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Fail to move data to "public" group

https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7377

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Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 11:13 am
by 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

Re: Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 12:22 pm
by 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.
...

Re: Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 1:15 pm
by 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

Re: Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 2:22 pm
by 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.

Re: Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 3:17 pm
by jmoore
Definitely the server log file. Sorry, I should have mentioned.

Thanks.
~Josh

Re: Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 3:52 pm
by 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.

Re: Fail to move data to "public" group

PostPosted: Mon Jan 06, 2014 4:41 pm
by 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

Re: Fail to move data to "public" group

PostPosted: Tue Jan 07, 2014 8:27 am
by 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

Re: Fail to move data to "public" group

PostPosted: Tue Jan 07, 2014 11:20 am
by 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.

Re: Fail to move data to "public" group

PostPosted: Tue Jan 07, 2014 12:44 pm
by 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.
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