wip

.github/workflows/spatial-image.yml

@@ -0,0 +1,25 @@
+name: Docker Spatial Image
+on:
+  workflow_dispatch: null
+  push:
+    paths: ['images/*']
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v3
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'boettiger-lab/k8s'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Build the Docker image
+        if: github.repository == 'boettiger-lab/k8s'
+        run: docker build images/ -f images/Dockerfile.spatial --tag ghcr.io/boettiger-lab/spatial:latest
+      - name: Publish
+        if: github.repository == 'boettiger-lab/k8s'
+        run: docker push ghcr.io/boettiger-lab/spatial:latest
+

images/Dockerfile.spatial

@@ -0,0 +1,4 @@
+FROM ghcr.io/boettiger-lab/k8s 
+
+RUN pip install -U --find-links https://girder.github.io/large_image_wheels GDAL
+

initial-setup.sh

@@ -11,6 +11,9 @@
 # Otherwise, to use jupyter's cert manager, or manual caddy, do:
 curl -sfL https://get.k3s.io | sh -s - --disable=traefik 
 
+echo "export KUBECONFIG=/etc/rancher/k3s/k3s.yaml" >> ~/.bashrc
+source ~/.bashrc
+sudo chown $(id -u) /etc/rancher/k3s/k3s.yaml
 
 # Install Helm
 # ============================
@@ -19,15 +22,7 @@ curl https://raw.githubusercontent.com/helm/helm/main/scripts/get-helm-3 | bash
 # Enable GPU + timeslicing
 # ============================
 
-helm upgrade -i nvdp nvdp/nvidia-device-plugin \
-  --namespace nvidia-device-plugin \
-  --create-namespace \
-  --version 0.14.3 \
-  --wait \
-  --values nvidia/nvidia-device-plugin-config.yaml
-
-# identically:
-# bash nvidia/nvidia-device-plugin.sh
+bash nvidia/nvidia-device-plugin.sh
 
 
 

jupyterhub/jupyterhub.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+helm repo add jupyterhub https://hub.jupyter.org/helm-chart/
+helm repo update
 
 ## use your name for install name and namespace name
 helm upgrade --cleanup-on-fail \

jupyterhub/public-config.yaml

@@ -14,6 +14,7 @@ proxy:
     type: NodePort
 singleuser:
   storage:
+    capacity: 60Gi
     extraVolumeMounts:
       - name: "volume-{username}{servername}"
         mountPath: /home/rstudio
@@ -26,21 +27,21 @@ singleuser:
           display_name: Resource Allocation
           choices:
             small:
-              display_name: Small (1.9 GB RAM)
+              display_name: Small (8 GB RAM)
               kubespawner_override:
-                mem_guarantee: 1991341312
-                mem_limit: 1991341312
+                mem_guarantee: 7991341312
+                mem_limit: 7991341312
               default: true
             med:
-              display_name: Medium (14.8 GB RAM)
+              display_name: Medium (16 GB RAM)
               kubespawner_override:
                 mem_guarantee: 15930730496
                 mem_limit: 15930730496
             large:
-              display_name: Large (29.7 GB RAM)
+              display_name: Large (60 GB RAM)
               kubespawner_override:
-                mem_guarantee: 31861460992
-                mem_limit: 31861460992
+                mem_guarantee: 59861460992
+                mem_limit: 59861460992
       kubespawner_override:
         image: ghcr.io/boettiger-lab/k8s:latest
         default_url: /lab # change to /rstudio to go straight to RStudio
@@ -86,10 +87,10 @@ hub:
         - cboettig 
     GitHubOAuthenticator:
       allowed_organizations:
-        - espm-288 
+        - boettiger-lab
       scope:
         - read:org
-      oauth_callback_url: https://jupyterhub.thelio.carlboettiger.info/hub/oauth_callback
+      oauth_callback_url: https://jupyterhub.cirrus.carlboettiger.info/hub/oauth_callback
     JupyterHub:
       authenticator_class: github
 

nvidia/nvidia-device-plugin.sh

@@ -1,9 +1,12 @@
 #!/bin/bash
+helm repo add nvdp https://nvidia.github.io/k8s-device-plugin
+helm repo update
+
 helm upgrade -i nvdp nvdp/nvidia-device-plugin \
   --namespace nvidia-device-plugin \
   --create-namespace \
   --version 0.14.3 \
   --wait \
-  --values nvidia-device-plugin-config.yaml
+  --values nvidia/nvidia-device-plugin-config.yaml