Open Microscopy Environment

Public Continuation of discussions and OMERO QAs 7651 and 7659

Basically, there is a client side Ice::MemoryLimitException (See 7651) After this client error, the server continue to operate.

There is also a server side java.lang.OutOfMemoryError: Java heap space, which is likely related. I've uploaded 2 server OOM logs in a tar.bzip2 file here: https://www.openmicroscopy.org/qa2/qa/feedback/7693/

Existing relevant settings:

<property name="Ice.MessageSizeMax" value="131072"/>
<option>-Xmx2048M</option>
<option>-XX:MaxPermSize=1024M</option>

Here are the OOMs in the provided log files:

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OOM.log:2013-10-08 07:39:34,525
OOM2.log:2013-10-14 17:34:59,807
OOM2.log:2013-10-14 17:35:08,463
OOM2.log:2013-10-14 17:42:03,802
OOM2.log:2013-10-14 17:45:36,377


Ignoring the one from the 8th, I noticed that this starts during a delete operation (perhaps by another user). Helio, can you try to describe specifically the steps that led to the crash? Also, when were the times of the other failures?

Cheers,
~Josh

The deletion operation was made by me at the same time. The deletion operation concluded successfully while the import failed.
I've tried these imports at different times during the day, but mostly in the evening, and leaving it running during night (have also done it during the day and it also fail). I've tried this with Importer and Insight-importer.
This import stays quite a lot of hours analyzing the data before trying to import something.
Sorry not being more precise but hope this helps.
Helio

Looking through the related QA feedback items, I can only assume that for now, it actually is going to require more memory to get this dataset in. If you can provide a heap dump of the OOM, then we can investigate how to prevent this in the future. You can activate heap dumps via:

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bin/omero admin deploy heap-dump


or

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bin/omero admin deploy heap-dump-tmp


See https://github.com/openmicroscopy/openmicroscopy/blob/v.4.4.9/etc/grid/templates.xml#L184

This will restart the server. On the next restart or the next call to:

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bin/omero admin deploy


(with no options), then heap dumps will be disabled to save disk space.

Cheers,
~Josh

Ok, I've changed tthe settings to:

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<option>-Xmx16384M</option>
<option>-XX:MaxPermSize=1024M</option>
<property name="Ice.MessageSizeMax" value="524288"/>


I've left XX:MaxPermSize alone as obviously it's not the Classes themselves that's overloading memory.

To recap:

This should deal with the Ice::MemoryLimitException because the metadata is being sent as a single message that exceeds Ice's current limit? I guess something to look at would be breaking up large metadata into multiple messages or whatever Ice magic can give you.

The OOM still remains somewhat of a mystery, I've activated heap-dump so next time it happens we'll hopefully have more data. Although I guess now it may never happen if it's a concurrent problem and not a leak. At least not until more users start doing more stuff like this at the same time.

Thanks, Douglas. Sounds like a plan. FYI: in OMERO5, there will be a server-side import queue, so there should not be an uncontrolled number of "saveToDB" actions at any one time.

Cheers,
~Josh

Hi all,

Redid the import and it failed again. Starting importing last evening around ~19h and it failed somewhere during the night. Server wasn't down from what I can tell.
Here is the error:

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Ice.ConnectionLostException
    error = 0
   at IceInternal.Outgoing.invoke(Outgoing.java:147)
   at omero.api._ServiceFactoryDelM.getAdminService(_ServiceFactoryDelM.java:627)
   at omero.api.ServiceFactoryPrxHelper.getAdminService(ServiceFactoryPrxHelper.java:705)
   at omero.api.ServiceFactoryPrxHelper.getAdminService(ServiceFactoryPrxHelper.java:677)
   at ome.formats.OMEROMetadataStoreClient.initializeServices(OMEROMetadataStoreClient.java:413)
   at ome.formats.OMEROMetadataStoreClient.createRoot(OMEROMetadataStoreClient.java:1049)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:769)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6736)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:230)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1475)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:695)

   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6790)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:230)
   at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1475)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
   at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
   at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
   at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
   at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
   at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
   at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
   at java.lang.Thread.run(Thread.java:695)
Caused by: Ice.ConnectionLostException
    error = 0
   at IceInternal.Outgoing.invoke(Outgoing.java:147)
   at omero.api._ServiceFactoryDelM.getAdminService(_ServiceFactoryDelM.java:627)
   at omero.api.ServiceFactoryPrxHelper.getAdminService(ServiceFactoryPrxHelper.java:705)
   at omero.api.ServiceFactoryPrxHelper.getAdminService(ServiceFactoryPrxHelper.java:677)
   at ome.formats.OMEROMetadataStoreClient.initializeServices(OMEROMetadataStoreClient.java:413)
   at ome.formats.OMEROMetadataStoreClient.createRoot(OMEROMetadataStoreClient.java:1049)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:769)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6736)
   ... 12 more


Could I get your ~/omero/log/omeroinsight.log file as well as the server logs and the heap dump if available? Thanks, ~Josh

Not sure how to upload the files here!
It does not seem to work. Is there a size limit?
anyway here is a link to the log.

https://www.dropbox.com/s/mrd347eyjylyy ... nsight.log

Thanks for the log, Helio.

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...SNIP...
2013-11-06 18:58:01,300 INFO  [   ome.formats.importer.ImportCandidates] ( Thread-33) 74589 file(s) parsed into 1 group(s) with 2 call(s) to setId in 183097ms. (304743ms total) [1 unknowns]
2013-11-06 18:58:01,590 INFO  [       ome.formats.importer.ImportConfig] ( Thread-33) OMERO Version: 4.4.8-ice33-b256
2013-11-06 18:58:01,590 INFO  [       ome.formats.importer.ImportConfig] ( Thread-33) Bioformats version: 4.4.8 revision: 660f607 date: 1 May 2013
...SNIP...
Caused by: Ice.ConnectionLostException
    error = 0
   at IceInternal.Outgoing.invoke(Outgoing.java:147)
   at omero.api._ServiceFactoryDelM.getAdminService(_ServiceFactoryDelM.java:627)
   at omero.api.ServiceFactoryPrxHelper.getAdminService(ServiceFactoryPrxHelper.java:705)
   at omero.api.ServiceFactoryPrxHelper.getAdminService(ServiceFactoryPrxHelper.java:677)
   at ome.formats.OMEROMetadataStoreClient.initializeServices(OMEROMetadataStoreClient.java:413)
   at ome.formats.OMEROMetadataStoreClient.createRoot(OMEROMetadataStoreClient.java:1049)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:769)
   at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6736)
   ... 12 more
Exception in thread "Thread-33"


The above looks like an error in the long-running connection code which we fixed in 4.4.9. Could you try upgrading to the latest release (4.4.9) and see if that gets you past this issue?

Thanks for your patience!
~Josh