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LEAP prometheus server is down/scheduler faiiling #2248

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pnasrat opened this issue Feb 23, 2023 · 21 comments
Closed

LEAP prometheus server is down/scheduler faiiling #2248

pnasrat opened this issue Feb 23, 2023 · 21 comments
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@pnasrat

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@pnasrat
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pnasrat commented Feb 23, 2023 •
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Prometheus in leap server is down

Reported via ticket https://2i2c.freshdesk.com/a/tickets/482
@pnasrat
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pnasrat commented Feb 23, 2023 

Name:             support-prometheus-server-548d55b8bc-mhppb
Namespace:        support
Priority:         0
Service Account:  support-prometheus-server
Node:             <none>
Labels:           app=prometheus
                  chart=prometheus-19.4.0
                  component=server
                  heritage=Helm
                  pod-template-hash=548d55b8bc
                  release=support
Annotations:      <none>
Status:           Pending
IP:               
IPs:              <none>
Controlled By:    ReplicaSet/support-prometheus-server-548d55b8bc
Containers:
  prometheus-server-configmap-reload:
    Image:      jimmidyson/configmap-reload:v0.8.0
    Port:       <none>
    Host Port:  <none>
    Args:
      --volume-dir=/etc/config
      --webhook-url=http://127.0.0.1:9090/-/reload
    Environment:  <none>
    Mounts:
      /etc/config from config-volume (ro)
      /var/run/secrets/kubernetes.io/serviceaccount from kube-api-access-wc84b (ro)
  prometheus-server:
    Image:      quay.io/prometheus/prometheus:v2.41.0
    Port:       9090/TCP
    Host Port:  0/TCP
    Args:
      --storage.tsdb.retention.time=366d
      --config.file=/etc/config/prometheus.yml
      --storage.tsdb.path=/data
      --web.console.libraries=/etc/prometheus/console_libraries
      --web.console.templates=/etc/prometheus/consoles
      --web.enable-lifecycle
    Limits:
      cpu:     3900m
      memory:  22Gi
    Requests:
      cpu:        3
      memory:     20Gi
    Liveness:     http-get http://:9090/-/healthy delay=30s timeout=10s period=15s #success=1 #failure=3
    Readiness:    http-get http://:9090/-/ready delay=30s timeout=4s period=5s #success=1 #failure=3
    Environment:  <none>
    Mounts:
      /data from storage-volume (rw)
      /etc/config from config-volume (rw)
      /var/run/secrets/kubernetes.io/serviceaccount from kube-api-access-wc84b (ro)
Conditions:
  Type           Status
  PodScheduled   False 
Volumes:
  config-volume:
    Type:      ConfigMap (a volume populated by a ConfigMap)
    Name:      support-prometheus-server
    Optional:  false
  storage-volume:
    Type:       PersistentVolumeClaim (a reference to a PersistentVolumeClaim in the same namespace)
    ClaimName:  support-prometheus-server
    ReadOnly:   false
  kube-api-access-wc84b:
    Type:                    Projected (a volume that contains injected data from multiple sources)
    TokenExpirationSeconds:  3607
    ConfigMapName:           kube-root-ca.crt
    ConfigMapOptional:       <nil>
    DownwardAPI:             true
QoS Class:                   Burstable
Node-Selectors:              <none>
Tolerations:                 node.kubernetes.io/not-ready:NoExecute op=Exists for 300s
                             node.kubernetes.io/unreachable:NoExecute op=Exists for 300s
Events:
  Type     Reason             Age                   From                                   Message
  ----     ------             ----                  ----                                   -------
  Warning  FailedScheduling   13m                   gke.io/optimize-utilization-scheduler  0/212 nodes are available: 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 Insufficient cpu, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 8 Insufficient memory. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
  Normal   NotTriggerScaleUp  13m                   cluster-autoscaler                     pod didn't trigger scale-up: 4 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 2 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 2 Insufficient memory, 1 Insufficient cpu, 2 max node group size reached
  Warning  FailedScheduling   11m (x15 over 13m)    gke.io/optimize-utilization-scheduler  0/212 nodes are available: 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 Insufficient cpu, 7 Insufficient memory, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
  Normal   NotTriggerScaleUp  8m42s (x7 over 13m)   cluster-autoscaler                     pod didn't trigger scale-up: 3 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 2 max node group size reached
  Normal   NotTriggerScaleUp  3m39s (x52 over 12m)  cluster-autoscaler                     (combined from similar events): pod didn't trigger scale-up: 3 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 4 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 1 node(s) had untolerated taint {nvidia.com/gpu: present}, 2 max node group size reached
  Warning  FailedScheduling   52s (x32 over 11m)    gke.io/optimize-utilization-scheduler  0/212 nodes are available: 11 Insufficient cpu, 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 7 Insufficient memory, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.

@pnasrat
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pnasrat commented Feb 23, 2023

I'm still learning about the system but my expectation about the support namespace is that it would just be for monitoring, etc and I'm seeing a lot of gke nodes in the namespace

kubectl get nodes -n support 

NAME                                       STATUS   ROLES    AGE     VERSION
gke-leap-cluster-core-pool-1cc6bf7d-5fnp   Ready       132d    v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-5fwt   Ready       64d     v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-7wg2   Ready       34d     v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-g77w   Ready       27h     v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-vlbq   Ready       45h     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-24j4   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-29kn   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2dxm   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2g5c   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2gc4   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2khr   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2tzz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2vcj   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-2wzw   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-465z   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-46df   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-46zs   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-49x2   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-49zh   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-4hfp   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-4jdv   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-4v49   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-4vsf   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-4wbr   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-4zd9   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-574h   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-59tc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5glt   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5k64   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5lmk   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5mb2   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5v5s   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5wks   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5zbh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-5zjr   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-6mkt   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-6q4b   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-6shh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-7cbz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-7dk6   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-7h7g   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-7ptq   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-7vjc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-84d6   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-88rc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-8hks   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-8pzd   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-8s7b   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-8wvn   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-9js4   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-9l9h   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-9vbf   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-9w2f   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-b7lc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-b86b   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-bknz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-blnl   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-bmrb   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-brzw   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-c4mc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-c58s   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-c68s   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-c92c   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-clbd   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-cnjz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-cnr4   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-djjm   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-djz2   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-dppr   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-dr7q   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-dv9d   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-dvxx   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-f4w9   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-f7mm   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-f9mc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-fbpp   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-fj2z   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-fljh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-fmr2   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-fr2c   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-fwnp   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-g6c9   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-g6ph   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gdll   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gf6p   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gfbl   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gkrr   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-glvb   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-grp2   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gvpq   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gxkv   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-gzbd   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-h67b   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-h9kc   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-hkd6   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-hkwm   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-hrwh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-hrzd   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-hvpb   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-j729   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-jbqb   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-jglq   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-jk72   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-jkj5   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-jlfc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-js67   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-jsvf   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-k7rp   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-k8k9   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-k9kg   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-kn65   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-kqdw   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-kvlm   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-l7j6   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-lpdm   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-lrx4   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-lwzr   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-m2kg   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-m6hj   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-m7vx   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-mk8k   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-mt8t   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-n5w6   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-n8js   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-n92c   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-ncgt   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-nfws   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-nkw4   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-nqqx   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-nqt5   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-nr6s   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-nx2v   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-p7sj   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-pdkm   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-pn8q   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-ppd8   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-q8nt   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-q9cb   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qb6k   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qg9r   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qh9g   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qm5b   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qngf   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qpdb   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qrmv   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qtz6   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qv46   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qv8q   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qxnf   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-qzcq   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-r4f7   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-r826   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rbw7   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rg2m   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rg5l   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rgv7   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rqsz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rrww   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-rtrh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-s7x5   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-sk5v   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-slbj   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-srpz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-ss25   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-swlb   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-swqf   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-t2k9   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-t68d   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-t7wg   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-t92m   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-td44   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-tdbk   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-thzt   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-tmxx   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-tzs6   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vbrd   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vc6g   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vhwq   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vkk2   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vnxq   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vsp5   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vw6w   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-vxfp   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-wbpj   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-wkb5   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-wmj8   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-wq8f   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-wrml   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-wwqk   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-x4rz   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-x972   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-xd4s   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-xl7d   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-xlhh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-xlr8   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-xp58   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-xxrq   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-z2mf   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-z6c7   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-z6xh   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-zdbs   Ready       28m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-zjh4   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-zwkn   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-zwmc   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-dask-huge-b3a90f26-zx6b   Ready       29m     v1.24.5-gke.600
gke-leap-cluster-nb-huge-cf099c13-2zkf     Ready       58m     v1.24.5-gke.600
gke-leap-cluster-nb-huge-cf099c13-zssb     Ready       5h7m    v1.24.5-gke.600
gke-leap-cluster-nb-large-3ab858ce-gmz9    Ready       20m     v1.24.5-gke.600
gke-leap-cluster-nb-large-3ab858ce-l7dv    Ready       34m     v1.24.5-gke.600
gke-leap-cluster-nb-medium-b9c8ba20-7thc   Ready       131m    v1.24.5-gke.600
gke-leap-cluster-nb-medium-b9c8ba20-hrhk   Ready       3h15m   v1.24.5-gke.600
gke-leap-cluster-nb-medium-b9c8ba20-wjmj   Ready       4h15m   v1.24.5-gke.600

@pnasrat
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pnasrat commented Feb 23, 2023

Adding a node to the core pool to see if can get prometheus scheduled

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pnasrat commented Feb 23, 2023

Added server is gke-leap-cluster-core-pool-1cc6bf7d-tmq0

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pnasrat commented Feb 23, 2023 

kubectl get pods --field-selector=status.phase=Pending -n support
NAME                                         READY   STATUS              RESTARTS   AGE
support-cryptnono-6rmkq                      0/1     Init:0/1            0          10s
support-prometheus-node-exporter-bzh9k       0/1     ContainerCreating   0          10s
support-prometheus-server-548d55b8bc-mhppb   0/2     Pending             0          30m

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pnasrat commented Feb 23, 2023 

 kubectl get pods -l app=prometheus,component=server -n supportNAME                                         READY   STATUS    RESTARTS   AGE
support-prometheus-server-548d55b8bc-mhppb   1/2     Running   0          31m

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pnasrat commented Feb 23, 2023 

kubectl get deployment -l app=prometheus,component=server -n support 
NAME                        READY   UP-TO-DATE   AVAILABLE   AGE
support-prometheus-server   1/1     1            1           302d
kubectl get pods -l app=prometheus,component=server -n support 
NAME                                         READY   STATUS    RESTARTS   AGE
support-prometheus-server-548d55b8bc-mhppb   2/2     Running   0          33m

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pnasrat commented Feb 23, 2023

@damianavila and @yuvipanda as the formal oncalls tagging you here. I've added (from 5 to 6) nodes to gke-leap-cluster-core-pool-1cc6bf7d-grp this clears the paging condition but I've not done an extensive analysis of why this occurs

TODO:

  • Diagnose scheduling failure
  • Reduce core pool size down

@pnasrat pnasrat self-assigned this Feb 23, 2023
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pnasrat commented Feb 23, 2023

Looking at the events it looks like it was prempted (longer logs below) extract here. It looks like scheduling failed and then scale-up faiiled/was not triggered and max group size reached.

55m         Normal    Preempted                pod/support-prometheus-server-548d55b8bc-hfkvk    Preempted by kube-system/calico-node-rnths on node gke-leap-cluster-core-pool-1cc6bf7d-g77w
55m         Normal    Killing                  pod/support-prometheus-server-548d55b8bc-hfkvk    Stopping container prometheus-server-configmap-reload
55m         Normal    Killing                  pod/support-prometheus-server-548d55b8bc-hfkvk    Stopping container prometheus-server
55m         Warning   FailedScheduling         pod/support-prometheus-server-548d55b8bc-mhppb    0/212 nodes are available: 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 Insufficient cpu, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 8 Insufficient memory. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
55m         Normal    NotTriggerScaleUp        pod/support-prometheus-server-548d55b8bc-mhppb    pod didn't trigger scale-up: 4 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 2 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 2 Insufficient memory, 1 Insufficient cpu, 2 max node group size reached
k get events -n support 

LAST SEEN   TYPE      REASON                   OBJECT                                            MESSAGE
26m         Normal    Scheduled                pod/support-cryptnono-6rmkq                       Successfully assigned support/support-cryptnono-6rmkq to gke-leap-cluster-core-pool-1cc6bf7d-tmq0
26m         Warning   FailedCreatePodSandBox   pod/support-cryptnono-6rmkq                       Failed to create pod sandbox: rpc error: code = Unknown desc = failed to setup network for sandbox "f53c22cf29bd154c5839d963af765266c5c2076f94b490a251100ab3693f5c7e": plugin type="calico" failed (add): stat /var/lib/calico/nodename: no such file or directory: check that the calico/node container is running and has mounted /var/lib/calico/
26m         Normal    Pulling                  pod/support-cryptnono-6rmkq                       Pulling image "yuvipanda/kubectl-trace-init:9af18f1197b1b377be4816c2761049745b64c6b8"
26m         Normal    Pulled                   pod/support-cryptnono-6rmkq                       Successfully pulled image "yuvipanda/kubectl-trace-init:9af18f1197b1b377be4816c2761049745b64c6b8" in 6.317139676s
26m         Normal    Created                  pod/support-cryptnono-6rmkq                       Created container kubectl-trace-init
26m         Normal    Started                  pod/support-cryptnono-6rmkq                       Started container kubectl-trace-init
24m         Normal    Pulling                  pod/support-cryptnono-6rmkq                       Pulling image "quay.io/iovisor/bpftrace:1c295d899035aaded34d5861375051ec1add1d3a-vanilla_llvm12_clang_glibc2.23"
24m         Normal    Pulled                   pod/support-cryptnono-6rmkq                       Successfully pulled image "quay.io/iovisor/bpftrace:1c295d899035aaded34d5861375051ec1add1d3a-vanilla_llvm12_clang_glibc2.23" in 3.724225512s
24m         Normal    Created                  pod/support-cryptnono-6rmkq                       Created container trace
24m         Normal    Started                  pod/support-cryptnono-6rmkq                       Started container trace
18m         Normal    Killing                  pod/support-cryptnono-jxqgh                       Stopping container trace
18m         Warning   FailedPreStopHook        pod/support-cryptnono-jxqgh                       Exec lifecycle hook ([/bin/bash -c kill -SIGINT $(pidof bpftrace) && sleep 30]) for Container "trace" in Pod "support-cryptnono-jxqgh_support(668e877f-e240-454f-b701-969e684aaa12)" failed - error: command '/bin/bash -c kill -SIGINT $(pidof bpftrace) && sleep 30' exited with 137: , message: ""
16m         Normal    Scheduled                pod/support-cryptnono-k9lvj                       Successfully assigned support/support-cryptnono-k9lvj to gke-leap-cluster-dask-huge-b3a90f26-574h
16m         Warning   FailedCreatePodSandBox   pod/support-cryptnono-k9lvj                       Failed to create pod sandbox: rpc error: code = Unknown desc = failed to setup network for sandbox "68bd292ac298b53878944d07d1fdb1a4b221ab7b2a4269474d2c80ffe787bb88": plugin type="calico" failed (add): stat /var/lib/calico/nodename: no such file or directory: check that the calico/node container is running and has mounted /var/lib/calico/
16m         Normal    Pulling                  pod/support-cryptnono-k9lvj                       Pulling image "yuvipanda/kubectl-trace-init:9af18f1197b1b377be4816c2761049745b64c6b8"
16m         Normal    Pulled                   pod/support-cryptnono-k9lvj                       Successfully pulled image "yuvipanda/kubectl-trace-init:9af18f1197b1b377be4816c2761049745b64c6b8" in 4.904876655s
16m         Normal    Created                  pod/support-cryptnono-k9lvj                       Created container kubectl-trace-init
16m         Normal    Started                  pod/support-cryptnono-k9lvj                       Started container kubectl-trace-init
15m         Normal    Pulling                  pod/support-cryptnono-k9lvj                       Pulling image "quay.io/iovisor/bpftrace:1c295d899035aaded34d5861375051ec1add1d3a-vanilla_llvm12_clang_glibc2.23"
15m         Normal    Pulled                   pod/support-cryptnono-k9lvj                       Successfully pulled image "quay.io/iovisor/bpftrace:1c295d899035aaded34d5861375051ec1add1d3a-vanilla_llvm12_clang_glibc2.23" in 3.016818465s
15m         Normal    Created                  pod/support-cryptnono-k9lvj                       Created container trace
15m         Normal    Started                  pod/support-cryptnono-k9lvj                       Started container trace
57m         Normal    Scheduled                pod/support-cryptnono-pqfxr                       Successfully assigned support/support-cryptnono-pqfxr to gke-leap-cluster-nb-large-3ab858ce-gmz9
57m         Warning   FailedCreatePodSandBox   pod/support-cryptnono-pqfxr                       Failed to create pod sandbox: rpc error: code = Unknown desc = failed to setup network for sandbox "e87524ae545827b1bb95712db0b0d42131f31faf0bb35d58f9cc798d40c46b41": plugin type="calico" failed (add): stat /var/lib/calico/nodename: no such file or directory: check that the calico/node container is running and has mounted /var/lib/calico/
57m         Normal    Pulling                  pod/support-cryptnono-pqfxr                       Pulling image "yuvipanda/kubectl-trace-init:9af18f1197b1b377be4816c2761049745b64c6b8"
53m         Normal    Pulled                   pod/support-cryptnono-pqfxr                       Successfully pulled image "yuvipanda/kubectl-trace-init:9af18f1197b1b377be4816c2761049745b64c6b8" in 3m50.935963258s
53m         Normal    Created                  pod/support-cryptnono-pqfxr                       Created container kubectl-trace-init
53m         Normal    Started                  pod/support-cryptnono-pqfxr                       Started container kubectl-trace-init
51m         Normal    Pulling                  pod/support-cryptnono-pqfxr                       Pulling image "quay.io/iovisor/bpftrace:1c295d899035aaded34d5861375051ec1add1d3a-vanilla_llvm12_clang_glibc2.23"
49m         Normal    Pulled                   pod/support-cryptnono-pqfxr                       Successfully pulled image "quay.io/iovisor/bpftrace:1c295d899035aaded34d5861375051ec1add1d3a-vanilla_llvm12_clang_glibc2.23" in 1m29.808725295s
49m         Normal    Created                  pod/support-cryptnono-pqfxr                       Created container trace
49m         Normal    Started                  pod/support-cryptnono-pqfxr                       Started container trace
57m         Normal    SuccessfulCreate         daemonset/support-cryptnono                       (combined from similar events): Created pod: support-cryptnono-pqfxr
26m         Normal    SuccessfulCreate         daemonset/support-cryptnono                       Created pod: support-cryptnono-6rmkq
18m         Warning   FailedDaemonPod          daemonset/support-cryptnono                       Found failed daemon pod support/support-cryptnono-jxqgh on node gke-leap-cluster-dask-huge-b3a90f26-574h, will try to kill it
18m         Normal    SuccessfulDelete         daemonset/support-cryptnono                       Deleted pod: support-cryptnono-jxqgh
16m         Normal    SuccessfulCreate         daemonset/support-cryptnono                       Created pod: support-cryptnono-k9lvj
16m         Normal    UpdatedLoadBalancer      service/support-ingress-nginx-controller          Updated load balancer with new hosts
26m         Normal    Scheduled                pod/support-prometheus-node-exporter-bzh9k        Successfully assigned support/support-prometheus-node-exporter-bzh9k to gke-leap-cluster-core-pool-1cc6bf7d-tmq0
26m         Normal    Pulling                  pod/support-prometheus-node-exporter-bzh9k        Pulling image "quay.io/prometheus/node-exporter:v1.5.0"
26m         Normal    Pulled                   pod/support-prometheus-node-exporter-bzh9k        Successfully pulled image "quay.io/prometheus/node-exporter:v1.5.0" in 11.452735399s
26m         Normal    Created                  pod/support-prometheus-node-exporter-bzh9k        Created container node-exporter
26m         Normal    Started                  pod/support-prometheus-node-exporter-bzh9k        Started container node-exporter
16m         Normal    Scheduled                pod/support-prometheus-node-exporter-hnhmf        Successfully assigned support/support-prometheus-node-exporter-hnhmf to gke-leap-cluster-dask-huge-b3a90f26-574h
16m         Normal    Pulling                  pod/support-prometheus-node-exporter-hnhmf        Pulling image "quay.io/prometheus/node-exporter:v1.5.0"
16m         Normal    Pulled                   pod/support-prometheus-node-exporter-hnhmf        Successfully pulled image "quay.io/prometheus/node-exporter:v1.5.0" in 4.595472136s
16m         Normal    Created                  pod/support-prometheus-node-exporter-hnhmf        Created container node-exporter
16m         Normal    Started                  pod/support-prometheus-node-exporter-hnhmf        Started container node-exporter
18m         Normal    Killing                  pod/support-prometheus-node-exporter-pgd4t        Stopping container node-exporter
57m         Normal    Scheduled                pod/support-prometheus-node-exporter-s967n        Successfully assigned support/support-prometheus-node-exporter-s967n to gke-leap-cluster-nb-large-3ab858ce-gmz9
57m         Normal    Pulling                  pod/support-prometheus-node-exporter-s967n        Pulling image "quay.io/prometheus/node-exporter:v1.5.0"
57m         Normal    Pulled                   pod/support-prometheus-node-exporter-s967n        Successfully pulled image "quay.io/prometheus/node-exporter:v1.5.0" in 5.175019332s
57m         Normal    Created                  pod/support-prometheus-node-exporter-s967n        Created container node-exporter
57m         Normal    Started                  pod/support-prometheus-node-exporter-s967n        Started container node-exporter
57m         Normal    SuccessfulCreate         daemonset/support-prometheus-node-exporter        (combined from similar events): Created pod: support-prometheus-node-exporter-s967n
26m         Normal    SuccessfulCreate         daemonset/support-prometheus-node-exporter        Created pod: support-prometheus-node-exporter-bzh9k
18m         Warning   FailedDaemonPod          daemonset/support-prometheus-node-exporter        Found failed daemon pod support/support-prometheus-node-exporter-pgd4t on node gke-leap-cluster-dask-huge-b3a90f26-574h, will try to kill it
18m         Normal    SuccessfulDelete         daemonset/support-prometheus-node-exporter        Deleted pod: support-prometheus-node-exporter-pgd4t
16m         Normal    SuccessfulCreate         daemonset/support-prometheus-node-exporter        Created pod: support-prometheus-node-exporter-hnhmf
57m         Normal    Preempted                pod/support-prometheus-server-548d55b8bc-hfkvk    Preempted by kube-system/calico-node-rnths on node gke-leap-cluster-core-pool-1cc6bf7d-g77w
57m         Normal    Killing                  pod/support-prometheus-server-548d55b8bc-hfkvk    Stopping container prometheus-server-configmap-reload
57m         Normal    Killing                  pod/support-prometheus-server-548d55b8bc-hfkvk    Stopping container prometheus-server
57m         Warning   FailedScheduling         pod/support-prometheus-server-548d55b8bc-mhppb    0/212 nodes are available: 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 Insufficient cpu, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 8 Insufficient memory. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
57m         Normal    NotTriggerScaleUp        pod/support-prometheus-server-548d55b8bc-mhppb    pod didn't trigger scale-up: 4 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 2 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 2 Insufficient memory, 1 Insufficient cpu, 2 max node group size reached
52m         Normal    NotTriggerScaleUp        pod/support-prometheus-server-548d55b8bc-mhppb    pod didn't trigger scale-up: 3 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 2 max node group size reached
54m         Warning   FailedScheduling         pod/support-prometheus-server-548d55b8bc-mhppb    0/212 nodes are available: 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 Insufficient cpu, 7 Insufficient memory, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
36m         Normal    NotTriggerScaleUp        pod/support-prometheus-server-548d55b8bc-mhppb    pod didn't trigger scale-up: 5 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 3 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 2 max node group size reached
31m         Normal    NotTriggerScaleUp        pod/support-prometheus-server-548d55b8bc-mhppb    (combined from similar events): pod didn't trigger scale-up: 2 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 1 Insufficient cpu, 1 Insufficient memory, 2 max node group size reached, 5 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}
29m         Warning   FailedScheduling         pod/support-prometheus-server-548d55b8bc-mhppb    0/212 nodes are available: 11 Insufficient cpu, 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 7 Insufficient memory, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
26m         Warning   FailedScheduling         pod/support-prometheus-server-548d55b8bc-mhppb    0/213 nodes are available: 1 node(s) had volume node affinity conflict, 11 Insufficient cpu, 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 7 Insufficient memory, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}. preemption: 0/213 nodes are available: 208 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
26m         Normal    SuccessfulAttachVolume   pod/support-prometheus-server-548d55b8bc-mhppb    AttachVolume.Attach succeeded for volume "pvc-9f8c30e3-b63f-4c82-a819-80ea211e77fe"
26m         Normal    Pulling                  pod/support-prometheus-server-548d55b8bc-mhppb    Pulling image "jimmidyson/configmap-reload:v0.8.0"
26m         Normal    Pulled                   pod/support-prometheus-server-548d55b8bc-mhppb    Successfully pulled image "jimmidyson/configmap-reload:v0.8.0" in 950.407348ms
26m         Normal    Created                  pod/support-prometheus-server-548d55b8bc-mhppb    Created container prometheus-server-configmap-reload
26m         Normal    Started                  pod/support-prometheus-server-548d55b8bc-mhppb    Started container prometheus-server-configmap-reload
26m         Normal    Pulling                  pod/support-prometheus-server-548d55b8bc-mhppb    Pulling image "quay.io/prometheus/prometheus:v2.41.0"
26m         Normal    Pulled                   pod/support-prometheus-server-548d55b8bc-mhppb    Successfully pulled image "quay.io/prometheus/prometheus:v2.41.0" in 5.241799705s
26m         Normal    Created                  pod/support-prometheus-server-548d55b8bc-mhppb    Created container prometheus-server
26m         Normal    Started                  pod/support-prometheus-server-548d55b8bc-mhppb    Started container prometheus-server
24m         Warning   Unhealthy                pod/support-prometheus-server-548d55b8bc-mhppb    Readiness probe failed: HTTP probe failed with statuscode: 503
57m         Normal    SuccessfulCreate         replicaset/support-prometheus-server-548d55b8bc   Created pod: support-prometheus-server-548d55b8bc-mhppb

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consideRatio commented Feb 24, 2023 •
edited
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Guessed diagnosis

  1. Leap started 200 dask worker nodes and possibly even more worker pods via dask-gateway.
  2. Since each node comes with a support-prometheus-node-exporter daemonset replica that prometheus-server detects, it will start scraping 200 additional endpoints at which it crashes or gets evicted because its memory limit is larger than its requests.
  3. Since there are 200+ nodes, the calico-typha-horizontal-autoscaler adds a few cailco-typha replicas based on configuration in a configmap, and when that happens they start eating CPU from the core node pools where they can schedule - even though they do their best to avoid each other when scheduling which also makes them spread out.
  4. Since there are 200+ nodes, the calico-typha-vertical-autoscaler may have increased the CPU requests for calico-typha pods as well eating up more CPU capacity on each node.
  5. prometheus-server that was evicted from its previous node can no longer fit on the existing nodes, and it also fails to start on new nodes as the group size is reached.

Mitigation ideas

  • I think we need to consider how to handle calico-typha or re-evaluate if in-cluster GKE managed network policy enforcement is worth it since it forces scaleups like this when bursting nodes.
  • I think we should help leap use larger nodes more effectively for dask-workers as we can't be stable for X nodes but should aim for up to for example 100 nodes and instead increased their capacity instead.
  • I think we should trim node-exporter to expose only relevant metrics, or to make prometheus-server only scrape relevant metrics depending on how that works.

@consideRatio consideRatio mentioned this issue Feb 24, 2023
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@pnasrat
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pnasrat commented Feb 24, 2023

@consideRatio thanks for you input, I was planning to look at this further today as the issue came in late in my day yesterday.

Can you walk me through the diagnosis steps to get the timeline for 1 - eg what logs and graphs did you consult, commands run etc. This would be helpful in learning effective debugging techniques for the system.

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In this case, I extracted information you had provided above and deduced most things from that based on previous experience.

In these k8s Event's associated with the prometheus-server pod, we get informed about a huge number of nodes are running which could also be discovered via https://grafana.leap.2i2c.cloud under the "Cluster something" dashboard that lists nodes.

55m         Normal    Preempted                pod/support-prometheus-server-548d55b8bc-hfkvk    Preempted by kube-system/calico-node-rnths on node gke-leap-cluster-core-pool-1cc6bf7d-g77w
55m         Normal    Killing                  pod/support-prometheus-server-548d55b8bc-hfkvk    Stopping container prometheus-server-configmap-reload
55m         Normal    Killing                  pod/support-prometheus-server-548d55b8bc-hfkvk    Stopping container prometheus-server
55m         Warning   FailedScheduling         pod/support-prometheus-server-548d55b8bc-mhppb    0/212 nodes are available: 200 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 5 Insufficient cpu, 7 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 8 Insufficient memory. preemption: 0/212 nodes are available: 207 Preemption is not helpful for scheduling, 5 No preemption victims found for incoming pod.
55m         Normal    NotTriggerScaleUp        pod/support-prometheus-server-548d55b8bc-mhppb    pod didn't trigger scale-up: 4 node(s) had untolerated taint {hub.jupyter.org_dedicated: user}, 2 node(s) had untolerated taint {k8s.dask.org_dedicated: worker}, 2 Insufficient memory, 1 Insufficient cpu, 2 max node group size reached

Looking at this again, I see that it seems that prometheus-server was pre-empted/evicted to free up CPU for calico-node which is a system critical daemonset, that perhaps got an increased CPU request via vertical autoscaler logic. I'm not sure.

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pnasrat commented Feb 24, 2023

Autoscaler logs are in GCP and can be queried eg

https://cloudlogging.app.goo.gl/a7oNtLZ5QNSZBZv5A

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pnasrat commented Feb 24, 2023 

resource.type="k8s_cluster"
resource.labels.project_id="leap-pangeo"
resource.labels.location="us-central1"
resource.labels.cluster_name="leap-cluster"
jsonPayload.decision: *
logName="projects/leap-pangeo/logs/container.googleapis.com%2Fcluster-autoscaler-visibility" severity>=DEFAULT
timestamp >= "2023-02-23T18:00:00Z" timestamp < "2023-02-23T20:00:00Z"

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pnasrat commented Feb 24, 2023

Pod logs https://cloudlogging.app.goo.gl/sPqyHAPpjpg8pxJ19

@damianavila damianavila moved this to Waiting 🕛 in Sprint Board Feb 27, 2023
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pnasrat commented Feb 27, 2023

Given there are tracking items #2209 and #2222 for sizing the core pool more robustly, I think the last action before doing this is deciding if leaving the additional node running is necessary to keep in the short term. It looks like the number of nodes has scaled down

Image

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pnasrat commented Feb 27, 2023 •
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7d core pool commitments

Image

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pnasrat commented Feb 27, 2023

Oh it looks like the node pool has already been reduced, I don't see an update in this issue (or the checklist item checked for doing this)

kubectl get node -l  cloud.google.com/gke-nodepool=core-pool
NAME                                       STATUS   ROLES    AGE     VERSION
gke-leap-cluster-core-pool-1cc6bf7d-5fnp   Ready    <none>   136d    v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-5fwt   Ready    <none>   68d     v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-g77w   Ready    <none>   4d23h   v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-rmgj   Ready    <none>   2d21h   v1.24.5-gke.600
gke-leap-cluster-core-pool-1cc6bf7d-vlbq   Ready    <none>   5d17h   v1.24.5-gke.600

Time of downsize is 06:16UTC

image

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pnasrat commented Feb 27, 2023

Ok terraform core_node_max_count = 5 so that got rolled back. If overriding that and running terraform is the correct way to temporarily increase a pool manually that probably should be documented. Searching for core_node_max_count in infra guide that should be documented.

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pnasrat commented Feb 27, 2023

I only see one scale down in the time window

logName="projects/leap-pangeo/logs/container.googleapis.com%2Fcluster-autoscaler-visibility" severity>=DEFAULT
jsonPayload.decision.scaleDown.nodesToBeRemoved: *
core-pool

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pnasrat commented Mar 7, 2023

Given the autoscaler has downsized and the mitigation issues filed as per #2248 (comment) I am closing this as no longer active.

@pnasrat pnasrat closed this as completed Mar 7, 2023
@github-project-automation github-project-automation bot moved this from Waiting 🕛 to Done 🎉 in Sprint Board Mar 7, 2023
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