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Testing mkngff on idr-testing #672
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Install
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Going to test idr0051 (3 images), following IDR/omero-mkngff#2 workflow... idr0051.csv
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Image above is not viewable...
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Was the bucket mounted both on the read-write VM and the read-only VMs (which are the ones accessed by the idr-testing endpoint)? |
Update ZarrReader to include all current PRs, as described... IDR/omero-mkngff#2 (comment)
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@sbesson no, I'll try... - I also wondered if the ZarrReader updates need to be applied across all VMs? |
If you are departing from the release 0.3.1 artifact was deployed as part of IDR/deployment#380, the same JAR will definitely need to be copied under |
Mount
@sbesson What about the creation of symlinks by |
That should work out of the box as the OMERO binary repository should be shared between the read-write VM and all read-only VMs. |
I updated
But I'm still seeing I'was trying to check the Blitz.log on |
On
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David (slack) "Kryo will be related to the memoizer, I haven’t seen that particular issue though, perhaps a version mismatch with the dependency? |
One thing worth investigating is that the latest OMERO.server release, 5.6.8, was deployed on Would it be worth to revert |
@sbesson yes, if that's the easiest option to get this working, and we don't need the 5.6.8, that would be great |
Thanks @sbesson that's working now. After updating ZarrReader again on the 4 servers I can see NGFF images. NB: I noticed a couple of warnings when restarting servers on
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That's the HAproxy application which is balancing the load between read-only servers and responding to the service getting restarted. If you look at
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Going to test a plate on idr-testing...
oops - forgot to remove whitespace from the csv above, but it still seems to find the right strings eventually...
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Viewed first plate image (to start memo file generation - 11:42)... |
ON http://localhost:1080/webclient/ got this while waiting on memo file....
https://idr-testing.openmicroscopy.org/webclient/?show=image-5025551 https://idr-testing.openmicroscopy.org/webclient/imgData/3260451/ takes time and fails with
restart all servers... and web servers...
But still see Gateway Timeout at https://idr-testing.openmicroscopy.org/webclient/imgData/3260451/ |
Going to update ZarrReader to hopefully improve performance... for each of
Then restarted all 5 servers in loop as above.
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Now try set-id on the 2nd Plate of idr0025 above (only tried Plate 1 so far)...
First checked Plate 1 image above http://localhost:1080/webclient/?show=image-3260451 and this was viewable!
However - this isn't the original memo file regeneration, which I attempted to start this morning. Now tried viewing image on Plate 2... |
Image from Plate 2 of idr0025 is now "viewable" (Preview panel loads in webclient)...
Unfortunately the Images are rendering black: https://idr-testing.openmicroscopy.org/webclient/?show=image-3261251 |
Testing with today's merge
244964 ms is 4 minutes |
As discussed during the weekly IDR calls, the following commands aim to measure the initialization time for several of the IDR datasets converted to NGFF in order to benchmark/assess the current performance of ZarrReader against the original reader (
Overall, these timings should be used for an informal comparison with the initialization times described in the issue description. Note a few comments:
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Comparing the first initialisation time for pattern files above with the times to create bfmemo for equivalent NGFF filesets (from description above):
So, NGFF is ~ 2x quicker for idr0016 but ~ 4x slower for the others. |
👍 for the data but still concerning. |
Seb: "
test120
now deployed with OMERO.server and available at https://idr-testing.openmicroscopy.org/".As discussed at IDR meeting 11th September, good to test
mkngff
with ALL the NGFF filesets:View on https://idr-testing.openmicroscopy.org - Updated ZarrReader on 2023.09.25
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