zalando / zalando/postgres-operator

K8s: Restart in the middle of reinit of replica db node -> manual fixing of db node needed

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Description

Image: registry.opensource.zalan.do/acid/postgres-operator:v1.6.0
patroni==2.0.1
spilo-13:2.0-p4
PostgreSQL 13.2

Running it in Kubernetes
Running Postgres operator in Test pipe Environment
Issue: Feature request

Main Error: Data dir for the cluster is not empty, but system ID is invalid; consider doing reinitialize

There was 20 million rows in the DB cluster.

Following is quite a simple test execution.
Steps,
reinit:

Are you sure you want to reinitialize members rdbms-pg-cluster-2? [y/N]: y
Success: reinitialize for member rdbms-pg-cluster-2

Then the same replica pod was restarted in the middle of the reinit process:

kubectl delete po rdbms-pg-cluster-2
pod "rdbms-pg-cluster-2" deleted

Then the pod got in mentioned error state:

"data dir for the cluster is not empty, but system ID is invalid; consider doing reinitialize"

Such needs manual fixing.

Larger the database → Higher the probability for these kinds of problems.

Patroni REST interface of the problematic DB pod / DB pod works at that time:

curl --max-time 10 "http://xxxx.xx.xx.xx:8008/cluster"
{"members": ... {"name": "rdbms-pg-cluster-2", "role": "replica", "state": "stopped", "api_url": "http://xx.xx.xx.xx:8008/patroni", "host": "xxx.xx.xx.xx", "port": 5432, "lag": "unknown"}]}

And it is possible to reinitialize that pod with curl:

curl --max-time 10 -s -X POST "http://xxx.xx.xx.xx:8008/reinitialize"

So, in theory, it would be possible to write our own script for automatic re initialization for some cases. But is it wise, I do not know.

Q: What could be done for this problem?

I think, in source codes of Patroni, the error message comes from following place:

(https://github.com/zalando/patroni/blob/master/patroni/ha.py)

if not self.sysid_valid(data_sysid):
# data directory is not empty, but no valid sysid, cluster must be broken, suggest reinit
return ("data dir for the cluster is not empty, "
"but system ID is invalid; consider doing reinitialize")

Attached Logs, CRD and manifest files here for reference :
reinit-error.txt
manifest.txt
crd.txt

remove_data_directory_on_diverged_timelines: 'true'
remove_data_directory_on_rewind_failure: 'true'

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the attached reinit-error.txt, manifest.txt, and crd.txt, then inspect the referenced Patroni entry point in patroni/ha.py. Determine whether the operator should handle a replica restart during reinitialization and document the safe completion criteria for any proposed recovery behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
go, kubernetes, postgresql
Domain
databases, devops, infrastructure
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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