Open Microscopy Environment

Hi All,

My omero install has been up and running for a bit, but I am just now starting to load it with image data. I have not noticed any obvious issues, but I am seeing quite a few errors in my Blitz log. Hopefully someone can let me know if I am missing a big problem somewhere. Here is my diagnostics:

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================================================================================
OMERO Diagnostics 5.0.5-ice35-b47
================================================================================

Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.6.6     (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.3.5     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 26131, enabled)
Server:     DropBox                        active (pid = 26149, enabled)
Server:     FileServer                     active (pid = 26168, enabled)
Server:     Indexer-0                      active (pid = 26150, enabled)
Server:     MonitorServer                  active (pid = 26184, enabled)
Server:     OMERO.Glacier2                 active (pid = 26151, enabled)
Server:     OMERO.IceStorm                 active (pid = 26185, enabled)
Server:     PixelData-0                    active (pid = 26154, enabled)
Server:     Processor-0                    active (pid = 26173, enabled)
Server:     Tables-0                       active (pid = 26158, enabled)
Server:     TestDropBox                    inactive (enabled)

OMERO:      SSL port                       4064
OMERO:      TCP port                       4063

Log dir:    /home/omero/OMERO.server-5.0.5-ice35-b47/var/log exists

Log files:  Blitz-0.log                    140.0 MB      errors=601  warnings=3780
Log files:  DropBox.log                    30.0 KB       errors=0    warnings=11
Log files:  FileServer.log                 3.0 KB
Log files:  Indexer-0.log                  946.0 KB      errors=25   warnings=0
Log files:  MonitorServer.log              16.0 KB
Log files:  OMEROweb.log                   762.0 KB      errors=1    warnings=4
Log files:  OMEROweb_request.log           0.0 KB        errors=0    warnings=4
Log files:  PixelData-0.log                482.0 KB      errors=22   warnings=0
Log files:  Processor-0.log                22.0 KB       errors=0    warnings=8
Log files:  Tables-0.log                   21.0 KB       errors=0    warnings=7
Log files:  TestDropBox.log                n/a
Log files:  master.err                     5.0 KB        errors=0    warnings=4
Log files:  master.out                     0.0 KB
Log files:  Total size                     142.45 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/OMERO'   Exists? True   Is writable? True
OMERO temp dir: '/home/omero/omero/tmp'   Exists? True   Is writable? True   (Size: 0)
OMERO.web status... [RUNNING] (PID 26446)

And here are some of the errors I see repeated in Blitz:

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2014-10-28 16:56:55,545 ERROR [                      omero.cmd.SessionI] (2-thread-1) Error destroying servant: a9380702-33a3-4751-af48-8bb1155c4a85omero.api.RawFileStore=ome.services.blitz.impl.RawFileStoreI$OpsDelegate@4a030524
2014-10-28 16:56:55,547 ERROR [o.s.blitz.impl.RawFileStoreI$OpsDelegate] (2-thread-1) Error on close, stage1

I have checked the errors in my other logs and they seem to be from an unrelated, older date when my NFS was unmounted for a bit. Any insight into the Blitz errors would be greatly appreciated.

Thanks!
Blair

Hi Blair,

how are you loading the data? The most likely cause of the error you're seeing is an unclosed service which is failing to be cleaned up. If you'd like to email or upload your full var/log/Blitz-0.log, though, we can take a look.

Cheers,
~Josh.

Hi Josh,

Thank you very much for your suggestion. Did you happen to get the email of the log file? I have noticed that I still get the same errors.

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2014-12-05 18:32:33,502 ERROR [o.s.blitz.impl.RawFileStoreI$OpsDelegate] (rver-40677) Error on close, stage1
2014-12-05 18:32:33,503 ERROR [                      omero.cmd.SessionI] (rver-40677) Error destroying servant: 0f35090e-b0ae-4724-adfb-8f8b1768872eomero.api.RawFileStore=ome.services.blitz.impl.RawFileStoreI$OpsDelegate@2ae37bdd
2014-12-05 18:32:33,504 ERROR [o.s.blitz.impl.RawFileStoreI$OpsDelegate] (rver-40677) Error on close, stage1
2014-12-05 18:32:33,505 ERROR [                      omero.cmd.SessionI] (rver-40677) Error destroying servant: 01c41a92-bcce-438f-988c-14865b0dd4a0omero.api.RawFileStore=ome.services.blitz.impl.RawFileStoreI$OpsDelegate@801a202

We are uploading the data via the OMERO.insight client. Any suggestions for resolving these errors would be greatly appreciated.

Thanks!
Blair

Hi Blair,

Did you happen to get the email of the log file?

No! Sorry. And searching through mail I couldn't find any from you which match. Perhaps it died in my spam folder?! Could you possibly resend?

Thanks, and again, sorry for the trouble.
~Josh.

Hi Josh,

Thanks for checking! I just resent the log file (subject: Blitz Log Errors). Thanks again for your help!

Cheers,
Blair

Hi Blair,

thanks for the log file. Do you know off-hand what client version is being used?

Looking threw the logs, it seems there were 2 heavy periods of failures:

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~/Downloads$ grep ERROR Blitz-0.log  | grep stage1 | cut -f1-2 -d: | uniq -c
126 2014-10-28 10:2x
   1 2014-10-28 13:4x
  24 2014-10-28 16:5x


Does this correspond to ALL the imports that were performed? Or only particular ones?

Cheers,
~Josh.

Hi Josh,

Thanks for looking at the log file. I have been using a variety of computer for uploading, so I decided to test a few methods of uploading to see which produced errors.

Using OMERO.insight client version 5.0.5-ice35-b47 on OSX and Windows, I get a warning when I uploaded a single image:

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2014-12-10 13:07:03,069 WARN  [    ome.formats.model.ReferenceProcessor] (2-thread-3) Unknown target class for LSID: Image:0

Using OMERO.insight via webstart, I get 200 errors like the following:

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2014-12-10 13:21:59,087 ERROR [o.s.blitz.impl.RawFileStoreI$OpsDelegate] (2-thread-1) Error on close, stage1
2014-12-10 13:21:59,089 ERROR [                      omero.cmd.SessionI] (2-thread-1) Error destroying servant: 6c249bec-33c5-4b50-b96f-db31c9144cd6omero.api.RawFileStore=ome.services.blitz.impl.RawFileStoreI$OpsDelegate@2fecb9d4

So, it looks like using OMERO.insight from webstart is causing the issues with the errors.

-Blair

Blair,

thanks for letting us know. There's certainly a possibility that something's going awry in the WebStart stack, but our attempts to reproduce the errors haven't yet shown anything similar. Could you let us know more about that environment?

• Operating system
• Browser version
• Java version
• any other differences between the two client usages

Thanks for helping us to track this down!
~Josh.

Hi Josh,

Ok, I think I got to the bottom of the errors! It does not appear to be an issue with WebStart or OMERO.insight client (at least not directly). The errors occur every time I upload a spectral Zeiss CZI file. I tried uploading on a variety of platforms (OSX/Windows 7) with both WebStart and the OMERO.insight client. I do not get errors when uploading JPGs or TIFFs, but I get two errors for every CZI image uploaded.

As I mentioned, these are spectral images. I tried uploading a non-spectral CZI file and I did not receive an error. If you would like to recreate this, I would be happy to send you a file.

Thanks!
Blair

Hi Blair,

that would be great, if you could upload the file. I've been trying to reproduce these errors, but without success yet. You can upload the file here: http://qa.openmicroscopy.org.uk/qa/upload/

Cheers,
Dominik