[ome-users] Error instantiating pixel buffer

[Sebastien Besson]

Hi Mark,

our suggestion when increasing the PixelDataTemplate is to use 1024M as of
https://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-installation.html#jvm-memory-settings
I would definitely start with this memory value and report if this is insufficient.

To remove the empty pyramids files on the server, you should be able to use the `admin fixpyramids`
command via CLI:
$ bin/omero admin fixpyramids -h

Then clicking on the CZI from a client should re-trigger the pyramid generation. Since this operation will likely
take a while, you may want to watch the Pixel-Data0.log during generation to catch any error.

Best,
Sebastien

On 14 Mar 2014, at 13:10, Mark Woodbridge <m.woodbridge at imperial.ac.uk<mailto:m.woodbridge at imperial.ac.uk>> wrote:

That makes sense. It looks like I didn't change the heap/permgen settings from the defaults when doing the upgrade. Do you have any suggestions for values that would enable the pyramid file to be generated for an image of this size? And is there a way to trigger its generation now without re-uploading the czi?

Thanks!

Mark.

On 14/03/14 12:46, Josh Moore wrote:

On Mar 14, 2014, at 1:20 PM, Mark Woodbridge wrote:

Hi,

Hi Mark,

We've uploaded a ~30GB czi file to OMERO 5, which seemed to complete successfully (file sizes match), but it can't be viewed in Insight. There is a corresponding exception in the server logs which I've attached. The 63624_pyramid file referenced is empty.

Does anyone have any suggestions regarding the cause? We'd be really grateful for any help.

My guess would be that during generation of the pyramid file for the CZI the PixelData-0 process threw an OutOfMemoryException. You should be able to check for that in var/log/PixelData-0.log. If so, how much memory is it allocated?

Thanks,
Mark.

Cheers,
~Josh.

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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096
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