We're Hiring!

Slow/stalled creation of thumbnails and pyramids?

Having a problem deploying OMERO? Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.

Slow/stalled creation of thumbnails and pyramids?

Postby dsudar » Wed Apr 08, 2015 12:01 am

Hi,
This is on OMERO 5.0.8. Many hours after importing a mixture of 240 TIFFS and JPGs (all 2200 by 6000 pixels in size), the thumbnail panel shows the "clock" for many of the images:
Clocks.PNG
Clocks.PNG (141.19 KiB) Viewed 3207 times


and for many of them, the "Pyramid being generated" message shows when opening them in full view. Is there a way to make that process quicker? The system is pretty lightly loaded so it's not busy doing something else.

Thanks,
- Damir
dsudar
 
Posts: 235
Joined: Mon May 14, 2012 8:43 pm
Location: Berkeley, CA, USA

Re: Slow/stalled creation of thumbnails and pyramids?

Postby sbesson » Wed Apr 08, 2015 8:04 am

Hi Damir,

the issue you describe here looks very similar to the one from this forum thread.

Are you importing single tile TIFF files? If so, performance improvements for the pyramid generation have been included in OMERO 5.1.0 and you may want to test this import workflow on a development 5.1.0 server. You might also want to increase the number of pixeldata threads in the server configuration and check if this speeds up the pyramid generation process.

Best regards,
Sebastien
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm

Re: Slow/stalled creation of thumbnails and pyramids?

Postby dsudar » Wed Apr 08, 2015 10:02 pm

Hi Sebastien,

Yes, you are right that there are many similarities with the earlier thread. Apologies that I hadn't looked at that first. I'll look carefully at the suggestions in there and in your reply here for my 5.0.8 server.

I just tried the import of (yes, indeed these are all single-tile TIFFs and single-tile JPGs) on my new server running OMERO 5.1.0 and the pyramid creation is definitely much much faster so that's great for when all my servers are upgraded to 5.1

One glitch that remains in 5.1 is the following: even though the pyramids are generated and the thumbnails are as well, the thumbnail display in the web client still shows many clocks even if I refresh the display using the OMERO refresh button. However, when I refresh the webpage using the browser refresh, all the thumbnails will show up. I guess this has something to do with the browser caching things or is there something else in play?

Thanks,
- Damir
dsudar
 
Posts: 235
Joined: Mon May 14, 2012 8:43 pm
Location: Berkeley, CA, USA

Re: Slow/stalled creation of thumbnails and pyramids?

Postby jburel » Fri Apr 10, 2015 7:59 am

Hi Damir

It could also be the thumbnail version check in place i.e. the version is checked after for example changing the rendering settings so an update is started.
We will have to investigate.

Thanks for your feedback

Jmarie
User avatar
jburel
Team Member
 
Posts: 348
Joined: Thu May 21, 2009 6:38 pm
Location: dundee

Re: Slow/stalled creation of thumbnails and pyramids?

Postby PaulVanSchayck » Mon Apr 13, 2015 7:16 am

Hi Jmarie,

I've reported this problem (Browser not refreshing thumbnails by using the webclient builtin refresh button) before in this thread (this thread mainly talks about the pixel generation problem also described in this thread, but also mentions the second problem):
viewtopic.php?f=4&t=7593

I believe at the time Will Moore actually looked into this specific issue, also created a Trac ticket for it. But I cannot retrieve it anymore.

I think the issue is that going from no thumbnail to the first thumbnail does not actually increase the version, and thus not the URL.

Thanks,

Paul
PaulVanSchayck
 
Posts: 41
Joined: Tue May 20, 2014 7:04 am

Re: Slow/stalled creation of thumbnails and pyramids?

Postby wmoore » Mon Apr 13, 2015 9:07 am

Hi All,

Paul is correct (see ticket at http://trac.openmicroscopy.org/ome/ticket/12538). When you refresh the tree in web, it does now check to see if there is a new version of the thumbnail and if so then the browser will load it. The problem now is the fact that there are no new thumbnails automatically generated (and no change in thumb version number) when pyramid generation completes.
Therefore, web does not know to request a new thumbnail (see discussion on ticket).

Currently the ticket is scheduled for 5.1.1, so hopefully this will be fixed soon.

Regards,

Will.
User avatar
wmoore
Team Member
 
Posts: 674
Joined: Mon May 18, 2009 12:46 pm

Re: Slow/stalled creation of thumbnails and pyramids?

Postby wmoore » Mon Apr 27, 2015 9:19 am

Just an update - thumbnails refresh in web during pyramid generation should now be fixed for 5.1.1. See post at viewtopic.php?f=6&t=7747&p=15690#p15690

Regards,

Will.
User avatar
wmoore
Team Member
 
Posts: 674
Joined: Mon May 18, 2009 12:46 pm


Return to Installation and Deployment

Who is online

Users browsing this forum: No registered users and 1 guest