FAQ

Question: Every Pod, Job, Deployment, and any other type that runs a container must have the resources attribute set, otherwise the deploy will fail with a similar error:

Pods "master-685f855ff-gg9sr" is forbidden: failed quota: default-w2qv7: must specify limits.cpu,limits.memory,requests.cpu,requests.memory:Deployment does not have minimum availability.

Answer: Pod, Job, Deployment is missing the following resource section with appropriate values:

resources:
  requests:
    cpu: 1
    memory: 512Mi
  limits:
    cpu: 1
    memory: 512Mi
 

Question: Deployment returns message simmilar to:

pods cz-iocb-nextprot-loader-loaderspark-1649322652207-driver" is forbidden: 
exceeded quota: default-sq5kt, requested: limits.cpu=1,limits.memory=2432Mi,requests.cpu=1,requests.memory=2432Mi, 
used: limits.cpu=0,limits.memory=0,requests.cpu=0,requests.memory=0,
limited:limits.cpu=0,limits.memory=0,requests.cpu=0,requests.memory=0.

Answer: The deployment is being made to a Namespace that is running out of quota or even has quota set to zero. You need to increase the Namespace quota, which may require decreasing the quotas of your other Namespaces or requesting an explicit Project. See Projects, Namespaces, and Quotas.

Question: No GPU found, nvidia-smi returns command not found.

Answer: The deployment is missing request for GPU like:

resources:
  limits:
    nvidia.com/gpu: 1

or

resources:   
  limits:
    cerit.io/gpu-mem: 1

Question: Deployment returns message similar to:

CreateContainerConfigError (container has runAsNonRoot and image will run as root (pod: "mongo-db-846b7bfc7-qrlqt_namespace-ns(5d3538ab-7493-41ab-bd94-a4256c236f6f)", container: mongo-db-test))

Answer: The deployment is missing the securityContext section and the container image (in this case mongo) does not contain numeric USER. To fix this, just extend the deployment definition like this:

image: cerit.io/nextflowproxy:v1.2
imagePullPolicy: Always
securityContext:
  runAsUser: 1000
  runAsGroup: 1000
resources:
  limits:
    cpu: 4
    memory: 8192Mi

The runAsUser and runAsGroup lines are important.

See full security context settings here.

Question: Helm deployment returns error code 413

Answer: HTML code 413 means entity too larger. Helm stores whole deployment (including all the local files in the chart no matter if they have .yaml suffix) and values into a Secret object. Limit of the Secret size is about 1.5MB. Verify, if there is no big file in the whole chart.