Deploy ms image region by khaledk2 · Pull Request #430 · IDR/deployment

khaledk2 · 2024-08-14T18:24:42Z

This PR adds an Ansible playbook to deploy the MS image region. It uses the ansible-role-omero-ms-image-region, and it has been added to the requirements. It should be altered once the PRs are merged and the role is published.

sbesson

A few suggestions to integration the role into the existing deployment logic.

sbesson · 2024-08-14T20:10:56Z

+          }}
+    - name: get database password
+      set_fact: >-
+        database_user_password: "{{ idr_secret_postgresql_password_ro | default('omero') }}"


Is there a reason to use set_fact rather than using "{{ idr_secret_postgresql_password_ro | default('omero') }}" directly in the variable?

sbesson · 2024-08-14T20:12:48Z

+# this should be updated after merging the PRs and publich the role
+- name: ome.omero_ms_image_region
+  src: https://github.com/khaledk2/ansible-role-omero-ms-image-region/
+  version: new_ms_release


For the prod122 update we can certainly use the in-progress version but for future deployments this role will need to be released in order to merge this step

sbesson · 2024-08-15T09:28:28Z

Another thought here while working through the prod122 upgrade with @dominikl. Are we limiting the deployment of the micro-service to production environments or should it also be deployed on pilot environments? In the latter case, the role will also need to be configured to work against the omeroreadwrite hosts

khaledk2 · 2024-08-26T11:09:51Z

The download URL for a task inside the ome.analysis_tools role was broken (system packages | analysis utils]). I have fixed it and created a PR to fix that, i.e. ome/ansible-role-analysis-tools#7
I have edited the requirements file to use the branch for the ome.analysis_tools PR.

sbesson

This was successfully deployed on test123 and ready for a quick round of functional testing @pwalczysko @jburel @khaledk2 @dominikl @will-moore

The primary issue I ran into is that the initial data access via the micro-service failed with a FileNotFoundException / Permission denied when accessing the data

2024-08-27 16:16:48,376 [render-image-region-pool-8] ERROR ome.io.nio.PixelsService - Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-08/11/11-22-30.109/IMG_0006-0060 Diplophyllum albicans stature ventral side (2.5x).ome.tiff
java.lang.RuntimeException: java.io.FileNotFoundException: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-08/11/11-22-30.109/IMG_0006-0060 Diplophyllum albicans stature ventral side (2.5x).ome.tiff (Permission denied)
        at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:79)
        at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:124)
        at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:898)
        at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:606)
        at com.glencoesoftware.omero.zarr.ZarrPixelsService.getPixelBuffer(ZarrPixelsService.java:373)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.getPixelBuffer(ImageRegionRequestHandler.java:419)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.render(ImageRegionRequestHandler.java:516)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.getRegion(ImageRegionRequestHandler.java:349)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.renderImageRegion(ImageRegionRequestHandler.java:326)
        at com.glencoesoftware.omero.ms.core.OmeroRequest.execute(OmeroRequest.java:109)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionVerticle.renderImageRegion(ImageRegionVerticle.java:187)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionVerticle.lambda$start$0(ImageRegionVerticle.java:133)
        at io.vertx.core.eventbus.impl.HandlerRegistration.deliver(HandlerRegistration.java:271)
        at io.vertx.core.eventbus.impl.HandlerRegistration.handle(HandlerRegistration.java:249)
        at io.vertx.core.eventbus.impl.EventBusImpl$InboundDeliveryContext.next(EventBusImpl.java:573)
        at io.vertx.core.eventbus.impl.EventBusImpl.lambda$deliverToHandler$5(EventBusImpl.java:532)
        at io.vertx.core.impl.ContextImpl.executeTask(ContextImpl.java:369)
        at io.vertx.core.impl.WorkerContext.lambda$wrapTask$0(WorkerContext.java:35)
        at io.vertx.core.impl.TaskQueue.run(TaskQueue.java:76)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
        at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.io.FileNotFoundException: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-08/11/11-22-30.109/IMG_0006-0060 Diplophyllum albicans stature ventral side (2.5x).ome.tiff (Permission denied)
        at java.base/java.io.RandomAccessFile.open0(Native Method)
        at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345)
        at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:259)
        at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:214)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:130)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:151)
        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:165)
        at loci.common.Location.getHandle(Location.java:522)
        at loci.common.Location.getHandle(Location.java:462)
        at loci.common.Location.getHandle(Location.java:443)
        at loci.common.Location.getHandle(Location.java:426)
        at loci.common.Location.checkValidId(Location.java:551)
        at loci.formats.ImageReader.getReader(ImageReader.java:183)
        at loci.formats.ImageReader.setId(ImageReader.java:859)
        at ome.io.nio.PixelsService$3.setId(PixelsService.java:869)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:258)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
        at loci.formats.Memoizer.setId(Memoizer.java:726)
        at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:52)
        at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:73)
        ... 22 common frames omitted
2024-08-27 16:16:48,377 [render-image-region-pool-8] INFO  c.g.omero.ms.core.LogSpanReporter - {"traceId":"76755e09a50af5a8","parentId":"23a63d7e555009f4","id":"74c40ee9d1857b13","name":"get_pixel_buffer","timestamp":1724775408355957,"duration":21133,"localEndpoint":{"serviceName":"omero-ms-image-region","ipv4":"10.35.199.90"},"tags":{"error":"Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-08/11/11-22-30.109/IMG_0006-0060 Diplophyllum albicans stature ventral side (2.5x).ome.tiff","omero.pixels_id":"14234493"}}
2024-08-27 16:16:48,377 [render-image-region-pool-8] INFO  c.g.omero.ms.core.LogSpanReporter - {"traceId":"76755e09a50af5a8","parentId":"80b226d96a9da92a","id":"23a63d7e555009f4","name":"render_as_packed_int","timestamp":1724775408355922,"duration":21635,"localEndpoint":{"serviceName":"omero-ms-image-region","ipv4":"10.35.199.90"},"tags":{"omero.pixels_id":"14234493"}}
2024-08-27 16:16:48,377 [render-image-region-pool-8] ERROR c.g.o.m.i.r.ImageRegionRequestHandler - Exception while retrieving image region
ome.conditions.ResourceError: Error instantiating pixel buffer: /data/OMERO/ManagedRepository/demo_2/Blitz-0-Ice.ThreadPool.Server-12/2022-08/11/11-22-30.109/IMG_0006-0060 Diplophyllum albicans stature ventral side (2.5x).ome.tiff
        at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:907)
        at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:606)
        at com.glencoesoftware.omero.zarr.ZarrPixelsService.getPixelBuffer(ZarrPixelsService.java:373)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.getPixelBuffer(ImageRegionRequestHandler.java:419)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.render(ImageRegionRequestHandler.java:516)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.getRegion(ImageRegionRequestHandler.java:349)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionRequestHandler.renderImageRegion(ImageRegionRequestHandler.java:326)
        at com.glencoesoftware.omero.ms.core.OmeroRequest.execute(OmeroRequest.java:109)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionVerticle.renderImageRegion(ImageRegionVerticle.java:187)
        at com.glencoesoftware.omero.ms.image.region.ImageRegionVerticle.lambda$start$0(ImageRegionVerticle.java:133)
        at io.vertx.core.eventbus.impl.HandlerRegistration.deliver(HandlerRegistration.java:271)
        at io.vertx.core.eventbus.impl.HandlerRegistration.handle(HandlerRegistration.java:249)
        at io.vertx.core.eventbus.impl.EventBusImpl$InboundDeliveryContext.next(EventBusImpl.java:573)
        at io.vertx.core.eventbus.impl.EventBusImpl.lambda$deliverToHandler$5(EventBusImpl.java:532)
        at io.vertx.core.impl.ContextImpl.executeTask(ContextImpl.java:369)
        at io.vertx.core.impl.WorkerContext.lambda$wrapTask$0(WorkerContext.java:35)
        at io.vertx.core.impl.TaskQueue.run(TaskQueue.java:76)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
        at java.base/java.lang.Thread.run(Thread.java:829)

Restarting the micro-service via systemctl on all read-only servers was sufficient to fix the problem. We encountered something very similar in the past with the omero-server service needing a restart at the end of the deployment. This has been mitigated by the introduction of the monitoring playbook which is restarting the omero-server service

The Permission denied error is likely related to the sequence of the IDR deployment:

the idr-01-install-idr.yml playbook creates the service user, installs the OMERO services and and starts the omero-server, omero-web, omero-ms-image-region services
a later internal phase creates internal symlinks from /uod/idr/filesets to /nfs/bioimage/drop with the correct ownerships (omero-server) so that the services can access the in-place imported data

Listing possible options:

add instructions to restart the image-region micro-services by hand at the end of the deployment
add a step at the end of the monitoring playbook to restart the image-region micro-service
move the micro-service deployment to the idr-02-services.yml phase and ensure the links are created before their deployment
rearchitect the deployment phases to create the links before idr-01-install-idr.yml
investigate what causes the Permission denied in the first place e.g. does another service need to be restarted during the link creation phase

khaledk2 · 2024-09-05T09:32:10Z

If no one has an obligation, as @sbesson suggested (option 2), I have added a step to ansible/idr-09-monitoring.yml to restart the image-region micro-service.
We have tested the Idr-testing with microservices today and it works fine. So, we think microservices deployment should be applied to the Idr-next.
I have made some Nginx configuration changes on the `Idr-testing to return the Omero read-only instance which handles the request and to improve the performance, I will open a dedicated PR for it.

sbesson · 2024-09-05T11:48:12Z

Thanks @khaledk2, bb0a48f makes sense to me and should fix the issue I ran across while spinning up test123. This will be tested as part of the next full deployment and we can iterate if we encounter issues.

Code-wise, the only outstanding action is to release the underlying Ansible roles and update requirements.yml. Ideally, everything should be merged before upgrading prod123 but being mindful of timelines, we can certainly upgrade the software on prod123 from this branch like test123 /cc @francesw @jburel

jburel · 2024-09-05T12:08:30Z

@khaledk2 could you open a PR for the ansible roles?
The deployment is based on 2 of your branches and nothing has been opened

khaledk2 · 2024-09-05T12:23:46Z

@jburel There is an open PR to fix ansible-role-analysis-tools
ome/ansible-role-analysis-tools#7
@sbesson has already approved it, could you please check it?

I have made some changes in the ansible-role-omero-ms-image-region , based on your PR
ome/ansible-role-omero-ms-image-region#4
I have already referenced that in the PR
ome/ansible-role-omero-ms-image-region#4 (comment)

jburel · 2024-09-05T12:33:38Z

If you have made changes based on my branch, please open a PR and we close mine

khaledk2 · 2024-09-05T12:44:41Z

@jburel I have opened the new ome/ansible-role-omero-ms-image-region#5 PR

sbesson · 2024-09-06T08:17:13Z

Thanks all. Deployed on prod123

khaledk2 added 2 commits August 14, 2024 18:57

deploy ms-image-region

a9884b0

use pre_tasks

15052eb

sbesson requested changes Aug 14, 2024

View reviewed changes

move ms deployment to omero read only

45693d7

sbesson requested changes Aug 26, 2024

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Comment thread ansible/group_vars/omeroreadonly-hosts.yml Outdated

Comment thread ansible/group_vars/omeroreadonly-hosts.yml Outdated

Comment thread ansible/group_vars/omeroreadonly-hosts.yml Outdated

khaledk2 added 2 commits August 26, 2024 11:55

fix syntex issue

eb89e47

use branch for ome.analysis_tools role

832d695

sbesson self-requested a review August 26, 2024 15:46

sbesson reviewed Aug 28, 2024

View reviewed changes

add restart ms service

bb0a48f

use ms_image_region and analysis_tools roles from Ansible Galaxy

59dbd88

sbesson approved these changes Sep 6, 2024

View reviewed changes

sbesson merged commit 911bc8f into IDR:master Sep 6, 2024

sbesson mentioned this pull request Oct 7, 2024

Micro-service deployment & NGINX configuration #436

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