Container ot-es is Unhealthy

[shaileshchaudhary11]

Hi,

I am encountering an issue with the ot-es container in my setup. When I attempt to run the application, the container is marked as unhealthy, and I receive the following error:

make: *** [Makefile:123: platform_up] Error 1

I've tried restarting the container and checking the logs for any clues, but I am unable to resolve the issue. I am attaching
ot-es.log
log file for further details below.

Here are the details of my setup:

Docker version 27.3.1, build ce12230
Operating System: Ubuntu 22.04.5 LTS
Profile: config.2406-gcs
OpenJDK version 11.0.24

I am following blog ( https://blog.opentargets.org/standalone-deployment-tool/ )
for setting up open target.

Could any one please assist me in troubleshooting this issue? Any help would be greatly appreciated!

Thank you!

[mbdebian]

Thanks for reporting @shaileshchaudhary11 , would you mind providing the configuration profile you're using, so we can reproduce the issue on our side and investigate what may be happening?
Thanks!

[remo87]

It could be a permissions issue with the es try making the deployment folder readable for everyone chmod 777 -R deployment and re start the container

[shaileshchaudhary11]

Thanks for reporting @shaileshchaudhary11 , would you mind providing the configuration profile you're using, so we can reproduce the issue on our side and investigate what may be happening? Thanks!

Profile : config.2406-gcs

I tried by giving permission: chmod 777 -R deployment
still getting same error

[shaileshchaudhary11]

Hi @mbdebian, any updates on above issue, have you try to run it?

[remo87]

You're right @shaileshchaudhary11 the permission change solves a different issue. I just tried cleaning my env and running the standalone with the same profile as you but it worked. I ran it in a Ubuntu 22.04.5 LTS which is the same version as yours. Could you please share console output to see if there's potential issues?

[shaileshchaudhary11]

Hii @remo87

Can you please tell me what commands did you run in sequence in the terminal?
I would like to try the exact same thing. Also, what did you mean by cleaning the env in the last response?

Also, Is there any other even a slight change in any file of the project that you made?

[remo87]

sure thing!

 8281  2024-09-30 09:22:39 make platform_down
 8283  2024-09-30 09:23:00 sudo make clean
 8285  2024-09-30 09:23:52 make set_profile profile=2406-gcs
 8286  2024-09-30 09:24:09 make platform_up

I was testing with a different profile so I had different data and versions in my local environment. To test your configuration I ran make platform_down to destroy the containers and sudo make clean to delete the local files.

I did not changed the profile config.2406-gcs did a pull from master and my local repo has no changes.

[remo87]

I forgot to mention that after the previous steps I also performed the chmod operation. after running the platform_up I end up with all healthy and running containers but opensearch (ot-es) doesn't work, then I apply the chmod and re start the container and then it works

[remo87]

@shaileshchaudhary11 we've done a fix that might help you if you pull the latest version

[mbdebian]

This has now been addressed, please, let us know in case you face any more issues.
Thanks!

[shaileshchaudhary11]

Thank you, now I am able to run the Open Target platform at my local machine using standalone-deployment-platform. I have a doubt there is Open Target Genetics platform, is there any repository to run this platform also on my local machine .

…

On Thu, Oct 3, 2024 at 8:08 PM remo87 ***@***.***> wrote: @shaileshchaudhary11 <https://github.com/shaileshchaudhary11> we've done a fix that might help you if you pull the latest version — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANQJVHUI2P3LT3LXFS2MLGTZZVJHTAVCNFSM6AAAAABO62YYF6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJRGU4TIMRQGE> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

[mbdebian]

@shaileshchaudhary11 , I noticed that you are using the configuration profile config.2406-gcs, this profile pulls the Elasticsearch and Clickhouse data volumes off of a Google Cloud Storage bucket where, although it's open to the public, it is set on requester pays, which may affect the capability of actually downloading the tarballs with the data for Elasticsearch and Clickhouse on your end.

This is also related to what's happening to @kenibrewer in #8 . And, actually, the file not found exception he mentions would make total sense.

Please, allow me to verify this hypothesis and I'll let you know soon.

Thanks!

[mbdebian]

I have reproduce this environment in Google Cloud, as we don't have yet an allocation in AWS, specs:

Distributor ID:	Ubuntu
Description:	Ubuntu 22.04.5 LTS
Release:	22.04
Codename:	jammy

Docker version 27.3.1, build ce12230
docker-compose version 1.29.2, build unknown

I've run this using the profile config.2406-gcs, which downloads the data volumes from our bucket in Google Cloud, and profile config.2406, which is the same, but the tarballs are downloaded from our EBI FTP location.

No JDK is needed, as everything is run via docker images.

When installing Docker, the regular user has been added to the docker group, so no root permission is needed for running the containers.

The changes can be found in branch local_issue_6_and_8.

@kenibrewer, would you mind trying this branch, with profile '2406' in your EC2 instance?

Thank you guys!

[kenibrewer]

Thanks @mbdebian . Your theory about the requester pays bucket seems solid to me. I'll test out the changes and let you know.

[kenibrewer]

Hi @mbdebian This fixed the problem for me, and I was able to get a working deployment. Thanks so much!