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

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  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...>
> 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

o....@dk... <mailto:o....@dk...>
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