Minimal update error

[treitpeter]

Using the docker container installation During running the minimal update I get the error message in docker desktop log:

[2021-09-07 07:13:45,753: WARNING/ForkPoolWorker-1] Done Parsing database phosphositeplus [2021-09-07 07:13:46,701: INFO/ForkPoolWorker-1] Parsing database drugbank [D 2021-09-07 07:14:46.643 SingleUserNotebookApp mixins:518] Notifying Hub of activity 2021-09-07T07:09:27.427800Z [I 2021-09-07 07:14:48.110 JupyterHub log:189] 200 POST /hub/api/users/ckguser/activity ([email protected]) 857.21ms [2021-09-07 07:18:02,487: ERROR/MainProcess] Process 'ForkPoolWorker-1' pid:652 exited with 'signal 9 (SIGKILL)' [2021-09-07 07:18:02,801: ERROR/MainProcess] Task handler raised error: WorkerLostError('Worker exited prematurely: signal 9 (SIGKILL) Job: 0.') Traceback (most recent call last): File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 1267, in mark_as_worker_lost human_status(exitcode), job._job), billiard.exceptions.WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL) Job: 0. 07:18:40.547 [ConfigProxy] info: 200 GET /api/routes [I 2021-09-07 07:18:40.822 JupyterHub proxy:347] Checking routes [D 2021-09-07 07:19:20.875 SingleUserNotebookApp mixins:518] Notifying Hub of activity 2021-09-07T07:09:27.427800Z [I 2021-09-07 07:19:21.119 JupyterHub log:189] 200 POST /hub/api/users/ckguser/activity ([email protected]) 96.73ms

Desktop

• OS: iOS Catalina version 10.15.7
• Browser chrome
• Version [e.g. 22]

** Not sure what worker exited prematurely means but I didn't quit anything during installation, neo4j desktop is still running, and I can access all the jupyter notebooks and neo4j online services.

I did make a user before the minimal update was done - I hope this is not an issue.

[treitpeter]

Couple of ideas based on a short troubleshooting session

https://stackoverflow.com/questions/22805079/celery-workerlosterror-worker-exited-prematurely-signal-9-sigkill

This sounds like exactly the problem I am having, but not sure of how to check.

[xuel12]

@treitpeter I have exact same error of "signal 9 kill during drugbank parsing". Have you found any solution?

[treitpeter]

No I have not unfortunately. Will get back to you in the coming weeks.

On Fri, Feb 11, 2022 at 3:15 AM Liang Xue @.***> wrote:

@treitpeter https://github.com/treitpeter I have exact same error of "signal 9 kill during drugbank parsing". Have you found any solution?

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[frederikbyl]

We had the same issue. We are running the docker installation and saw that during the minimal update the container hits the memory limits. We increased a couple of times and saw it running stable with 25 GB memory assigned to it. The top was at about 17 GB. It solved our issue. Seem like it's loading all the files in memory before processing, but we are not completely sure and didn't go into depth in the code. Permanent solution could be to change the parsing so it doesn't need to load everything in memory at once, but process in batches imho.