Merge pull request #13 from shubhMaheshwari/main

Adding YAML files to run syncthing on Nautilus clusters

k8s/first_login.yaml

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+apiVersion: v1
+kind: Pod
+metadata:
+  name: test-pod
+spec:
+  containers:
+  - name: mypod
+    image: ubuntu
+    resources:
+      limits:
+        memory: 100Mi
+        cpu: 100m
+      requests:
+        memory: 100Mi
+        cpu: 100m
+    command: ["sh", "-c", "echo 'Im a new pod' && sleep infinity"]

k8s/persistent-storage.yaml

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+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: sports-analytics-database
+spec:
+  storageClassName: rook-cephfs-central
+  accessModes:
+    - ReadWriteMany 
+  resources:
+    requests:
+      storage: 30Gi

k8s/run_muscle_activation.yaml

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+apiVersion: batch/v1
+kind: Job
+metadata:
+  namespace: spatiotemporal-decision-making
+  name: syncthing-setup
+spec:
+  template:
+    spec:
+      affinity:
+        nodeAffinity:
+          preferredDuringSchedulingIgnoredDuringExecution:
+            - weight: 1
+              preference:
+                matchExpressions:
+              # - key: topology.kubernetes.io/region
+              #   operator: In
+              #   values:
+              #   - us-west
+                - key: nautilus.io/group
+                  operator: In
+                  values:
+                  - ry
+
+      containers:
+      - name: shubh-container
+        image: gitlab-registry.nrp-nautilus.io/prp/jupyter-stack/minimal
+        command:
+        - /bin/bash
+        - -c
+        args:
+        - "echo 'Hello, World!'"
+
+        resources:
+          limits:
+            memory: 20Gi
+            cpu: 8
+            nvidia.com/gpu: "1"
+          requests:
+            memory: 15Gi
+            cpu: 4
+            nvidia.com/gpu: "1"
+
+        volumeMounts:
+        - mountPath: /dev/shm
+          name: dshm
+        - mountPath: /vol
+          name: sports-analytics-database
+
+      tolerations:
+      - key: "nautilus.io/ry-reservation"
+        operator: "Equal"
+        value: "true"
+        effect: "NoSchedule"  
+      restartPolicy: Never
+
+      volumes:
+      - name: dshm
+        emptyDir:
+          medium: Memory
+      - name: sports-analytics-database
+        persistentVolumeClaim:
+          claimName: sports-analytics-database
+  backoffLimit: 0

k8s/sync-data.sh

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+#!/bin/bash
+
+# Usage instructions
+# This script deploys Syncthing to a Kubernetes cluster to synchronize data between a local machine and a Kubernetes Pod.
+# It requires the DEVICE_ID environment variable to be set to the Syncthing device ID of the local machine.
+#
+# Usage:
+#   export DEVICE_ID="your-device-id"
+#   ./sync-data.sh
+
+# Check if DEVICE_ID is set
+if [ -z "$DEVICE_ID" ]; then
+  echo "Error: DEVICE_ID environment variable is not set. Used by Syncthing to identify the master machine."
+  echo "Set: export DEVICE_ID=\"your-device-id\""
+  exit 1
+fi
+
+# Delete the existing Pod if it exists
+kubectl delete pod data-transfer-pod --ignore-not-found
+
+# Apply the ConfigMap
+kubectl apply -f sync-data/syncthing-config.yaml
+
+# Apply the Pod
+kubectl apply -f sync-data/syncthing-setup.yaml
+
+# Wait for the Pod to be running
+echo "Waiting for the Pod to be running..."
+sleep 20
+
+# Check Pod status
+POD_STATUS=$(kubectl get pod data-transfer-pod -o jsonpath='{.status.phase}')
+if [ "$POD_STATUS" != "Running" ]; then
+  echo "Error: Pod is not running. Current status=$POD_STATUS"
+  echo "Describing the Pod..."
+  kubectl describe pod data-transfer-pod
+  echo "Fetching Pod logs..."
+  kubectl logs data-transfer-pod
+  exit 1
+fi
+
+echo "Syncthing deployment complete."
+echo "To access the Syncthing web GUI, run the following command:"
+echo "kubectl port-forward pod/data-transfer-pod 32000:8384"
+echo "Then open your browser and go to http://localhost:32000"

k8s/sync-data/syncthing-config.yaml

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+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: syncthing-config
+data:
+  config.xml: |
+    <configuration version="30">
+        <folder id="MCS_DATA" label="MCS_DATA" path="/mnt/data/MCS_DATA" type="readwrite">
+            <filesystemType>basic</filesystemType>
+            <device id="${DEVICE_ID}"/>
+        </folder>
+        <device id="${DEVICE_ID}" name="KubernetesPod" compression="metadata" introducer="false" skipIntroductionRemovals="false">
+            <address>dynamic</address>
+            <paused>false</paused>
+            <autoAcceptFolders>false</autoAcceptFolders>
+            <maxSendKbps>0</maxSendKbps>
+            <maxRecvKbps>0</maxRecvKbps>
+            <maxRequestKiB>0</maxRequestKiB>
+            <untrusted>false</untrusted>
+        </device>
+    </configuration>

k8s/sync-data/syncthing-service.yaml

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+apiVersion: v1
+kind: Service 
+metadata:
+  name: syncthing-service # Exposes the Syncthing web GUI port.
+spec:
+  selector:
+    app: syncthing
+  ports:
+    - protocol: TCP
+      port: 8384
+      targetPort: 8384
+  type: NodePort

k8s/sync-data/syncthing-setup.yaml

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+apiVersion: v1
+kind: Pod
+metadata:
+  name: data-transfer-pod
+  labels:
+    app: syncthing
+spec:
+  containers:
+  - name: syncthing
+    image: syncthing/syncthing:latest
+    ports:
+    - containerPort: 8384  # Syncthing web GUI port
+    - containerPort: 22000 # Syncthing sync port
+    - containerPort: 21027 # Syncthing discovery port
+    env:
+    - name: DEVICE_ID
+      value: "${DEVICE_ID}"
+    volumeMounts:
+    - mountPath: /mnt/data
+      name: sports-analytics-database
+    - mountPath: /var/syncthing/config
+      name: syncthing-config
+    command: ["/bin/sh"]
+    args: ["-c", "mkdir -p /mnt/data/MCS_DATA && /bin/syncthing -home=/var/syncthing/config"]
+  volumes:
+  - name: sports-analytics-database
+    persistentVolumeClaim:
+      claimName: sports-analytics-database
+  - name: syncthing-config
+    emptyDir: {}
+  restartPolicy: Never