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Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
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From: Chipster <chi...@cs...> - 2025-07-22 11:53:08
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Hi Oli,
well, that’s certainly interesting. Let’s find out what’s the difference.
** Do you have the latest deployment scripts?
$ git log
commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD -> k3s, tag: v4.15.0, origin/k3s-ubuntu24, origin/k3s)
Author: Petri Klemela pet...@cs...<mailto:pet...@cs...>
Date: Wed May 14 09:41:59 2025 +0300
Fix typo
…
** Do we have the same K3s version?
$ k3s -v
k3s version v1.32.4+k3s1 (6b330558)
go version go1.23.6
** Does K3s have any extra namespaces that could hide something from us?
$ kubectl get namespace
NAME STATUS AGE
default Active 52m
kube-node-lease Active 52m
kube-public Active 52m
kube-system Active 52m
** Or IngressRoutes?
ubuntu@chipster-dev-86-50-168-180-1:~/git/chipster-openshift/k3s$ kubectl get ingressroute
NAME AGE
chipster 56m
** Or middlewares?
$ kubectl get middleware
NAME AGE
chipster-https-redirect 56m
chipster-stripprefix 56m
** Is the kubectl configured to control this this node and not some other remote server? Check that both commands show the same hostname:
$ kubectl get node
NAME STATUS ROLES AGE VERSION
<hostname> Ready control-plane,master 54m v1.32.4+k3s1
$ hostname
<hostname>
** Is K3s using SQLite as datastore?
$ journalctl -u k3s.service --no-pager | grep "database"
May 26 06:50:12 chipster-dev-86-50-168-180-1 k3s[3427]: time="2025-05-26T06:50:12Z" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
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** The SQLite stores its data in /var/lib/rancher/k3s/server/db/ . Was it cleared when K3s was uninstalled?
sudo ls -l /var/lib/rancher/k3s/server/db/
total 30736
drwx------ 2 root root 4096 Jul 22 10:44 etcd
-rw-r--r-- 1 root root 19906560 Jul 22 11:46 state.db
-rw-r--r-- 1 root root 32768 Jul 22 11:48 state.db-shm
-rw-r--r-- 1 root root 11519552 Jul 22 11:48 state.db-wal
Best regards,
Petri / Chipster Team
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Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...
From: Oliver Heil <o....@dk...>
Date: Tuesday, 22. July 2025 at 14.25
To: chi...@li... <chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
Hi Petri,
I did as you suggested (I hope you believe me), but the result stays the same:
At this point:
ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash --set host=172.XX.26.XXX
Error: INSTALLATION FAILED: unable to build kubernetes objects from release manifest: [resource mapping not found for name: "chipster" namespace: "" from "": no matches for kind "IngressRoute" in version "traefik.containo.us/v1alpha1"
ensure CRDs are installed first, resource mapping not found for name: "chipster-stripprefix" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1"
ensure CRDs are installed first, resource mapping not found for name: "chipster-https-redirect" namespace: "" from "": no matches for kind "Middleware" in version "traefik.containo.us/v1alpha1"
ensure CRDs are installed first]
Oli
Am 22.07.2025 um 13:03 schrieb Chipster:
Hi Oli,
sorry, you had shown already in the first message that you have deleted all Kubernetes secrets.
I’m not sure where the K3s still finds those old definitions. Anyway, if nothing needs to be saved, would it be easiest just to uninstall K3s (https://docs.k3s.io/installation/uninstall):
/usr/local/bin/k3s-uninstall.sh
Then reinstall K3s: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/prerequisites.md#install-k3s-helm-and-other-utils
And Chipster: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#deploy
Best regards,
Petri / Chipster Team
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Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...<mailto:chi...@cs...>
From: Oliver Heil <o....@dk...><mailto:o....@dk...>
Date: Tuesday, 22. July 2025 at 12.29
To: chi...@li...<mailto:chi...@li...> <chi...@li...><mailto:chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster
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Oliver Heil (er/ihm,he/him)
Microarray Core Facility
Bioinformatics
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
o....@dk...<mailto:o....@dk...>
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