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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 11:03:27
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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 -- Petri Klemelä Chipster Team, CSC – IT Center for Science chi...@cs... From: Oliver Heil <o....@dk...> Date: Tuesday, 22. July 2025 at 12.29 To: chi...@li... <chi...@li...> Subject: Re: [Chipster-tech] [Extern] - Ubuntu 24.04 and K3s v1.32 updates in Chipster Hi Petri, I followed the procedure already. I did it now again, with the only difference, that I upgraded the servers Ubuntu as usual, because since then, 18 more updates have been waiting. Ok, after doing it again I am now at this point: ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f ~/values.yaml 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] Before that I did the bash pull-images.bash and it finished without any problems. And now ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret NAME TYPE DATA AGE passwords Opaque 1 14d which looks good. Best regards, Oli PS: there is nothing on the server which needs to be saved! Am 22.07.2025 um 06:53 schrieb Chipster: Hi Oli, unfortunately your error message looks a lot like the errors that I got when I tried to update the K3s before uninstalling Chipster. Luckily at least the update of the first server went through, so you have at least one working server. Does this second server store any analysis sessions that shouldn’t be lost? If it does, please do not make any further changes before we have verified where those are stored and how we can do this as safely as possible without losing them. If you are not too worried about losing the data stored on the server, then I would start by trying to delete the Helm releases like shown in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#recovering-from-failed-k3s-v1324-update . 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: Monday, 7. July 2025 at 19.09 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 Dear Petri, I updated one server successfully, but the second one did not well. I am stuck here: ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ bash deploy.bash -f ~/values.yaml 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] but ubuntu@chipstervm1:~/git/chipster-openshift/k3s$ kubectl get secret NAME TYPE DATA AGE passwords Opaque 1 37m I did already kubectl delete secret passwords but this did not resolve the issue. Of course I did helm uninstall chipster at first but yet I run into above known issue anyways. What can I do ? Best regards, Oli -- 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 The information in this email may be confidential and is intended solely for the use of the individual or entity to whom it is intended. If you are not the intended recipient of this message, please delete the message and notify the sender immediately. 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