Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

Hi Oli,

yay, finally this makes sense. There are two extra files:

        helm/chipster/templates/ingress.yaml.backup
        helm/chipster/values.yaml.backup

Those are probably copies of some older version of the ingress.yaml and values.yaml. Helm apparently finds them and tries to deploy them, causing problems with their old API definitions. I may have even instructed you to create these files at some point without realising that Helm will find them.

When we run the command “git pull” to get the latest versions, it doesn’t warn about those files, because it assumes those are your modifications that you want to keep.

Please delete or move those two files outside of helm directory, where Helm can’t find them. After that it’s probably best to uninstall K3s once more to remove all old crud and install K3s and Chipster again.

Best regards,
Petri / Chipster Team

--
Petri Klemelä
Chipster Team, CSC – IT Center for Science
chi...@cs...

From: Oliver Heil <o....@dk...>
Date: Wednesday, 23. July 2025 at 10.23
To: chi...@li... <chi...@li...>
Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster

Ah perhaps here is something wrong:

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git status
HEAD detached at v4.15.0
Untracked files:
  (use "git add <file>..." to include in what will be committed)
        helm/chipster/Chart.lock
        helm/chipster/charts/
        helm/chipster/templates/ingress.yaml.backup
        helm/chipster/values.yaml.backup

nothing added to commit but untracked files present (use "git add" to track)

Am 23.07.2025 um 07:34 schrieb Chipster:
Hi Oli,

I got your email through the email list eventually, so apparently the list just had some temporary glitch.

I guess missing IngressRoutes and Middlewares are expected, because that’s where the deployment fails.

** Let’s check that you don’t have any local changes in those files:

$ git status
On branch k3s
Your branch is up to date with 'origin/k3s'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        k3s/helm/chipster/Chart.lock
        k3s/helm/chipster/charts/

nothing added to commit but untracked files present (use "git add" to track)

** If there are changes, you can check those with

$ git diff <file_path>

Best regards,
Petri / Chipster Team

--
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 15.25
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

 Problems start with the ingress thing:

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ git log
commit 46016f41f46905bb7fc2390b5d188464fc6b27da (HEAD, tag: v4.15.0, origin/k3s-ubuntu24, origin/k3s, k3s)
Author: Petri Klemela <pet...@cs...><mailto:pet...@cs...>
Date:   Wed May 14 09:41:59 2025 +0300

    Fix typo

commit d590b6d6ba349f2a7384ebd31491be1614237974

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ k3s -v
k3s version v1.32.4+k3s1 (6b330558)
go version go1.23.6

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get namespace
NAME              STATUS   AGE
default           Active   36m
kube-node-lease   Active   36m
kube-public       Active   36m
kube-system       Active   36m

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get ingressroute
No resources found in default namespace.

===================^^^^^^^^^^^^^^^^^^^^

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get middleware
No resources found in default namespace.

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get node
NAME          STATUS   ROLES                  AGE   VERSION
chipstervm1   Ready    control-plane,master   37m   v1.32.4+k3s1

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ hostname
chipstervm1

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ journalctl -u k3s.service --no-pager | grep "database"
Jun 18 10:20:36 chipstervm1 k3s[956]: time="2025-06-18T10:20:36+02:00" level=error msg="Compact failed: failed to compact to revision 41449638: database is locked"
Jun 20 01:45:36 chipstervm1 k3s[956]: time="2025-06-20T01:45:36+02:00" level=error msg="Compact failed: failed to compact to revision 41492579: database is locked"
Jun 24 11:25:36 chipstervm1 k3s[956]: time="2025-06-24T11:25:36+02:00" level=error msg="Compact failed: failed to compact to revision 41607701: database is locked"
Jun 28 23:20:36 chipstervm1 k3s[956]: time="2025-06-28T23:20:36+02:00" level=error msg="Compact failed: failed to compact to revision 41725264: database is locked"
Jun 30 18:35:36 chipstervm1 k3s[956]: time="2025-06-30T18:35:36+02:00" level=error msg="Compact failed: failed to compact to revision 41772386: database is locked"
Jul 07 15:02:12 chipstervm1 k3s[747637]: time="2025-07-07T15:02:12+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:02:12 chipstervm1 k3s[747637]: time="2025-07-07T15:02:12+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1295288538]: ---"Object deleted from database" 524ms (15:04:56.387)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[337602364]: ---"Object deleted from database" 542ms (15:04:56.413)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[147515258]: ---"Object deleted from database" 510ms (15:04:56.423)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[605196751]: ---"Object deleted from database" 521ms (15:04:56.428)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1750733902]: ---"Object deleted from database" 536ms (15:04:56.432)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[270507439]: ---"Object deleted from database" 570ms (15:04:56.440)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[513417525]: ---"Object deleted from database" 558ms (15:04:56.448)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[546947458]: ---"Object deleted from database" 590ms (15:04:56.453)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1353657320]: ---"Object deleted from database" 593ms (15:04:56.458)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1180849967]: ---"Object deleted from database" 600ms (15:04:56.465)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[512674873]: ---"Object deleted from database" 567ms (15:04:56.470)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1416147340]: ---"Object deleted from database" 574ms (15:04:56.475)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1199243352]: ---"Object deleted from database" 605ms (15:04:56.479)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[669529128]: ---"Object deleted from database" 600ms (15:04:56.483)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1342959763]: ---"Object deleted from database" 609ms (15:04:56.488)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1214239173]: ---"Object deleted from database" 580ms (15:04:56.493)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[783574743]: ---"Object deleted from database" 584ms (15:04:56.498)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1600294098]: ---"Object deleted from database" 595ms (15:04:56.502)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[985792831]: ---"Object deleted from database" 620ms (15:04:56.506)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[1107874578]: ---"Object deleted from database" 634ms (15:04:56.510)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[406458206]: ---"Object deleted from database" 616ms (15:04:56.515)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[654409944]: ---"Object deleted from database" 652ms (15:04:56.519)
Jul 07 15:04:56 chipstervm1 k3s[747637]: Trace[2001160119]: ---"Object deleted from database" 631ms (15:04:56.523)
Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:09:50 chipstervm1 k3s[935]: time="2025-07-07T15:09:50+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 15:48:41 chipstervm1 k3s[918]: time="2025-07-07T15:48:41+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 16:14:21 chipstervm1 k3s[1046]: time="2025-07-07T16:14:21+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 16:14:21 chipstervm1 k3s[1046]: time="2025-07-07T16:14:21+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 07 16:17:55 chipstervm1 k3s[4218]: time="2025-07-07T16:17:55+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 07 16:17:55 chipstervm1 k3s[4218]: time="2025-07-07T16:17:55+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 22 10:58:21 chipstervm1 k3s[1032]: time="2025-07-22T10:58:21+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 22 10:58:21 chipstervm1 k3s[1032]: time="2025-07-22T10:58:21+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."
Jul 22 13:18:00 chipstervm1 k3s[11626]: time="2025-07-22T13:18:00+02:00" level=info msg="Configuring sqlite3 database connection pooling: maxIdleConns=2, maxOpenConns=0, connMaxLifetime=0s"
Jul 22 13:18:00 chipstervm1 k3s[11626]: time="2025-07-22T13:18:00+02:00" level=info msg="Configuring database table schema and indexes, this may take a moment..."

ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ sudo ls -l /var/lib/rancher/k3s/server/db/
[sudo] password for ubuntu:
total 12056
drwx------ 2 root root    4096 Jul 22 13:18 etcd
-rw-r--r-- 1 root root 7655424 Jul 22 13:58 state.db
-rw-r--r-- 1 root root   32768 Jul 22 13:59 state.db-shm
-rw-r--r-- 1 root root 4647392 Jul 22 13:59 state.db-wal

Am 22.07.2025 um 13:52 schrieb Chipster:
Hi Oli,

well, that’s certainly interesting. Let’s find out what’s the difference.

--

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

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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...>
Support: " rel="nofollow">www.dkfz.de/gpcf/support/<https://www.dkfz.de/gpcf/support/>
www.dkfz.de<http://www.dkfz.de>
[Research for a Life without Cancer]

Management Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537