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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 04:53:29
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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... From: Oliver Heil <o....@dk...> Date: Monday, 7. July 2025 at 19.09 To: chi...@li... <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 Am 15.05.2025 um 08:53 schrieb chipster--- via Chipster-tech: Hi all Chipster maintainers, until now main Chipster components have been running in Ubuntu 20.04, which will reach end of support at May 31 2025. Our installation instructions now start from Ubuntu 24.04. We have also prepared instructions for this update, but please read this whole message before starting. The Ubuntu update itself seems to be relatively easy. You can either install a new server, or update your current one. Old Chipster containers seem to work just fine in the new Ubuntu and vice versa, so it doesn't matter whether you update first the Ubuntu or the Chipster version. However, we used this oportunity to update also the K3s. Due to earlier update issues, we had it pinned down to version v1.26. We now updated it to v1.32. The new version doesn't seem to tolerate our old apiVersion definition "traefik.containo.us/v1alpha1" in https://github.com/chipster/chipster-openshift/blob/k3s/k3s/helm/chipster/templates/ingress-route.yaml . We have updated the apiVersion definition in the current templates (Chipster v4.15.0), but the K3s still has problems with the old versions stored by Helm. If you install a new server, you will get Ubuntu 24.04, K3s v1.32 with our new templates, and everything will work just fine. But if you try to upgrade an old server, read our migration instructions carefully. The easiest solution that we found is to uninstall Chipster before the new K3s is installed. Without this the server ended up in a state where even downgrading of K3s didn't fix it. K3s v1.32 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-k3s-v1324 Ubuntu 24.04 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/migration.md#update-to-ubuntu-2404 Chipster v4.15.0 update instructions: https://github.com/chipster/chipster-openshift/blob/k3s/k3s/README.md#updates Best regards, Petri / Chipster team _______________________________________________ Chipster-tech mailing list Chi...@li...<mailto:Chi...@li...> https://lists.sourceforge.net/lists/listinfo/chipster-tech -- 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. 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