Fail to move data to "public" group

[yuriy_alexandrov]

Hi All, - and Happy New Year,

Recently we moved some data to the “public” group (with the help of Omero Insight), and now I need to move some more.
However this time the operation failed.

The moving option was right click->Move to->public, or right click->Copy and then Paste to public.
The data were in the "default" group.
Insight “Activities” message window displayed “Unable to transfer data” error.

When trying Omero Web for this purpose, it didn’t work either.
Error messages were longer, and different when Omero.Web failed to move a Dataset to the (public) Project, or a Plate to the (public) Screen.
I paste these messages below.

Thanks,
Y.

Dataset to Project

STEP ERR step: 6170, stacktrace: ome.services.graphs.GraphException(message=Release at depth 0!
at ome.services.graphs.GraphState.rollback(GraphState.java:536)
at ome.services.graphs.GraphStep.rollback(GraphStep.java:336)
at ome.services.graphs.GraphState.handleException(GraphState.java:384)
at ome.services.graphs.GraphState.execute(GraphState.java:362)
at omero.cmd.graphs.ChgrpI.step(ChgrpI.java:155)
at omero.cmd.basic.DoAllI$X.step(DoAllI.java:100)
at omero.cmd.basic.DoAllI.step(DoAllI.java:301)
at omero.cmd.HandleI.steps(HandleI.java:443)
at omero.cmd.HandleI.doRun(HandleI.java:418)
at omero.cmd.HandleI$1.doWork(HandleI.java:365)
at omero.cmd.HandleI$1.doWork(HandleI.java:361)
at sun.reflect.GeneratedMethodAccessor252.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:566)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy68.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at omero.cmd.HandleI.run(HandleI.java:359)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at ome.services.util.Executor$Impl$1.call(Executor.java:488)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
, message: , id: 5754

Plate to Screen:

STEP ERR step: 7904, stacktrace: ome.services.graphs.GraphException(message=Release at depth 0!
at ome.services.graphs.GraphState.rollback(GraphState.java:536)
at ome.services.graphs.GraphStep.rollback(GraphStep.java:336)
at ome.services.graphs.GraphState.handleException(GraphState.java:384)
at ome.services.graphs.GraphState.execute(GraphState.java:362)
at omero.cmd.graphs.ChgrpI.step(ChgrpI.java:155)
at omero.cmd.basic.DoAllI$X.step(DoAllI.java:100)
at omero.cmd.basic.DoAllI.step(DoAllI.java:301)
at omero.cmd.HandleI.steps(HandleI.java:443)
at omero.cmd.HandleI.doRun(HandleI.java:418)
at omero.cmd.HandleI$1.doWork(HandleI.java:365)
at omero.cmd.HandleI$1.doWork(HandleI.java:361)
at sun.reflect.GeneratedMethodAccessor252.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:566)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy68.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:447)
at omero.cmd.HandleI.run(HandleI.java:359)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at ome.services.util.Executor$Impl$1.call(Executor.java:488)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
, message: , id: 1103

[yuriy_alexandrov]

we now tried another computer (Mac - thanks Ian!) - got the same error when tried to move Dataset to Project.
our server is 4.4.9, Ian used 4.4.9 Insight, I used 4.4.8 Insight from my PC.
...

[jmoore]

Can you attach var/log/Blitz-0.log (possibly zipped)? If that doesn't work, you can upload to http://qa.openmicroscopy.org.uk/qa/upload/

Thanks,
~Josh

[yuriy_alexandrov]

Thanks Josh,

I didn't find var/log/Blitz-0.log anywhere on my machine.
Could it be that this log-file is on the server? - then I'll ask Administrator.

Cheers,
Y.

[jmoore]

Definitely the server log file. Sorry, I should have mentioned.

Thanks.
~Josh

[yuriy_alexandrov]

Hi again,

Mark Woodbridge placed this log file here, by my request -
http://cisbic.bioinformatics.ic.ac.uk/files/omero/Blitz-0.log.zip

Is it downloadable? - if not, I'll use Your link.

Best,
Y.

[yuriy_alexandrov]

I hope the log file (that Josh requested) uploaded via that qa link is accessible here -
http://qa.openmicroscopy.org.uk/qa/feedback/7800/?token=ccebbfe33230e13013b95a1e4c96f634

[jmoore]

Thanks for the logs. (Both methods of uploading worked fine). However, I can't find any mention of a chgrp operation in it. Is it possible that there was a log rotation? Blitz-0.log becomes Blitz-0.log.1 etc. This file only covers the times between 1300 and 1500:

Code: Select all

head -n 1 Blitz-0.log; tail -n 1 Blitz-0.log
2014-01-06 13:16:12,842 INFO  [             ome.io.nio.RomioPixelBuffer] (l.Server-1) Retrieving plane: 0x14x0
2014-01-06 15:30:23,200 INFO  [ome.services.sessions.state.SessionCache] (2-thread-3) Synchronization took 78 ms.


Cheers,
~Josh

[yuriy_alexandrov]

Good morning Josh,

I asked Mark for new version of the log, it is here again
http://cisbic.bioinformatics.ic.ac.uk/files/omero/Blitz-0.log.zip

It contains chgrp string.
Today, I tried the data moving operation twice - one failed around 10:35 and another at 10:46

Best,
Y.

[jmoore]

Hi Yuriy,

there's at least one instance of the server running out of memory on a chgrp:

Code: Select all

07 10:46:03,514 INFO  [       ome.security.basic.CurrentDetails] (2-thread-5) Adding log:CHGRP-VALIDATION,class ome.model.core.Pixels,61121
2014-01-07 10:46:03,514 INFO  [       ome.security.basic.CurrentDetails] (2-thread-5) Adding log:CHGRP-VALIDATION,class ome.model.core.Pixels,61120
2014-01-07 10:46:04,041 INFO  [        omero.cmd.basic.DoAllI.@5db0a0d8] (2-thread-5) Cancelled
2014-01-07 10:46:04,041 INFO  [                 org.perf4j.TimingLogger] (2-thread-5) start[1389091554660] time[9381] tag[omero.request.step.6653]
2014-01-07 10:46:04,041 INFO  [                 org.perf4j.TimingLogger] (2-thread-5) start[1389091196160] time[367881] tag[omero.request]
2014-01-07 10:46:06,553 ERROR [.support.TransactionSynchronizationUtils] (2-thread-5) TransactionSynchronization.afterCompletion threw exception
java.lang.OutOfMemoryError: GC overhead limit exceeded


How much memory is this configured to use?

Cheers,
~Josh

P.S. the upcoming 4.4.10 release should improve the memory usage of chgrp.