Many Pyramid Files with 0 kB

[jmoore]

2013-08-23 12:26:02,836 ERROR [ ome.io.nio.PixelsService] (.Server-15) Error instantiating pixel buffer: /home/ict/apps/OMERO/OMERO.data/Pixels/Dir-024/24371_pyramid
java.lang.RuntimeException: java.io.IOException: Permission denied
at ome.io.bioformats.BfPyramidPixelBuffer.isLockedByOthers(BfPyramidPixelBuffer.java:377)
[/code]

Are there also hidden files lying about? (.123*lock) ?

What I changed as well was
"omero.pixeldata.threads=4
omero.pixeldata.max_plane_height=5000
omero.pixeldata.max_plane_width=5000"

Currently I only increased memory for the BlitzTemplate, should I also increase memory on other server-templates (PixelDataTemplate for instance?)?

If your goal is to not require creating the pyramids, then just modifying BlitzTemplate should suffice. If, however, PixelData will be handling files, then its Xmx setting will also need to be increased.

[rdccmemg]

no lock files but I do find these files

.24274_pyramid4595592949458934508.tmp

they seem to correspond to the pyramids that were failing.

Best,
Raf

[rdccmemg]

I've played around a bit with threads. I experience the following. When I set omero.pixeldata.threads to 1. You can see clearly in pixeldata log that he starts to process. It goes nicely until I click an image in the webinterface (center pane). An extra "bad file descriptor" is thrown and we have our 0kb file created. Pyramid creation continues but will fail with the message ..._pyramid already exists in the end.
In fact if I try to delete these 0kb files I cannot (Text file busy).

When I add more threads the creation of 0kb files accelarates.

I don't see any problems memory wise.
Best,
Raf

[jmoore]

What kind of filesystem is /Files on?

[rdccmemg]

It is a CIFS share (on netapp filer) mounted on an ubuntu system.

Best,
Raf

[jmoore]

This is likely then all a result of locking issues. See "Locking and remote shares" for more information. Sorry for not having thought of this sooner.

Cheers,
~Josh