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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,229 @@ | ||
| # The config file for the dask-enabled hub with GPU node pool | ||
| jupyterhub: | ||
| hub: | ||
| extraEnv: | ||
| DASK_DISTRIBUTED__DASHBOARD_LINK: '/user/{JUPYTERHUB_USER}/proxy/{port}/status' | ||
| config: | ||
| GitHubOAuthenticator: | ||
| client_id: <get from GitHub when you define the oauth> | ||
| client_secret: <get from GitHub when you define the oauth> | ||
| oauth_callback_url: https://<url to your hub>/hub/oauth_callback | ||
| allowed_organizations: | ||
| - <org>:<team> | ||
| - myghorg:team1 | ||
| scope: | ||
| - read:org | ||
| Authenticator: | ||
| admin_users: | ||
| - <GitHub user name> | ||
| = JupyterHub: | ||
| authenticator_class: github | ||
| KubeSpawner: | ||
| working_dir: /home/jovyan | ||
| allowNamedServers: true | ||
| networkPolicy: | ||
| # FIXME: For dask gateway | ||
| enabled: false | ||
| readinessProbe: | ||
| enabled: false | ||
| initContainers: | ||
| # Optional if you want a custom landing page | ||
| # copy https://github.com/nmfs-opensci/jupyterhub-templates as example | ||
| # template repo must be PUBLIC | ||
| - name: git-clone-templates | ||
| image: alpine/git | ||
| command: | ||
| - /bin/sh | ||
| - -c | ||
| args: | ||
| - >- | ||
| git clone --branch=master https://github.com/<your GitHub org>/jupyterhub-templates.git && | ||
| cp -r jupyterhub-templates/templates/* /templates && | ||
| cp -r jupyterhub-templates/extra-assets/* /extra-assets | ||
| volumeMounts: | ||
| - name: custom-templates | ||
| mountPath: /templates | ||
| - name: custom-templates-static | ||
| mountPath: /extra-assets | ||
| extraVolumes: | ||
| - name: custom-templates | ||
| emptyDir: {} | ||
| - name: custom-templates-static | ||
| emptyDir: {} | ||
| extraVolumeMounts: | ||
| - name: custom-templates | ||
| mountPath: /usr/local/share/jupyterhub/custom_templates | ||
| - name: custom-templates-static | ||
| mountPath: /usr/local/share/jupyterhub/static/extra_assets | ||
| extraConfig: | ||
| templates: | | ||
| c.JupyterHub.template_paths = ['/usr/local/share/jupyterhub/custom_templates/'] | ||
| proxy: | ||
| https: | ||
| enabled: true | ||
| hosts: | ||
| - fish.opensci.live | ||
| letsencrypt: | ||
| contactEmail: [email protected] | ||
| singleuser: | ||
| startTimeout: 600 | ||
| defaultUrl: /lab | ||
| storage: | ||
| capacity: 50Gi | ||
| extraVolumes: | ||
| - name: jupyterhub-shared | ||
| persistentVolumeClaim: | ||
| claimName: safshub-pvc | ||
| extraVolumeMounts: | ||
| - name: jupyterhub-shared | ||
| mountPath: /home/jovyan/shared | ||
| image: | ||
| name: openscapes/python | ||
| tag: 6ee57a9 | ||
| pullPolicy: Always | ||
| profileList: | ||
| - display_name: "Intel Xeon - Select image and RAM" | ||
| description: &profile_list_description "Start a container with at least a chosen share of capacity on a node of this type" | ||
| default: true | ||
| slug: small | ||
| profile_options: | ||
| image: &profile_options_image | ||
| display_name: Image | ||
| choices: | ||
| pyrbase: | ||
| display_name: PyR - base image R vrs 4.4 and Python vrs 3.10 | ||
| slug: pyrbase | ||
| kubespawner_override: | ||
| image: ghcr.io/nmfs-opensci/container-images/py-rocket-base:latest | ||
| pyrgeo: | ||
| display_name: PyR - Geospatial Python and R - py-rocket-geospatial latest | ||
| slug: pyrgeo | ||
| default: true | ||
| kubespawner_override: | ||
| image: ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial:latest | ||
| coastwatch: | ||
| display_name: PyR - CoastWatch - nmfs-opensci coastwatch latest | ||
| slug: coastwatch | ||
| kubespawner_override: | ||
| image: ghcr.io/nmfs-opensci/container-images/coastwatch:latest | ||
| iopython: | ||
| display_name: Py - Python w tensorflow - eeholmes iopython 20230714 | ||
| slug: iopython | ||
| kubespawner_override: | ||
| image: eeholmes/iopython:20230714 | ||
| iorocker: | ||
| display_name: R - Geospatial w sdmTMB - r-geospatial-sdm latest | ||
| slug: rgeospatialsdm | ||
| kubespawner_override: | ||
| image: ghcr.io/nmfs-opensci/container-images/r-geospatial-sdm:latest | ||
| echopype: | ||
| display_name: Py - Echopype with pangeo nmfs-opensci echopype latest | ||
| slug: echopype | ||
| kubespawner_override: | ||
| image: ghcr.io/nmfs-opensci/container-images/echopype:latest | ||
| arcgis: | ||
| display_name: Py - ArcGIS Python 3.9 | ||
| slug: arcgis | ||
| kubespawner_override: | ||
| image: ghcr.io/nmfs-opensci/container-images/arcgis:latest | ||
| requests: &profile_options_resource_allocation | ||
| display_name: Resource Allocation | ||
| choices: | ||
| mem_1_9: | ||
| display_name: 1.9 GB RAM up to 3 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 1991244775 | ||
| mem_limit: 1991244775 | ||
| cpu_guarantee: 0.2328125 | ||
| cpu_limit: 3 | ||
| default: true | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E4s_v5 | ||
| mem_3_7: | ||
| display_name: 3.7 GB RAM up to 3 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 3982489550 | ||
| mem_limit: 3982489550 | ||
| cpu_guarantee: 0.465625 | ||
| cpu_limit: 3 | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E4s_v5 | ||
| mem_7_4: | ||
| display_name: 7.4 GB RAM up to 3 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 7964979101 | ||
| mem_limit: 7964979101 | ||
| cpu_guarantee: 0.93125 | ||
| cpu_limit: 3 | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E4s_v5 | ||
| mem_14_8: | ||
| display_name: 15.1 GB RAM up to 3 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 15929958203 | ||
| mem_limit: 15929958203 | ||
| cpu_guarantee: 1.8625 | ||
| cpu_limit: 3 | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E4s_v5 | ||
| mem_28_0: | ||
| display_name: 27.3 GB RAM up to 3 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 28673924765 | ||
| mem_limit: 28673924765 | ||
| cpu_guarantee: 3 | ||
| cpu_limit: 3 | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E4s_v5 | ||
| mem_53_5: | ||
| display_name: 64 GB RAM, upto 15 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 68576867914 | ||
| mem_limit: 68576867914 | ||
| cpu_guarantee: 8 | ||
| cpu_limit: 15 | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E16s_v5 | ||
| mem_112: | ||
| display_name: 112 GB RAM, upto 15 CPUs | ||
| kubespawner_override: | ||
| mem_guarantee: 118471896889 | ||
| mem_limit: 118471896889 | ||
| cpu_guarantee: 15 | ||
| cpu_limit: 15 | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_E16s_v5 | ||
| - display_name: NVIDIA Tesla T4, 28 GB, 4 CPUs | ||
| description: "Start a container on a dedicated node with a GPU" | ||
| slug: "gpu" | ||
| profile_options: | ||
| image: | ||
| display_name: Image | ||
| choices: | ||
| pytorch: | ||
| display_name: Pangeo PyTorch ML Notebook | ||
| default: true | ||
| slug: "pytorch" | ||
| kubespawner_override: | ||
| image: "quay.io/pangeo/pytorch-notebook:2024.06.24" | ||
| tensorflow: | ||
| display_name: Pangeo TensorFlow ML Notebook | ||
| default: true | ||
| slug: "tensorflow" | ||
| kubespawner_override: | ||
| image: "quay.io/pangeo/ml-notebook:2024.06.24" | ||
| kubespawner_override: | ||
| environment: | ||
| NVIDIA_DRIVER_CAPABILITIES: compute,utility | ||
| mem_limit: null | ||
| mem_guarantee: 14G | ||
| node_selector: | ||
| node.kubernetes.io/instance-type: Standard_NC4as_T4_v3 | ||
| extra_resource_limits: | ||
| nvidia.com/gpu: "1" | ||
| dask-gateway: | ||
| gateway: | ||
| extraConfig: | ||
| idle: |- | ||
| # timeout after 30 minutes of inactivity | ||
| c.KubeClusterConfig.idle_timeout = 1800 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| To restart hub after changing `dconfig2.yaml` | ||
| ``` | ||
| helm upgrade --cleanup-on-fail --render-subchart-notes dhub dask/daskhub --namespace dhub --version=2023.1.0 --values dconfig-resource.yaml | ||
| ``` | ||
|
|
||
| `dconfig-resource.yaml` has resources | ||
|
|
||
| To get the pods | ||
| ``` | ||
| kubectl get pods -n dhub | ||
| ``` | ||
|
|
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