From: Chipster <chi...@cs...> - 2023-09-08 05:03:05
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Hi Oli, interesting. It looks like you still have the old tool scripts somehow. Have you mounted the tool scripts from the host (https://github.com/chipster/chipster-openshift/blob/master/k3s/tool-script-dev.md#mount-tool-scripts-from-the-host) , i.e. something like this in your values.yaml? tools: hostPath: /opt/chipster/toolbox/tools In that case you would have to also update the tool scripts on your host: cd ~/git/chipster-tools/ git pull bash reload.bash Unfortunately the reload script hasn't been very reliable. It should print some logs. If the log timestamps are not from the current UTC time, then the reload didn't happen. In that case, restart the whole toolbox and wait for the old pod to disappear: kubectl rollout restart deployment/toolbox watch kubectl get pod Or if you have your own git branch (check with 'git status'): cd ~/git/chipster-tools/ git switch master git pull git switch <your-own-branch> git merge master bash reload.bash If you haven't mounted the tools scripts from the host, then the tool scripts should come directly from the toolbox container image and the version tag should make sure you are running the latest version of it. I guess we should then check how to toolbox deployment looks like: kubectl get deployment/toolbox -o yaml Best regards, Petri > On 7. Sep 2023, at 16.06, Oliver Heil <o....@dk...> wrote: > > Hi Petri, > The update to 4.7.5 worked flawless, but: > Still the docker image does not download, slightly different error: > > ... > QoS Class: Burstable > Node-Selectors: <none> > Tolerations: node.kubernetes.io/not-ready:NoExecuteop=Exists for 300s > node.kubernetes.io/unreachable:NoExecuteop=Exists for 300s > Events: > Type Reason Age From Message > ---- ------ ---- ---- ------- > Normal Scheduled 95s default-scheduler Successfully assigned default/comp-job-d6b3f450-3cd1-459a-ac8a-6cd70cbaa009-ordination-pca.r to chipstervm1 > Normal BackOff 13s (x5 over 94s) kubelet Back-off pulling image "docker-registry.rahti.csc.fi/chipster-images-release/comp-20.04-r-deps:v4.7.5" > Warning Failed 13s (x5 over 94s) kubelet Error: ImagePullBackOff > Normal Pulling 1s (x4 over 95s) kubelet Pulling image "docker-registry.rahti.csc.fi/chipster-images-release/comp-20.04-r-deps:v4.7.5" > Warning Failed 0s (x4 over 94s) kubelet Failed to pull image "docker-registry.rahti.csc.fi/chipster-images-release/comp-20.04-r-deps:v4.7.5": rpc error: code = NotFound desc = failed to pull and unpack image "docker-registry.rahti.csc.fi/chipster-images-release/comp-20.04-r-deps:v4.7.5": failed to resolve reference "docker-registry.rahti.csc.fi/chipster-images-release/comp-20.04-r-deps:v4.7.5":docker-registry.rahti.csc.fi/chipster-images-release/comp-20.04-r-deps:v4.7.5: not found > Warning Failed 0s (x4 over 94s) kubelet Error: ErrImagePull > ... > > > Am 07.09.2023 um 14:01 schrieb Chipster: >> Hi Oli, >> >> Good catch, thanks for spotting that! >> >> In v4.7.2 we renamed all period characters "." in the image names to dashes "-", because an OpenShift command line tool didn't like the periods. We changed these also in the so called "runtime" configuration in https://github.com/chipster/chipster-web-server/blob/master/src/main/resources/chipster-defaults.yaml , but there were two tools which had an overriding image name also in the tool itself. >> >> This is now fixed in Chipster version v4.7.5. >> >> Best regards, >> Petri >> > -- > Oliver Heil > Microarray Core Facility > Bioinformatics > German Cancer Research Center (DKFZ) > Foundation under Public Law > Im Neuenheimer Feld 580 > 69120 Heidelberg > Germany > o....@dk... > Support: www.dkfz.de/gpcf/support/ > www.dkfz.deManagement Board: Prof. Dr. med. Dr. h. c. Michael Baumann, Ursula Weyrich > VAT-ID No.: DE143293537 > _______________________________________________ > Chipster-tech mailing list > Chi...@li... > https://lists.sourceforge.net/lists/listinfo/chipster-tech |