimentergroup __g where __
g.id = group_id))
) and id=$7 and owner_id=$8
2014-06-03 08:43:19 EDT ERROR: current transaction is aborted, commands
ignored until end of transaction block
2014-06-03 08:43:19 EDT STATEMENT: drop table HT_job
The reason I am deleting file in OMERO is after import failure I need to
remove whatever existing in OMERO before doing import again.
Any comments? Anyone had similar issue before?
Thanks,
Yanling
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