Merge pull request 2i2c-org#3566 from yuvipanda/resource-alloc

yuvipanda · web-flow · commit e6ed45a2b47f · 2024-01-04T10:37:41.000-08:00
Use generated resource allocation options for veda hub
diff --git a/config/clusters/nasa-veda/common.values.yaml b/config/clusters/nasa-veda/common.values.yaml
@@ -59,31 +59,147 @@ basehub:
             - wildintellect
     singleuser:
       defaultUrl: /lab
-      image:
-        name: public.ecr.aws/nasa-veda/nasa-veda-singleuser
-        # Based off pangeo/pangeo-notebook:2023.07.05 which uses JupyterLab <4, so jupyterlab-git and dask-dashboard work
-        # If updating this tag, also update it in the `profile_options.image.options.pangeo.kubespawner_override.image`below
-        tag: "5068290376e8c3151d97a36ae6485bb7ff79650b94aecc93ffb2ea1b42d76460"
       profileList:
-        # NOTE: About node sharing
-        #
-        #       CPU/Memory requests/limits are actively considered still. This
-        #       profile list is setup to involve node sharing as considered in
-        #       https://github.com/2i2c-org/infrastructure/issues/2121.
-        #
-        #       - Memory requests are different from the description, based on:
-        #         whats found to remain allocate in k8s, subtracting 1GiB
-        #         overhead for misc system pods, and transitioning from GB in
-        #         description to GiB in mem_guarantee.
-        #       - CPU requests are lower than the description, with a factor of
-        #         10%.
-        #
-        - display_name: "Small: up to 4 CPU / 32 GB RAM"
-          description: &profile_list_description "Start a container with at least a chosen share of capacity on a node of this type"
-          slug: small
+        - display_name: "Modified Pangeo Notebook"
+          slug: modified-pangeo
+          description: Pangeo based notebook with a Python environment
           default: true
+          kubespawner_override:
+            image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:5068290376e8c3151d97a36ae6485bb7ff79650b94aecc93ffb2ea1b42d76460
+            init_containers:
+              # Need to explicitly fix ownership here, as otherwise these directories will be owned
+              # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
+              - name: volume-mount-ownership-fix
+                image: busybox:1.36.1
+                command:
+                  - sh
+                  - -c
+                  - id && chown 1000:1000 /home/jovyan /home/jovyan/shared && ls -lhd /home/jovyan
+                securityContext:
+                  runAsUser: 0
+                volumeMounts:
+                  - name: home
+                    mountPath: /home/jovyan
+                    subPath: "{username}"
+                  # mounted without readonly attribute here,
+                  # so we can chown it appropriately
+                  - name: home
+                    mountPath: /home/jovyan/shared
+                    subPath: _shared
+              # this container uses nbgitpuller to mount https://github.com/NASA-IMPACT/veda-docs/ for user pods
+              # image source: https://github.com/NASA-IMPACT/veda-jh-environments/tree/main/docker-images/base/nasa-veda-singleuser-init
+              - name: nasa-veda-singleuser-init
+                image: public.ecr.aws/nasa-veda/nasa-veda-singleuser-init:38e8998f9be64b0a59ac6c4d6d152d3403121dfc4be6d49bdf52ddc92827af8a
+                command:
+                  - "python3"
+                  - "/opt/k8s-init-container-nb-docs.py"
+                  - "/home/jovyan"
+                volumeMounts:
+                  - name: home
+                    mountPath: /home/jovyan
+                    subPath: "{username}"
+                securityContext:
+                  runAsUser: 1000
+                  runAsGroup: 1000
+          profile_options: &profile_options
+            resource_allocation: &profile_options_resource_allocation
+              display_name: Resource Allocation
+              choices:
+                mem_1_9:
+                  display_name: 1.9 GB RAM, upto 3.75 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 1991341312
+                    mem_limit: 1991341312
+                    cpu_guarantee: 0.234375
+                    cpu_limit: 3.75
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.xlarge
+                  default: true
+                mem_3_7:
+                  display_name: 3.7 GB RAM, upto 3.75 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 3982682624
+                    mem_limit: 3982682624
+                    cpu_guarantee: 0.46875
+                    cpu_limit: 3.75
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.xlarge
+                mem_7_4:
+                  display_name: 7.4 GB RAM, upto 3.75 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 7965365248
+                    mem_limit: 7965365248
+                    cpu_guarantee: 0.9375
+                    cpu_limit: 3.75
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.xlarge
+                mem_14_8:
+                  display_name: 14.8 GB RAM, upto 3.75 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 15930730496
+                    mem_limit: 15930730496
+                    cpu_guarantee: 1.875
+                    cpu_limit: 3.75
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.xlarge
+                mem_29_7:
+                  display_name: 29.7 GB RAM, upto 3.75 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 31861460992
+                    mem_limit: 31861460992
+                    cpu_guarantee: 3.75
+                    cpu_limit: 3.75
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.xlarge
+
+                mem_60_7:
+                  display_name: 60.7 GB RAM, upto 15.725 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 65147242496
+                    mem_limit: 65147242496
+                    cpu_guarantee: 7.8625
+                    cpu_limit: 15.725
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.4xlarge
+                mem_121_3:
+                  display_name: 121.3 GB RAM, upto 15.725 CPUs
+                  kubespawner_override:
+                    mem_guarantee: 130294484992
+                    mem_limit: 130294484992
+                    cpu_guarantee: 15.725
+                    cpu_limit: 15.725
+                    node_selector:
+                      node.kubernetes.io/instance-type: r5.4xlarge
+        - display_name: "Rocker Geospatial with RStudio"
+          slug: rocker
+          description: R environment with many geospatial libraries pre-installed
+          kubespawner_override:
+            image: rocker/binder:4.3
+            # Launch RStudio after the user logs in
+            default_url: /rstudio
+            # Ensures container working dir is homedir
+            # https://github.com/2i2c-org/infrastructure/issues/2559
+            working_dir: /home/rstudio
+          profile_options: *profile_options
+        - display_name: "QGIS on Linux Desktop"
+          slug: qgis
+          description: Linux desktop in the browser, with qgis installed
+          kubespawner_override:
+            # Explicitly unset this - we set this to 'jupyterhub-singleuser'
+            # in basehub/values.yaml. We instead want to leave this unset,
+            # so the default command for the docker image is used instead.
+            # This is required for .desktop files to show up correctly.
+            cmd: null
+            # Launch people directly into the Linux desktop when they start
+            default_url: /desktop
+            # Built from https://github.com/jupyterhub/jupyter-remote-desktop-proxy/pull/51
+            image: "quay.io/jupyter-remote-desktop-proxy/qgis:2023-09-27"
+          profile_options: *profile_options
+        - display_name: "Bring your own image"
+          description: Specify your own docker image (must have python and jupyterhub installed in it)
+          slug: custom
           profile_options:
-            image: &image_options
+            image:
               display_name: Image
               unlisted_choice:
                 enabled: True
@@ -92,200 +208,9 @@ basehub:
                 validation_message: "Must be a publicly available docker image, of form <image-name>:<tag>"
                 kubespawner_override:
                   image: "{value}"
-              choices:
-                pangeo:
-                  display_name: Modified Pangeo Notebook
-                  default: true
-                  slug: pangeo
-                  kubespawner_override:
-                    image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:5068290376e8c3151d97a36ae6485bb7ff79650b94aecc93ffb2ea1b42d76460
-                    init_containers:
-                      # Need to explicitly fix ownership here, as otherwise these directories will be owned
-                      # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
-                      - name: volume-mount-ownership-fix
-                        image: busybox:1.36.1
-                        command:
-                          - sh
-                          - -c
-                          - id && chown 1000:1000 /home/jovyan /home/jovyan/shared && ls -lhd /home/jovyan
-                        securityContext:
-                          runAsUser: 0
-                        volumeMounts:
-                          - name: home
-                            mountPath: /home/jovyan
-                            subPath: "{username}"
-                          # mounted without readonly attribute here,
-                          # so we can chown it appropriately
-                          - name: home
-                            mountPath: /home/jovyan/shared
-                            subPath: _shared
-                      # this container uses nbgitpuller to mount https://github.com/NASA-IMPACT/veda-docs/ for user pods
-                      # image source: https://github.com/NASA-IMPACT/veda-jh-environments/tree/main/docker-images/base/nasa-veda-singleuser-init
-                      - name: nasa-veda-singleuser-init
-                        image: public.ecr.aws/nasa-veda/nasa-veda-singleuser-init:38e8998f9be64b0a59ac6c4d6d152d3403121dfc4be6d49bdf52ddc92827af8a
-                        command:
-                          - "python3"
-                          - "/opt/k8s-init-container-nb-docs.py"
-                          - "/home/jovyan"
-                        volumeMounts:
-                          - name: home
-                            mountPath: /home/jovyan
-                            subPath: "{username}"
-                        securityContext:
-                          runAsUser: 1000
-                          runAsGroup: 1000
-                qgis:
-                  display_name: QGIS on Linux Desktop
-                  slug: qgis
-                  kubespawner_override:
-                    # Explicitly unset this - we set this to 'jupyterhub-singleuser'
-                    # in basehub/values.yaml. We instead want to leave this unset,
-                    # so the default command for the docker image is used instead.
-                    # This is required for .desktop files to show up correctly.
-                    cmd: null
-                    # Launch people directly into the Linux desktop when they start
-                    default_url: /desktop
-                    # Built from https://github.com/jupyterhub/jupyter-remote-desktop-proxy/pull/51
-                    image: "quay.io/jupyter-remote-desktop-proxy/qgis:2023-09-27"
-                rocker:
-                  display_name: Rocker Geospatial with RStudio
-                  slug: rocker
-                  kubespawner_override:
-                    image: rocker/binder:4.3
-                    # Launch RStudio after the user logs in
-                    default_url: /rstudio
-                    # Ensures container working dir is homedir
-                    # https://github.com/2i2c-org/infrastructure/issues/2559
-                    working_dir: /home/rstudio
-                    init_containers:
-                      # Need to explicitly fix ownership here, as otherwise these directories will be owned
-                      # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid
-                      - name: volume-mount-ownership-fix
-                        image: busybox:1.36.1
-                        command:
-                          [
-                            "sh",
-                            "-c",
-                            "id && chown 1000:1000 /home/rstudio && ls -lhd /home/rstudio ",
-                          ]
-                        securityContext:
-                          runAsUser: 0
-                        volumeMounts:
-                          - name: home
-                            mountPath: /home/rstudio
-                            subPath: "{username}"
-                      # this container uses nbgitpuller to mount https://github.com/NASA-IMPACT/veda-docs/ for user pods
-                      # image source: https://github.com/NASA-IMPACT/veda-jh-environments/tree/main/docker-images/base/nasa-veda-singleuser-init
-                      - name: nasa-veda-singleuser-init
-                        image: public.ecr.aws/nasa-veda/nasa-veda-singleuser-init:38e8998f9be64b0a59ac6c4d6d152d3403121dfc4be6d49bdf52ddc92827af8a
-                        command:
-                          - "python3"
-                          - "/opt/k8s-init-container-nb-docs.py"
-                          - "/home/rstudio"
-                        volumeMounts:
-                          - name: home
-                            mountPath: /home/rstudio
-                            subPath: "{username}"
-                        securityContext:
-                          runAsUser: 1000
-                          runAsGroup: 1000
-            requests:
-              # NOTE: Node share choices are in active development, see comment
-              #       next to profileList: above.
-              display_name: Node share
-              choices:
-                mem_1:
-                  default: true
-                  display_name: ~1 GB, ~0.125 CPU
-                  kubespawner_override:
-                    mem_guarantee: 0.904G
-                    cpu_guarantee: 0.013
-                mem_2:
-                  display_name: ~2 GB, ~0.25 CPU
-                  kubespawner_override:
-                    mem_guarantee: 1.809G
-                    cpu_guarantee: 0.025
-                mem_4:
-                  display_name: ~4 GB, ~0.5 CPU
-                  kubespawner_override:
-                    mem_guarantee: 3.617G
-                    cpu_guarantee: 0.05
-                mem_8:
-                  display_name: ~8 GB, ~1.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 7.234G
-                    cpu_guarantee: 0.1
-                mem_16:
-                  display_name: ~16 GB, ~2.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 14.469G
-                    cpu_guarantee: 0.2
-                mem_32:
-                  display_name: ~32 GB, ~4.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 28.937G
-                    cpu_guarantee: 0.4
-          kubespawner_override:
-            cpu_limit: null
-            mem_limit: null
-            node_selector:
-              node.kubernetes.io/instance-type: r5.xlarge
-        - display_name: "Medium: up to 16 CPU / 128 GB RAM"
-          description: *profile_list_description
-          slug: medium
-          profile_options:
-            image: *image_options
-            requests:
-              # NOTE: Node share choices are in active development, see comment
-              #       next to profileList: above.
-              display_name: Node share
-              choices:
-                mem_1:
-                  display_name: ~1 GB, ~0.125 CPU
-                  kubespawner_override:
-                    mem_guarantee: 0.942G
-                    cpu_guarantee: 0.013
-                mem_2:
-                  display_name: ~2 GB, ~0.25 CPU
-                  kubespawner_override:
-                    mem_guarantee: 1.883G
-                    cpu_guarantee: 0.025
-                mem_4:
-                  default: true
-                  display_name: ~4 GB, ~0.5 CPU
-                  kubespawner_override:
-                    mem_guarantee: 3.766G
-                    cpu_guarantee: 0.05
-                mem_8:
-                  display_name: ~8 GB, ~1.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 7.532G
-                    cpu_guarantee: 0.1
-                mem_16:
-                  display_name: ~16 GB, ~2.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 15.064G
-                    cpu_guarantee: 0.2
-                mem_32:
-                  display_name: ~32 GB, ~4.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 30.128G
-                    cpu_guarantee: 0.4
-                mem_64:
-                  display_name: ~64 GB, ~8.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 60.257G
-                    cpu_guarantee: 0.8
-                mem_128:
-                  display_name: ~128 GB, ~16.0 CPU
-                  kubespawner_override:
-                    mem_guarantee: 120.513G
-                    cpu_guarantee: 1.6
-          kubespawner_override:
-            cpu_limit: null
-            mem_limit: null
-            node_selector:
-              node.kubernetes.io/instance-type: r5.4xlarge
+              choices: {}
+            resource_allocation: *profile_options_resource_allocation
+
     scheduling:
       userScheduler:
         enabled: true
diff --git a/deployer/commands/generate/resource_allocation/instance_capacities.yaml b/deployer/commands/generate/resource_allocation/instance_capacities.yaml
@@ -131,9 +131,9 @@ r5.4xlarge:
   cpu_capacity_high: 16.0
   cpu_allocatable_low: 15.89
   cpu_allocatable_high: 15.89
-  mem_capacity_low: 124.364Gi
+  mem_capacity_low: 124.353Gi
   mem_capacity_high: 124.364Gi
-  mem_allocatable_low: 121.504Gi
+  mem_allocatable_low: 121.492Gi
   mem_allocatable_high: 121.504Gi
 m5.large:
   cpu_capacity_low: 2.0
diff --git a/deployer/commands/generate/resource_allocation/node-capacity-info.json b/deployer/commands/generate/resource_allocation/node-capacity-info.json
