Migrate Farallon Staging hub to this repository.

config/hubs/farallon.cluster.yaml

@@ -0,0 +1,196 @@
+name: farallon
+provider: kubeconfig
+kubeconfig:
+  file: secrets/farallon.yaml
+hubs:
+  - name: farallon-staging
+    domain: staging.farallon.2i2c.cloud
+    template: daskhub
+    auth0:
+      connection: github
+    config:
+      scratchBucket:
+        enabled: false
+      basehub:
+        nfsPVC:
+          nfs:
+            # from https://docs.aws.amazon.com/efs/latest/ug/mounting-fs-nfs-mount-settings.html
+            mountOptions:
+            - rsize=1048576
+            - wsize=1048576 
+            - timeo=600
+            - soft # We pick soft over hard, so NFS lockups don't lead to hung processes
+            - retrans=2
+            - noresvport
+            serverIP: fs-7b129903.efs.us-east-2.amazonaws.com
+            baseShareName: /homes/
+          shareCreator:
+            tolerations:
+            - key: node-role.kubernetes.io/master
+              operator: "Exists"
+              effect: "NoSchedule"
+        jupyterhub:
+          homepage:
+            templateVars:
+              org:
+                name: Farallon Institute
+                logo_url: https://2i2c.org/media/logo.png
+                url: http://www.faralloninstitute.org/
+              designed_by:
+                name: 2i2c
+                url: https://2i2c.org
+              operated_by:
+                name: 2i2c
+                url: https://2i2c.org
+              funded_by:
+                name: Farallon Institute
+                urL: http://www.faralloninstitute.org/
+          singleuser:
+            initContainers:
+              # Need to explicitly fix ownership here, since EFS doesn't do anonuid
+            - name: volume-mount-ownership-fix
+              image: busybox
+              command: ["sh", "-c", "id && chown 1000:1000 /home/jovyan && ls -lhd /home/jovyan"]
+              securityContext:
+                runAsUser: 0
+              volumeMounts:
+              - name: home
+                mountPath: /home/jovyan
+                subPath: "{username}"
+            image:
+              name: 677861182063.dkr.ecr.us-east-2.amazonaws.com/2i2c-hub/user-image
+              tag: 9cd76f1
+            profileList:
+              # The mem-guarantees are here so k8s doesn't schedule other pods
+              # on these nodes.
+              - display_name: "Default: m5.xlarge"
+                description: "~4CPUs & ~15GB RAM"
+                kubespawner_override:
+                  # Expllicitly unset mem_limit, so it overrides the default memory limit we set in
+                  # basehub/values.yaml
+                  mem_limit: null
+                  mem_guarantee: 14G
+                  cpu_guarantee: 3
+                  node_selector:
+                    hub.jupyter.org/pool-name: notebook-m5-xlarge
+              - display_name: "Default: m5.2xlarge"
+                description: "~8CPUs & ~30GB RAM"
+                kubespawner_override:
+                  # Expllicitly unset mem_limit, so it overrides the default memory limit we set in
+                  # basehub/values.yaml
+                  mem_limit: null
+                  mem_guarantee: 28G
+                  cpu_guarantee: 7
+                  node_selector:
+                    hub.jupyter.org/pool-name: notebook-m5-2xlarge
+          scheduling:
+            userPlaceholder:
+              enabled: false
+              replicas: 0
+            userScheduler:
+              enabled: false
+          proxy:
+            service:
+              type: LoadBalancer
+            https:
+              enabled: true
+              hosts:
+              - staging.farallon.2i2c.cloud 
+            chp:
+              nodeSelector: {}
+              tolerations:
+                - key:  "node-role.kubernetes.io/master"
+                  effect: "NoSchedule"
+            traefik:
+              nodeSelector: {}
+              tolerations:
+                - key:  "node-role.kubernetes.io/master"
+                  effect: "NoSchedule"
+          hub:
+            allowNamedServers: true
+            networkPolicy:
+              # FIXME: For dask gateway
+              enabled: false
+            readinessProbe:
+              enabled: false
+            nodeSelector: {}
+            tolerations:
+              - key:  "node-role.kubernetes.io/master"
+                effect: "NoSchedule"
+      dask-gateway:
+        traefik:
+          tolerations:
+            - key:  "node-role.kubernetes.io/master"
+              effect: "NoSchedule"
+        controller:
+          tolerations:
+            - key:  "node-role.kubernetes.io/master"
+              effect: "NoSchedule"
+        gateway:
+          tolerations:
+            - key:  "node-role.kubernetes.io/master"
+              effect: "NoSchedule"
+          backend:
+            scheduler:
+              extraPodConfig:
+                nodeSelector:
+                  hub.jupyter.org/pool-name: dask-worker
+                tolerations:
+                  - key: "k8s.dask.org/dedicated"
+                    operator: "Equal"
+                    value: "worker"
+                    effect: "NoSchedule"
+                  - key: "k8s.dask.org_dedicated"
+                    operator: "Equal"
+                    value: "worker"
+                    effect: "NoSchedule"
+            worker:
+              extraPodConfig:
+                nodeSelector:
+                  hub.jupyter.org/pool-name: dask-worker
+                tolerations:
+                  - key: "k8s.dask.org/dedicated"
+                    operator: "Equal"
+                    value: "worker"
+                    effect: "NoSchedule"
+                  - key: "k8s.dask.org_dedicated"
+                    operator: "Equal"
+                    value: "worker"
+                    effect: "NoSchedule"
+
+            # TODO: figure out a replacement for userLimits.
+          extraConfig:
+            optionHandler: |
+              from dask_gateway_server.options import Options, Integer, Float, String
+              def cluster_options(user):
+                def option_handler(options):
+                    if ":" not in options.image:
+                        raise ValueError("When specifying an image you must also provide a tag")
+                    extra_annotations = {
+                        "hub.jupyter.org/username": user.name,
+                        "prometheus.io/scrape": "true",
+                        "prometheus.io/port": "8787",
+                    }
+                    extra_labels = {
+                        "hub.jupyter.org/username": user.name,
+                    }
+                    return {
+                        "worker_cores_limit": options.worker_cores,
+                        "worker_cores": min(options.worker_cores / 2, 1),
+                        "worker_memory": "%fG" % options.worker_memory,
+                        "image": options.image,
+                        "scheduler_extra_pod_annotations": extra_annotations,
+                        "worker_extra_pod_annotations": extra_annotations,
+                        "scheduler_extra_pod_labels": extra_labels,
+                        "worker_extra_pod_labels": extra_labels,
+                    }
+                return Options(
+                    Integer("worker_cores", 2, min=1, max=16, label="Worker Cores"),
+                    Float("worker_memory", 4, min=1, max=32, label="Worker Memory (GiB)"),
+                    String("image", default="pangeo/pangeo-notebook:latest", label="Image"),
+                    handler=option_handler,
+                )
+              c.Backend.cluster_options = cluster_options
+            idle: |
+              # timeout after 30 minutes of inactivity
+              c.KubeClusterConfig.idle_timeout = 1800

config/hubs/schema.yaml

@@ -14,9 +14,23 @@ properties:
     type: string
     description: |
       Cloud provider this cluster is running on. Used to perform
-      authentication against the cluster. Currently supports gcp.
+      authentication against the cluster. Currently supports gcp
+      and raw kubeconfig files.
     enum: 
       - gcp
+      - kubeconfig
+  kubeconfig:
+    type: object
+    description: |
+      Configuration to connect to a cluster purely via a kubeconfig
+      file. 
+    additionalProperties: false
+    properties:
+      file:
+        type: string
+        descriptiON: |
+          Path to kubeconfig file (encrypted with sops) to use for
+          connecting to the cluster
   gcp:
     type: object
     additionalProperties: false

deployer/hub.py

@@ -37,12 +37,30 @@ def build_image(self):
 
     @contextmanager
     def auth(self):
-        with tempfile.NamedTemporaryFile() as kubeconfig:
-            # FIXME: This is dumb
-            os.environ['KUBECONFIG'] = kubeconfig.name
-            assert self.spec['provider'] == 'gcp'
-
+        if self.spec['provider'] == 'gcp':
             yield from self.auth_gcp()
+        elif self.spec['provider'] == 'kubeconfig':
+            yield from self.auth_kubeconfig()
+        else:
+            raise ValueError(f'Provider {self.spec["provider"]} not supported')
+
+
+    def auth_kubeconfig(self):
+        """
+        Context manager for authenticating with just a kubeconfig file
+
+        For the duration of the contextmanager, we:
+        1. Decrypt the file specified in kubeconfig.file with sops
+        2. Set `KUBECONFIG` env var to our decrypted file path, so applications
+           we call (primarily helm) will use that as config
+        """
+        config = self.spec['kubeconfig']
+        config_path = config['file']
+
+        with decrypt_file(config_path) as decrypted_key_path:
+            # FIXME: Unset this after our yield
+            os.environ['KUBECONFIG'] = decrypted_key_path
+            yield
 
     def auth_gcp(self):
         config = self.spec['gcp']
@@ -52,23 +70,23 @@ def auth_gcp(self):
         # Else, it'll just have a `zone` key set. Let's respect either.
         location = config.get('zone', config.get('region'))
         cluster = config['cluster']
+        with tempfile.NamedTemporaryFile() as kubeconfig:
+            with decrypt_file(key_path) as decrypted_key_path:
+                subprocess.check_call([
+                    'gcloud', 'auth',
+                    'activate-service-account',
+                    '--key-file', os.path.abspath(decrypted_key_path)
+                ])
 
-        with decrypt_file(key_path) as decrypted_key_path:
             subprocess.check_call([
-                'gcloud', 'auth',
-                'activate-service-account',
-                '--key-file', os.path.abspath(decrypted_key_path)
+                'gcloud', 'container', 'clusters',
+                # --zone works with regions too
+                f'--zone={location}',
+                f'--project={project}',
+                'get-credentials', cluster
             ])
 
-        subprocess.check_call([
-            'gcloud', 'container', 'clusters',
-            # --zone works with regions too
-            f'--zone={location}',
-            f'--project={project}',
-            'get-credentials', cluster
-        ])
-
-        yield
+            yield
 
 
 class Hub:

hub-templates/basehub/templates/cloud-resources/gcp/service-account.yaml

@@ -37,11 +37,4 @@ spec:
     apiVersion: resourcemanager.cnrm.cloud.google.com/v1beta1
     kind: Project
     external: projects/{{ .Values.jupyterhub.cloudResources.gcp.projectId }}
----
-apiVersion: v1
-kind: ServiceAccount
-metadata:
-  annotations:
-    iam.gke.io/gcp-service-account: {{ include "cloudResources.gcp.serviceAccountName" .}}@{{ .Values.jupyterhub.cloudResources.gcp.projectId }}.iam.gserviceaccount.com
-  name: user-sa
 {{- end }}

hub-templates/basehub/templates/nfs-pvc.yaml

@@ -11,10 +11,7 @@ spec:
   nfs:
     server: {{ .Values.nfsPVC.nfs.serverIP | quote}}
     path: "{{ .Values.nfsPVC.nfs.baseShareName }}{{ .Release.Name }}"
-  mountOptions:
-    - soft
-    - noatime
-    - vers=4.2
+  mountOptions: {{ .Values.nfsPVC.nfs.mountOptions | toJson }}
 ---
 apiVersion: v1
 kind: PersistentVolumeClaim

hub-templates/basehub/templates/nfs-share-creator.yaml

@@ -22,6 +22,8 @@ spec:
     spec:
       restartPolicy: Never
       terminationGracePeriodSeconds: 0
+      tolerations: {{ .Values.nfsPVC.shareCreator.tolerations | toJson }}
+
       containers:
         - name: dummy
           image: busybox

hub-templates/basehub/templates/user-sa.yaml

@@ -0,0 +1,10 @@
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  annotations:
+    {{ if .Values.jupyterhub.cloudResources.scratchBucket.enabled}}
+    {{ if eq .Values.jupyterhub.cloudResources.provider "gcp" }}
+    iam.gke.io/gcp-service-account: {{ include "cloudResources.gcp.serviceAccountName" .}}@{{ .Values.jupyterhub.cloudResources.gcp.projectId }}.iam.gserviceaccount.com
+    {{- end }}
+    {{- end }}
+  name: user-sa

hub-templates/basehub/values.yaml

@@ -19,6 +19,10 @@ nfsPVC:
   shareCreator:
     tolerations: []
   nfs:
+    mountOptions:
+      - soft
+      - noatime
+      - vers=4.2
     serverIP: nfs-server-01
     # MUST HAVE TRAILING SLASH
     baseShareName: /export/home-01/homes/