@Qiaoling Tang

This looks like a duplicate of https://bugzilla.redhat.com/show_bug.cgi?id=1873652

Can you confirm that the fix is included in the EO operator image you used?

@qiaoling Tang

Did you resolve this issue on this cluster: `'0/6 nodes are available: 2 node(s) had taint {node-role.kubernetes.io/master: }, that the pod didn''t tolerate, 2 node(s) had volume node affinity conflict, 2 node(s) were unschedulable.'`?

(In reply to Periklis Tsirakidis from comment #2)
> @Qiaoling Tang
> 
> This looks like a duplicate of
> https://bugzilla.redhat.com/show_bug.cgi?id=1873652
> 
> Can you confirm that the fix is included in the EO operator image you used?

Per https://bugzilla.redhat.com/show_bug.cgi?id=1873652#c13, the bz was verified on 2020-09-16, the image tag is 4.6.0-202009192030.p0, I think the image has the fix.


> Did you resolve this issue on this cluster: `'0/6 nodes are available: 2 node(s) had taint {node-role.kubernetes.io/master: }, that the pod didn''t 
> tolerate, 2 node(s) had volume node affinity conflict, 2 node(s) were unschedulable.'`?

The unschedulable events was generated when the cluster was under upgrading. 

Upgrading cluster from 4.5 to 4.6 needs to upgrade all the nodes, the nodes were unschedulable when they were under upgrading. After the nodes were upgraded successfully, they were schedulable.

@Qiaoling Tang

I've compiled a fix and the following routine to reproduce this BZ as well as to verify the fix:

To reproduce this bug, follow these instructions:

1. Fresh install 4.5.z on a cluster
2. Install clusterlogging with 3 nodes for ES - no need for selectors
3. Wait until the setup is fully workable.
4. Upgrade the ES resource in CL CR to make the ES nodes go "Unschedulable", e.g. set memory requests/limits to an astronomic number
5. Wait until the status.nodes fields marks at least one deployment as unschedulable.
6. Switch CL+ES CR to Unmanaged
7. Delete one of the three ES deployments

To verify the fix:

1. Upgrade the operators to 4.6.0
2. Switch resources in CL CR back to normal
3. Reset Unmanaged to Managed and see what happens.

For the record, this keeps happening because the deployments get garbage collected during the cluster upgrade by kube-system's GC. However, this should not happen at all because ownerReferences ensure that the deployments stay alive. Till today, we don't know which component keeps deleting our ClusterLogging/Elasticsearch CR on different scenarios like in one as well as in [1] and [2]

[1] https://bugzilla.redhat.com/show_bug.cgi?id=1868300
[2] https://bugzilla.redhat.com/show_bug.cgi?id=1873652

For the record, here are the audit logs, telling the story that our deployments get garbage collected:

{"kind":"Event","apiVersion":"audit.k8s.io/v1","level":"Metadata","auditID":"80e425e0-2165-4e55-a705-4fca893430ee","stage":"ResponseComplete","requestURI":"/apis/apps/v1/namespaces/openshift-logging/deployments/elasticsearch-cdm-2wg9lezz-3","verb":"delete","user":{"username":"system:serviceaccount:kube-system:generic-garbage-collector","uid":"54762d94-cf4c-4103-9813-4dc2c7a9f944","groups":["system:serviceaccounts","system:serviceaccounts:kube-system","system:authenticated"]},"sourceIPs":["10.0.0.6"],"userAgent":"kube-controller-manager/v1.19.0+f5121a6 (linux/amd64) kubernetes/f5121a6/system:serviceaccount:kube-system:generic-garbage-collector","objectRef":{"resource":"deployments","namespace":"openshift-logging","name":"elasticsearch-cdm-2wg9lezz-3","apiGroup":"apps","apiVersion":"v1"},"responseStatus":{"metadata":{},"status":"Success","code":200},"requestReceivedTimestamp":"2020-09-21T02:40:18.348424Z","stageTimestamp":"2020-09-21T02:40:18.415860Z","annotations":{"authentication.k8s.io/legacy-token":"system:serviceaccount:kube-system:generic-garbage-collector","authorization.k8s.io/decision":"allow","authorization.k8s.io/reason":"RBAC: allowed by ClusterRoleBinding \"system:controller:generic-garbage-collector\" of ClusterRole \"system:controller:generic-garbage-collector\" to ServiceAccount \"generic-garbage-collector/kube-system\""}}

{"kind":"Event","apiVersion":"audit.k8s.io/v1","level":"Metadata","auditID":"9ff43d02-7740-4423-a0cb-d8e057dc1e83","stage":"ResponseComplete","requestURI":"/apis/apps/v1/namespaces/openshift-logging/deployments/elasticsearch-cdm-2wg9lezz-2","verb":"delete","user":{"username":"system:serviceaccount:kube-system:generic-garbage-collector","uid":"54762d94-cf4c-4103-9813-4dc2c7a9f944","groups":["system:serviceaccounts","system:serviceaccounts:kube-system","system:authenticated"]},"sourceIPs":["10.0.0.6"],"userAgent":"kube-controller-manager/v1.19.0+f5121a6 (linux/amd64) kubernetes/f5121a6/system:serviceaccount:kube-system:generic-garbage-collector","objectRef":{"resource":"deployments","namespace":"openshift-logging","name":"elasticsearch-cdm-2wg9lezz-2","apiGroup":"apps","apiVersion":"v1"},"responseStatus":{"metadata":{},"status":"Success","code":200},"requestReceivedTimestamp":"2020-09-21T02:40:18.458157Z","stageTimestamp":"2020-09-21T02:40:18.502307Z","annotations":{"authentication.k8s.io/legacy-token":"system:serviceaccount:kube-system:generic-garbage-collector","authorization.k8s.io/decision":"allow","authorization.k8s.io/reason":"RBAC: allowed by ClusterRoleBinding \"system:controller:generic-garbage-collector\" of ClusterRole \"system:controller:generic-garbage-collector\" to ServiceAccount \"generic-garbage-collector/kube-system\""}}

{"kind":"Event","apiVersion":"audit.k8s.io/v1","level":"Metadata","auditID":"683e3884-6971-4b85-8a44-1571e7e8fedb","stage":"ResponseComplete","requestURI":"/apis/apps/v1/namespaces/openshift-logging/deployments/elasticsearch-cdm-2wg9lezz-1","verb":"delete","user":{"username":"system:serviceaccount:kube-system:generic-garbage-collector","uid":"54762d94-cf4c-4103-9813-4dc2c7a9f944","groups":["system:serviceaccounts","system:serviceaccounts:kube-system","system:authenticated"]},"sourceIPs":["10.0.0.6"],"userAgent":"kube-controller-manager/v1.19.0+f5121a6 (linux/amd64) kubernetes/f5121a6/system:serviceaccount:kube-system:generic-garbage-collector","objectRef":{"resource":"deployments","namespace":"openshift-logging","name":"elasticsearch-cdm-2wg9lezz-1","apiGroup":"apps","apiVersion":"v1"},"responseStatus":{"metadata":{},"status":"Success","code":200},"requestReceivedTimestamp":"2020-09-21T02:40:18.554628Z","stageTimestamp":"2020-09-21T02:40:18.624505Z","annotations":{"authentication.k8s.io/legacy-token":"system:serviceaccount:kube-system:generic-garbage-collector","authorization.k8s.io/decision":"allow","authorization.k8s.io/reason":"RBAC: allowed by ClusterRoleBinding \"system:controller:generic-garbage-collector\" of ClusterRole \"system:controller:generic-garbage-collector\" to ServiceAccount \"generic-garbage-collector/kube-system\""}}

(In reply to Periklis Tsirakidis from comment #5)
> @Qiaoling Tang
> 
> I've compiled a fix and the following routine to reproduce this BZ as well
> as to verify the fix:
> 
> To reproduce this bug, follow these instructions:
> 
> 1. Fresh install 4.5.z on a cluster
> 2. Install clusterlogging with 3 nodes for ES - no need for selectors
> 3. Wait until the setup is fully workable.
> 4. Upgrade the ES resource in CL CR to make the ES nodes go "Unschedulable",
> e.g. set memory requests/limits to an astronomic number
> 5. Wait until the status.nodes fields marks at least one deployment as
> unschedulable.
> 6. Switch CL+ES CR to Unmanaged
> 7. Delete one of the three ES deployments
> 
> To verify the fix:
> 
> 1. Upgrade the operators to 4.6.0
> 2. Switch resources in CL CR back to normal
> 3. Reset Unmanaged to Managed and see what happens.

I tested with clusterlogging.4.6.0-202010061132.p0 and elasticsearch-operator.4.6.0-202010081538.p0 

After I reset Unmanaged to Managed, the EO became CrashLoopBackOff, and it couldn't recreate the ES deployment.

$ oc get pod -n openshift-operators-redhat
NAME                                      READY   STATUS             RESTARTS   AGE
elasticsearch-operator-5d75f86c7d-x44c8   0/1     CrashLoopBackOff   5          7m10s

$ oc get pod -n openshift-operators-redhat
NAME                                      READY   STATUS             RESTARTS   AGE
elasticsearch-operator-5d75f86c7d-x44c8   0/1     CrashLoopBackOff   5          7m10s
[qitang@preserve-docker-slave gcp]$ oc logs -n openshift-operators-redhat elasticsearch-operator-5d75f86c7d-x44c8
{"level":"info","ts":1602229567.48116,"logger":"elasticsearch-operator","caller":"manager/main.go:45","msg":"starting up...","operator_version":"0.0.1","go_version":"go1.15.0","go_os":"linux","go_arch":"amd64","operator-sdk_version":"v0.18.1"}
I1009 07:46:08.533427       1 request.go:621] Throttling request took 1.015335812s, request: GET:https://172.30.0.1:443/apis/template.openshift.io/v1?timeout=32s
{"level":"info","ts":1602229572.7882924,"logger":"elasticsearch-operator","caller":"runtime/proc.go:204","msg":"Registering Components.","namespace":""}
I1009 07:46:18.749922       1 request.go:621] Throttling request took 1.046099375s, request: GET:https://172.30.0.1:443/apis/template.openshift.io/v1?timeout=32s
{"level":"info","ts":1602229582.7128692,"logger":"elasticsearch-operator","caller":"manager/main.go:173","msg":"Could not create ServiceMonitor object","error":"servicemonitors.monitoring.coreos.com \"elasticsearch-operator-metrics\" already exists"}
{"level":"info","ts":1602229582.7129803,"logger":"elasticsearch-operator","caller":"runtime/proc.go:204","msg":"This operator no longer honors the image specified by the custom resources so that it is able to properly coordinate the configuration with the image.","namespace":""}
{"level":"info","ts":1602229582.712998,"logger":"elasticsearch-operator","caller":"runtime/proc.go:204","msg":"Starting the Cmd.","namespace":""}
{"level":"info","ts":1602229584.7186341,"logger":"elasticsearch-operator","caller":"kibana/controller.go:256","msg":"Registering future events","name":"openshift-logging/kibana"}
{"level":"info","ts":1602229585.06746,"logger":"elasticsearch-operator","caller":"k8shandler/status.go:291","msg":"Pruning node status","cluster":"elasticsearch","namespace":"openshift-logging","node":{"deploymentName":"elasticsearch-cdm-8heixwh2-2","upgradeStatus":{"underUpgrade":"True","upgradePhase":"nodeRestarting"},"conditions":[{"type":"Unschedulable","status":"True","lastTransitionTime":"2020-10-09T07:31:38Z","reason":"Unschedulable","message":"0/6 nodes are available: 6 Insufficient memory."}]}}
E1009 07:46:25.067702       1 runtime.go:78] Observed a panic: runtime.boundsError{x:2, y:2, signed:true, code:0x0} (runtime error: index out of range [2] with length 2)
goroutine 1550 [running]:
k8s.io/apimachinery/pkg/util/runtime.logPanic(0x16efae0, 0xc000807cc0)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/runtime/runtime.go:74 +0xa6
k8s.io/apimachinery/pkg/util/runtime.HandleCrash(0x0, 0x0, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/runtime/runtime.go:48 +0x89
panic(0x16efae0, 0xc000807cc0)
	/usr/lib/golang/src/runtime/panic.go:969 +0x175
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).pruneStatus(0xc000b96200, 0xc0002dacf0, 0x2, 0xc000524be0, 0x1c, 0xc0028da000, 0x1, 0x1)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/status.go:300 +0xa10
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).updateNodeConditions(0xc000b96200, 0xc0002dacf0, 0xc00016eba0, 0xd)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/status.go:291 +0x46f
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).UpdateClusterStatus(0xc000b96200, 0x0, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/status.go:64 +0x205
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).CreateOrUpdateElasticsearchCluster(0xc000b96200, 0x0, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/cluster.go:63 +0x21e
github.com/openshift/elasticsearch-operator/pkg/k8shandler.Reconcile(0xc000528b40, 0x19ea8a0, 0xc00033b170, 0xc0005248a0, 0x11)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/reconciler.go:65 +0x5bd
github.com/openshift/elasticsearch-operator/pkg/controller/elasticsearch.(*ReconcileElasticsearch).Reconcile(0xc000017dc0, 0xc0005248a0, 0x11, 0xc00016eba0, 0xd, 0x3d132a567, 0xc000be2120, 0xc000be2008, 0xc000be2000)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/controller/elasticsearch/controller.go:112 +0x22a
sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).reconcileHandler(0xc0001e0b40, 0x16640e0, 0xc000110140, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:256 +0x166
sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).processNextWorkItem(0xc0001e0b40, 0x203000)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:232 +0xb0
sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).worker(0xc0001e0b40)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:211 +0x2b
k8s.io/apimachinery/pkg/util/wait.BackoffUntil.func1(0xc0004ca060)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:155 +0x5f
k8s.io/apimachinery/pkg/util/wait.BackoffUntil(0xc0004ca060, 0x19a1320, 0xc0006e0210, 0x1, 0xc000a15260)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:156 +0xad
k8s.io/apimachinery/pkg/util/wait.JitterUntil(0xc0004ca060, 0x3b9aca00, 0x0, 0x1, 0xc000a15260)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:133 +0x98
k8s.io/apimachinery/pkg/util/wait.Until(0xc0004ca060, 0x3b9aca00, 0xc000a15260)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:90 +0x4d
created by sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).Start.func1
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:193 +0x32d
panic: runtime error: index out of range [2] with length 2 [recovered]
	panic: runtime error: index out of range [2] with length 2

goroutine 1550 [running]:
k8s.io/apimachinery/pkg/util/runtime.HandleCrash(0x0, 0x0, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/runtime/runtime.go:55 +0x10c
panic(0x16efae0, 0xc000807cc0)
	/usr/lib/golang/src/runtime/panic.go:969 +0x175
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).pruneStatus(0xc000b96200, 0xc0002dacf0, 0x2, 0xc000524be0, 0x1c, 0xc0028da000, 0x1, 0x1)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/status.go:300 +0xa10
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).updateNodeConditions(0xc000b96200, 0xc0002dacf0, 0xc00016eba0, 0xd)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/status.go:291 +0x46f
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).UpdateClusterStatus(0xc000b96200, 0x0, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/status.go:64 +0x205
github.com/openshift/elasticsearch-operator/pkg/k8shandler.(*ElasticsearchRequest).CreateOrUpdateElasticsearchCluster(0xc000b96200, 0x0, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/cluster.go:63 +0x21e
github.com/openshift/elasticsearch-operator/pkg/k8shandler.Reconcile(0xc000528b40, 0x19ea8a0, 0xc00033b170, 0xc0005248a0, 0x11)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/k8shandler/reconciler.go:65 +0x5bd
github.com/openshift/elasticsearch-operator/pkg/controller/elasticsearch.(*ReconcileElasticsearch).Reconcile(0xc000017dc0, 0xc0005248a0, 0x11, 0xc00016eba0, 0xd, 0x3d132a567, 0xc000be2120, 0xc000be2008, 0xc000be2000)
	/go/src/github.com/openshift/elasticsearch-operator/pkg/controller/elasticsearch/controller.go:112 +0x22a
sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).reconcileHandler(0xc0001e0b40, 0x16640e0, 0xc000110140, 0x0)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:256 +0x166
sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).processNextWorkItem(0xc0001e0b40, 0x203000)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:232 +0xb0
sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).worker(0xc0001e0b40)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:211 +0x2b
k8s.io/apimachinery/pkg/util/wait.BackoffUntil.func1(0xc0004ca060)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:155 +0x5f
k8s.io/apimachinery/pkg/util/wait.BackoffUntil(0xc0004ca060, 0x19a1320, 0xc0006e0210, 0x1, 0xc000a15260)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:156 +0xad
k8s.io/apimachinery/pkg/util/wait.JitterUntil(0xc0004ca060, 0x3b9aca00, 0x0, 0x1, 0xc000a15260)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:133 +0x98
k8s.io/apimachinery/pkg/util/wait.Until(0xc0004ca060, 0x3b9aca00, 0xc000a15260)
	/go/src/github.com/openshift/elasticsearch-operator/vendor/k8s.io/apimachinery/pkg/util/wait/wait.go:90 +0x4d
created by sigs.k8s.io/controller-runtime/pkg/internal/controller.(*Controller).Start.func1
	/go/src/github.com/openshift/elasticsearch-operator/vendor/sigs.k8s.io/controller-runtime/pkg/internal/controller/controller.go:193 +0x32d

If deploy logging 4.6, and do the following steps:

1. Install clusterlogging with 3 nodes for ES - no need for selectors
2. Wait until the setup is fully workable.
3. Upgrade the ES resource in CL CR to make the ES nodes go "Unschedulable", e.g. set memory requests/limits to an astronomic number
4. Wait until the status.nodes fields marks at least one deployment as unschedulable.
5. Switch CL+ES CR to Unmanaged
6. Delete one of the three ES deployments
7. Switch resources in CL CR back to normal
8. Reset Unmanaged to Managed and see what happens.

The EO can running as usual, but it couldn't make the ES cluster back to normal.
Logs in the EO:
{"level":"info","ts":1602229844.2539637,"logger":"elasticsearch-operator","caller":"k8shandler/clusterrestart.go:492","msg":"Beginning restart of node","node":"elasticsearch-cdm-5dqdymyw-1","cluster":"elasticsearch","namespace":"openshift-logging"}
{"level":"error","ts":1602229845.446016,"logger":"elasticsearch-operator","caller":"k8shandler/clusterrestart.go:288","msg":"Unable to perform synchronized flush","namespace":"openshift-logging","name":"elasticsearch","error":"Failed to flush 7 shards in preparation for cluster restart"}
{"level":"info","ts":1602229845.4970524,"logger":"elasticsearch-operator","caller":"retry/util.go:51","msg":"failed to update node resource","node":"elasticsearch-cdm-5dqdymyw-1","error":"Operation cannot be fulfilled on deployments.apps \"elasticsearch-cdm-5dqdymyw-1\": the object has been modified; please apply your changes to the latest version and try again"}
{"level":"info","ts":1602229905.018403,"logger":"elasticsearch-operator","caller":"k8shandler/clusterrestart.go:519","msg":"Completed restart of node","node":"elasticsearch-cdm-5dqdymyw-1","cluster":"elasticsearch","namespace":"openshift-logging"}
{"level":"info","ts":1602229905.0530834,"logger":"elasticsearch-operator","caller":"k8shandler/clusterrestart.go:492","msg":"Beginning restart of node","node":"elasticsearch-cdm-5dqdymyw-2","cluster":"elasticsearch","namespace":"openshift-logging"}
{"level":"error","ts":1602229906.0889528,"logger":"elasticsearch-operator","caller":"k8shandler/clusterrestart.go:288","msg":"Unable to perform synchronized flush","namespace":"openshift-logging","name":"elasticsearch","error":"Failed to flush 4 shards in preparation for cluster restart"}
{"level":"error","ts":1602229940.184816,"logger":"elasticsearch-operator","caller":"k8shandler/cluster.go:131","msg":"failed to perform rolling update","error":"failed to get cluster state for \"elasticsearch\". Error code: true, map[error:map[reason:<nil> root_cause:[map[reason:<nil> type:master_not_discovered_exception]] type:master_not_discovered_exception] status:503]"}
{"level":"error","ts":1602229972.703489,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230004.35125,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230035.9973016,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230067.7721658,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230099.7733471,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230131.6252205,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230163.6494224,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230195.5667257,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230227.1968317,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230259.2925787,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230291.9073987,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230323.9044044,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230355.6235714,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230387.3924816,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230419.190769,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230451.3558466,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230483.1463294,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230514.8978357,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"info","ts":1602230585.3486938,"logger":"elasticsearch-operator","caller":"k8shandler/status.go:291","msg":"Pruning node status","cluster":"elasticsearch","namespace":"openshift-logging","node":{"deploymentName":"elasticsearch-cdm-5dqdymyw-3","upgradeStatus":{"scheduledUpgrade":"True"}}}
{"level":"error","ts":1602230616.3881042,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}
{"level":"error","ts":1602230619.3374827,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: connect: connection refused"}
{"level":"error","ts":1602230678.285918,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to update node","cluster":"elasticsearch","namespace":"openshift-logging","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.220.101:9200: i/o timeout"}

$ oc get elasticsearch elasticsearch -oyaml
apiVersion: logging.openshift.io/v1
kind: Elasticsearch
metadata:
  creationTimestamp: "2020-10-09T05:48:12Z"
  generation: 6
  name: elasticsearch
  namespace: openshift-logging
  ownerReferences:
  - apiVersion: logging.openshift.io/v1
    controller: true
    kind: ClusterLogging
    name: instance
    uid: 6901675c-b8c2-4bcb-9611-0f8a116b0eff
  resourceVersion: "293498"
  selfLink: /apis/logging.openshift.io/v1/namespaces/openshift-logging/elasticsearches/elasticsearch
  uid: 2fcaf92d-ac8c-414a-868a-a07c0528dc9d
spec:
  indexManagement:
    mappings:
    - aliases:
      - app
      - logs.app
      name: app
      policyRef: app-policy
    - aliases:
      - infra
      - logs.infra
      name: infra
      policyRef: infra-policy
    - aliases:
      - audit
      - logs.audit
      name: audit
      policyRef: audit-policy
    policies:
    - name: app-policy
      phases:
        delete:
          minAge: 7d
        hot:
          actions:
            rollover:
              maxAge: 8h
      pollInterval: 15m
    - name: infra-policy
      phases:
        delete:
          minAge: 7d
        hot:
          actions:
            rollover:
              maxAge: 8h
      pollInterval: 15m
    - name: audit-policy
      phases:
        delete:
          minAge: 7d
        hot:
          actions:
            rollover:
              maxAge: 8h
      pollInterval: 15m
  managementState: Managed
  nodeSpec:
    proxyResources:
      limits:
        memory: 64Mi
      requests:
        cpu: 100m
        memory: 64Mi
    resources:
      requests:
        memory: 2Gi
  nodes:
  - genUUID: 5dqdymyw
    nodeCount: 3
    proxyResources: {}
    resources: {}
    roles:
    - client
    - data
    - master
    storage: {}
  redundancyPolicy: SingleRedundancy
status:
  cluster:
    activePrimaryShards: 0
    activeShards: 0
    initializingShards: 0
    numDataNodes: 0
    numNodes: 0
    pendingTasks: 0
    relocatingShards: 0
    status: cluster health unknown
    unassignedShards: 0
  nodes:
  - deploymentName: elasticsearch-cdm-5dqdymyw-1
    upgradeStatus:
      upgradePhase: controllerUpdated
  - deploymentName: elasticsearch-cdm-5dqdymyw-2
    upgradeStatus:
      scheduledUpgrade: "True"
      underUpgrade: "True"
      upgradePhase: nodeRestarting
  pods:
    client:
      failed: []
      notReady:
      - elasticsearch-cdm-5dqdymyw-1-58c87fd6c8-kxh68
      - elasticsearch-cdm-5dqdymyw-2-59c8fd59cd-jvvkq
      ready: []
    data:
      failed: []
      notReady:
      - elasticsearch-cdm-5dqdymyw-1-58c87fd6c8-kxh68
      - elasticsearch-cdm-5dqdymyw-2-59c8fd59cd-jvvkq
      ready: []
    master:
      failed: []
      notReady:
      - elasticsearch-cdm-5dqdymyw-2-59c8fd59cd-jvvkq
      - elasticsearch-cdm-5dqdymyw-1-58c87fd6c8-kxh68
      ready: []
  shardAllocationEnabled: shard allocation unknown

Besides, the EO works well after doing a normal upgrade(from 4.5 to 4.6).

why is this only a medium?  ES failing after upgrades sounds very severe to me.

Tested with elasticsearch-operator.4.6.0-202010130127.p0, the EO didn't become CrashLoopBackOff, but it still couldn't recreate the ES deployments after reset Unmanaged to Managed.

EO log:
{"level":"error","ts":1602577056.8270836,"logger":"elasticsearch-operator","caller":"k8shandler/reconciler.go:65","msg":"unable to restart node","cluster":"elasticsearch","namespace":"openshift-logging","node":"elasticsearch-cdm-pw6l3eqr-3","error":"Get \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\": dial tcp 172.30.212.81:9200: i/o timeout"}

    nodes:
    - genUUID: pw6l3eqr
      nodeCount: 3
      proxyResources: {}
      resources: {}
      roles:
      - client
      - data
      - master
      storage:
        size: 20Gi
        storageClassName: standard
    redundancyPolicy: SingleRedundancy
  status:
    cluster:
      activePrimaryShards: 0
      activeShards: 0
      initializingShards: 0
      numDataNodes: 0
      numNodes: 0
      pendingTasks: 0
      relocatingShards: 0
      status: cluster health unknown
      unassignedShards: 0
    nodes:
    - conditions:
      - lastTransitionTime: "2020-10-13T07:54:24Z"
        message: '0/6 nodes are available: 1 node(s) were unschedulable, 5 Insufficient memory.'
        reason: Unschedulable
        status: "True"
        type: Unschedulable
      deploymentName: elasticsearch-cdm-pw6l3eqr-3
      upgradeStatus:
        underUpgrade: "True"
        upgradePhase: nodeRestarting

$ oc get pod
NAME                                            READY   STATUS                  RESTARTS   AGE
cluster-logging-operator-5747454486-86rpq       1/1     Running                 0          15m
elasticsearch-cdm-pw6l3eqr-3-787f9bfcf7-6sc89   1/2     Running                 0          11m
elasticsearch-delete-app-1602576900-wsvg7       0/1     Error                   0          4m29s
elasticsearch-delete-audit-1602576900-24jpp     0/1     Error                   0          4m29s
elasticsearch-delete-infra-1602576900-vjmhz     0/1     Error                   0          4m29s
elasticsearch-rollover-app-1602576900-s56dr     0/1     Error                   0          4m29s
elasticsearch-rollover-audit-1602576900-vpdb9   0/1     Error                   0          4m29s
elasticsearch-rollover-infra-1602576900-nmgxp   0/1     Error                   0          4m29s
fluentd-8qcmd                                   1/1     Running                 0          34m
fluentd-9l77k                                   0/1     Init:CrashLoopBackOff   5          11m
fluentd-bfh7s                                   1/1     Running                 0          34m
fluentd-bzdkt                                   1/1     Running                 0          34m
fluentd-qqkvq                                   1/1     Running                 0          34m
fluentd-rq8c8                                   1/1     Running                 0          34m
kibana-684cd479bd-bt82s                         2/2     Running                 0          14m

(In reply to Qiaoling Tang from comment #15)
> Tested with elasticsearch-operator.4.6.0-202010130127.p0, the EO didn't
> become CrashLoopBackOff, but it still couldn't recreate the ES deployments
> after reset Unmanaged to Managed.
> 
> EO log:
> {"level":"error","ts":1602577056.8270836,"logger":"elasticsearch-operator",
> "caller":"k8shandler/reconciler.go:65","msg":"unable to restart
> node","cluster":"elasticsearch","namespace":"openshift-logging","node":
> "elasticsearch-cdm-pw6l3eqr-3","error":"Get
> \"https://elasticsearch.openshift-logging.svc:9200/_cluster/state/nodes\":
> dial tcp 172.30.212.81:9200: i/o timeout"}
> 
>     nodes:
>     - genUUID: pw6l3eqr
>       nodeCount: 3
>       proxyResources: {}
>       resources: {}
>       roles:
>       - client
>       - data
>       - master
>       storage:
>         size: 20Gi
>         storageClassName: standard
>     redundancyPolicy: SingleRedundancy
>   status:
>     cluster:
>       activePrimaryShards: 0
>       activeShards: 0
>       initializingShards: 0
>       numDataNodes: 0
>       numNodes: 0
>       pendingTasks: 0
>       relocatingShards: 0
>       status: cluster health unknown
>       unassignedShards: 0
>     nodes:
>     - conditions:
>       - lastTransitionTime: "2020-10-13T07:54:24Z"
>         message: '0/6 nodes are available: 1 node(s) were unschedulable, 5
> Insufficient memory.'
>         reason: Unschedulable
>         status: "True"
>         type: Unschedulable
>       deploymentName: elasticsearch-cdm-pw6l3eqr-3
>       upgradeStatus:
>         underUpgrade: "True"
>         upgradePhase: nodeRestarting
> 
> $ oc get pod
> NAME                                            READY   STATUS              
> RESTARTS   AGE
> cluster-logging-operator-5747454486-86rpq       1/1     Running             
> 0          15m
> elasticsearch-cdm-pw6l3eqr-3-787f9bfcf7-6sc89   1/2     Running             
> 0          11m
> elasticsearch-delete-app-1602576900-wsvg7       0/1     Error               
> 0          4m29s
> elasticsearch-delete-audit-1602576900-24jpp     0/1     Error               
> 0          4m29s
> elasticsearch-delete-infra-1602576900-vjmhz     0/1     Error               
> 0          4m29s
> elasticsearch-rollover-app-1602576900-s56dr     0/1     Error               
> 0          4m29s
> elasticsearch-rollover-audit-1602576900-vpdb9   0/1     Error               
> 0          4m29s
> elasticsearch-rollover-infra-1602576900-nmgxp   0/1     Error               
> 0          4m29s
> fluentd-8qcmd                                   1/1     Running             
> 0          34m
> fluentd-9l77k                                   0/1    
> Init:CrashLoopBackOff   5          11m
> fluentd-bfh7s                                   1/1     Running             
> 0          34m
> fluentd-bzdkt                                   1/1     Running             
> 0          34m
> fluentd-qqkvq                                   1/1     Running             
> 0          34m
> fluentd-rq8c8                                   1/1     Running             
> 0          34m
> kibana-684cd479bd-bt82s                         2/2     Running             
> 0          14m


@Qiaoling

Could you please share the link to the cluster?

Putting this back to ON_QA, because this depends on backporting: https://bugzilla.redhat.com/show_bug.cgi?id=1887357

*** Bug 1887943 has been marked as a duplicate of this bug. ***

Verified with elasticsearch-operator.4.6.0-202010132327.p0

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory (OpenShift Container Platform 4.6.1 extras update), and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://access.redhat.com/errata/RHBA-2020:4198