Omero crashes under use with GC overhead limit exceeded

[Magic]

Josh...

Thanks for this! I've turned it on and hopefully I'll have something useful for you tomorrow.

Thanks
Sam

[Magic]

Josh...

I've got the file for you. It's 3.1 GB. I'll send you the link via email in about ten minutes, once it's done transferring to my server. Keep an eye out, and thank you! We appreciate all your help.

-Sam

[jmoore]

Hi Sam,

looking at your heap dump, there are 12 instances of JPEGImageWriter each 14 MB, which are likely the last images that were rendered. But then there are many, many more, each of which is 4MB. In all there are more than 1000 of these JPEG writers.

I can't find any OMERO object which is holding on to them, so my assumption is that you're experiencing a JVM bug similar to:

• http://marc.info/?l=openjdk-2d-dev&m=137279118601885
• http://bugs.sun.com/bugdatabase/view_bu ... id=8020983

Could you try a different JVM, possibly upgrading to Java 7, and see if the issue goes away?

[Magic]

Josh...

Thanks for the response. For future reference as we debug this issue, or as others come across it, I'm switching from:

java version "1.6.0_45"
Java(TM) SE Runtime Environment (build 1.6.0_45-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.45-b01, mixed mode)

to:
java version "1.7.0_40"
Java(TM) SE Runtime Environment (build 1.7.0_40-b43)
Java HotSpot(TM) 64-Bit Server VM (build 24.0-b56, mixed mode)

I also have the OpenJDK version available if you think it might work better:
java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1ubuntu0.12.04.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

Let me know if you think I might be better off with the OpenJDK version for some reason.

In the meantime I'll let you know how this works.

[jmoore]

Personally, I'd probably try the Oracle JDK first. But opinions likely vary.

[Lipplab]

Hi everybody it seems here we have a similar problem,
since we moved our server to OS X 10.9 Mavericks two months ago we experience some problems. Last week we udated the system to 5.0.2 and still the bugs persist.

When uploading larger tiffstacks of about 5000 images the client crashes and the upload fails. With small stacks of large size there is no problem. In the earlier versions of omero 5 the server was stuck too. Last changes I made were upgrade to jdk 7.40 and the omero upgrade.

Have you been able to solve your problem? Any other suggestions?

Best regards

Benjamin

[jmoore]

Hi Benjamin, this is quite an old thread. Could you start a new one and include your log files, etc? Both the importer log (insight or CLI) as well as the server logs would be useful.

Thanks,
~Josh.