Added kubernetes deployment.

Federated-Deployment/kubernetes/Chart.yaml

+apiVersion: v2
+name: exareme
+description: A helm chart for Kubernetes deployment of Exareme
+
+version: 0.1.0
+
+type: application
+

Federated-Deployment/kubernetes/DevDeployment.md

+# Exareme Development deployment with Kubernetes in one node
+
+## Configuration
+
+The following packages need to be installed:
+
+```
+docker
+kubectl
+helm
+```
+
+## Setup the kubernetes cluster with kind
+
+1. Create the cluster using the e2e_tests setup (you can create a custom one if you want) :
+```
+kind create cluster --config Federated-Deployment/kubernetes/kind_configuration/kind_cluster.yaml 
+```
+
+2. After the nodes are started, you need to taint them properly:
+```
+kubectl taint nodes kind-control-plane node-role.kubernetes.io/master-
+kubectl label node kind-control-plane nodeType=master
+kubectl label node kind-worker nodeType=worker
+kubectl label node kind-worker2 nodeType=worker
+```
+
+3. (Optional) Load the docker images to the kuberentes cluster, if not the images will be pulled from dockerhub:
+```
+kind load docker-image hbpmip/exareme:latest
+```
+
+4. Deploy the MIP-Engine kubernetes pods using helm charts:
+```
+helm install exareme Federated-Deployment/kubernetes/
+```

Federated-Deployment/kubernetes/README.md

-# Deploy exareme with Kubernetes
+# Exareme deployment with Kubernetes
 
+## Configuration
+
+The following packages need to be installed on **master/worker** nodes:
+
+```
+docker
+kubelet
+kubeadm
+```
+
+Packages needed on the **master** node only:
+
+```
+helm
+```
+
+To configure kubernetes to use docker you should also follow this [guide](https://kubernetes.io/docs/setup/production-environment/container-runtimes/#docker "guide") .
+
+## Cluster Management
+
+### Initialize the cluster
+
+On the **master** node:
+
+1. Run the following command to initialize the cluster:
+
+```
+sudo kubeadm init --pod-network-cidr=192.168.0.0/16
+```
+
+2. To enable kubectl run the following commands as prompted from the previous command:
+
+```
+mkdir -p $HOME/.kube
+sudo cp -i /etc/kubernetes/admin.conf $HOME/.kube/config
+sudo chown $(id -u):$(id -g) $HOME/.kube/config
+```
+
+3. Add calico network tool in the cluster:
+
+```
+kubectl apply -f https://docs.projectcalico.org/v3.20/manifests/calico.yaml
+```
+
+4. Allow master-specific pods to run on the **master** node with:
+
+```
+kubectl taint nodes --all node-role.kubernetes.io/master-
+kubectl label node <master-node-name> nodeType=master
+```
+
+### Add a worker node to the cluster
+
+1. On the **master** node, get the join token with the following command:
+
+```
+kubeadm token create --print-join-command
+```
+
+Use the provided on the **worker** node, with `sudo`, to join the cluster.
+
+2. Allow worker-specific pods to run on the **worker** node with:
+
+```
+kubectl label node <worker-node-name> nodeType=worker
+```
+
+3. If the node has status `Ready,SchedulingDisabled` run:
+
+```
+kubectl uncordon <node-name>
+```
+
+### Remove a worker node from the cluster
+
+On the **master** node execute the following commands:
+
+```
+kubectl drain <node-name> --ignore-daemonsets
+kubectl delete node <node-name>
+```
+
+## Deploy Exareme
+
+1. Configure the [helm chart values](values.yaml).
+
+   - The `exareme_images -> version` should be the exareme services' version in dockerhub.
+   - The `data_path` should be set to the path, in the workers' host machine, that contains the data. 
+   - The `workers` is a counter for the amount of workers in the cluster.
+
+1. From the `exareme` folder, deploy the services:
+
+```
+helm install exareme Federated-Deployment/kubernetes/
+```
+
+### Change the Exareme version running
+
+1. Modify the `exareme_images -> version` value in the [helm chart values](values.yaml) accordingly.
+
+1. Upgrade the helm chart with:
+
+```
+helm upgrade exareme Federated-Deployment/kubernetes/
+```
+
+### Increase/reduce the number of workers
+
+1. Modify the `workers` value in the [helm chart values](values.yaml) accordingly.
+
+1. Upgrade the helm chart with:
+
+```
+helm upgrade exareme Federated-Deployment/kubernetes/
+```
+
+### Restart the federation
+
+You can restart the federation with helm by running:
+
+```
+helm uninstall exareme
+helm install exareme Federated-Deployment/kubernetes/
+```
+
+## Firewall Configuration
+
+Using firewalld the following rules should apply,
+
+in the **master** node:
+
+```
+firewall-cmd --permanent --add-port=6443/tcp       # Kubelet api port
+firewall-cmd --permanent --add-port=30000/tcp      # MIPEngine Controller port
+```
+
+on all nodes:
+
+```
+firewall-cmd --zone=public --permanent --add-rich-rule='rule protocol value="ipip" accept'  # Protocol "4" for "calico"-network-plugin.
+```
+
+These rules allow for kubectl to only be run on the **master** node.

Federated-Deployment/kubernetes/kind_configuration/kind_cluster.yaml

+kind: Cluster
+apiVersion: kind.x-k8s.io/v1alpha4
+nodes:
+- role: control-plane
+  extraPortMappings:
+  - containerPort: 30000
+    hostPort: 9090
+  - containerPort: 30050
+    hostPort: 8500
+  extraMounts:
+  - hostPath: /opt/exareme_data_1
+    containerPath: /opt/data
+- role: worker
+  extraMounts:
+  - hostPath: /opt/exareme_data_2
+    containerPath: /opt/data
+- role: worker
+  extraMounts:
+  - hostPath: /opt/exareme_data_3
+    containerPath: /opt/data

Federated-Deployment/kubernetes/exareme-keystore.yaml → Federated-Deployment/kubernetes/templates/exareme-keystore.yaml

@@ -46,4 +46,4 @@ spec:
     - protocol: TCP
       port: 8500
       targetPort: 8500
-      nodePort: 30000
\ No newline at end of file
+      nodePort: 30050
\ No newline at end of file

Federated-Deployment/kubernetes/exareme-master.yaml → Federated-Deployment/kubernetes/templates/exareme-master.yaml

@@ -18,33 +18,34 @@ spec:
         nodeType: master
       containers:
       - name: exareme-master
-        image: hbpmip/exareme:24.1.2
+        image: {{ .Values.exareme_images.repository }}/exareme:{{ .Values.exareme_images.version }}
+        imagePullPolicy: IfNotPresent
         ports:
           - containerPort: 9090
         volumeMounts:
         - mountPath: /root/exareme/data
-          name: csvs
+          name: data
         env:
+        - name: ENVIRONMENT_TYPE
+          value: "{{ .Values.exareme.environment_type }}"
+        - name: LOG_LEVEL
+          value: "{{ .Values.exareme.log_level }}"
+        - name: CONVERT_CSVS
+          value: "{{ .Values.exareme.convert_csvs }}"
+        - name: TEMP_FILES_CLEANUP_TIME
+          value: "{{ .Values.exareme.temp_file_cleanup_time }}"
+        - name: NODE_COMMUNICATION_TIMEOUT
+          value: "{{ .Values.exareme.node_communication_timeout }}"
         - name: CONSULURL
           value: "exareme-keystore-service:8500"
         - name: FEDERATION_ROLE
           value: "master"
         - name: NODE_NAME
           value: "master"
-        - name: TEMP_FILES_CLEANUP_TIME
-          value: "30"
-        - name: NODE_COMMUNICATION_TIMEOUT
-          value: "30000"
-        - name: ENVIRONMENT_TYPE
-          value: "PROD"
-        - name: LOG_LEVEL
-          value: "INFO"
-        - name: CONVERT_CSVS
-          value: "TRUE"
       volumes:
-      - name: csvs
+      - name: data
         hostPath:
-          path: /etc/exareme
+          path: {{ .Values.data_path }}
 
 ---
 
@@ -60,4 +61,4 @@ spec:
     - protocol: TCP
       port: 9090
       targetPort: 9090
-      nodePort: 30090
+      nodePort: 30000

Federated-Deployment/kubernetes/exareme-worker.yaml → Federated-Deployment/kubernetes/templates/exareme-worker.yaml

@@ -5,7 +5,7 @@ metadata:
   labels:
     app: exareme-worker
 spec:
-  replicas: 2
+  replicas: {{ .Values.workers }}
   selector:
     matchLabels:
       app: exareme-worker
@@ -28,32 +28,33 @@ spec:
             topologyKey: "kubernetes.io/hostname"
       containers:
       - name: exareme-worker
-        image: hbpmip/exareme:24.1.2
+        image: {{ .Values.exareme_images.repository }}/exareme:{{ .Values.exareme_images.version }}
+        imagePullPolicy: IfNotPresent
         ports:
           - containerPort: 9090
         volumeMounts:
         - mountPath: /root/exareme/data
-          name: csvs
+          name: data
         env:
-        - name: NODE_NAME
-          valueFrom:
-            fieldRef:
-              fieldPath: spec.nodeName
+        - name: ENVIRONMENT_TYPE
+          value: "{{ .Values.exareme.environment_type }}"
+        - name: LOG_LEVEL
+          value: "{{ .Values.exareme.log_level }}"
+        - name: CONVERT_CSVS
+          value: "{{ .Values.exareme.convert_csvs }}"
+        - name: TEMP_FILES_CLEANUP_TIME
+          value: "{{ .Values.exareme.temp_file_cleanup_time }}"
+        - name: NODE_COMMUNICATION_TIMEOUT
+          value: "{{ .Values.exareme.node_communication_timeout }}"
         - name: CONSULURL
           value: "exareme-keystore-service:8500"
         - name: FEDERATION_ROLE
           value: "worker"
-        - name: TEMP_FILES_CLEANUP_TIME
-          value: "30"
-        - name: NODE_COMMUNICATION_TIMEOUT
-          value: "30000"
-        - name: ENVIRONMENT_TYPE
-          value: "PROD"
-        - name: LOG_LEVEL
-          value: "INFO"
-        - name: CONVERT_CSVS
-          value: "TRUE"
+        - name: NODE_NAME
+          valueFrom:
+            fieldRef:
+              fieldPath: spec.nodeName
       volumes:
-      - name: csvs
+      - name: data
         hostPath:
-          path: /etc/exareme
+          path: {{ .Values.data_path }}

Federated-Deployment/kubernetes/values.yaml

+exareme_images:
+  repository: hbpmip
+  version: 24.2.0
+
+data_path: /opt/data
+
+exareme:
+  log_level: INFO
+  environment_type: PROD
+  convert_csvs: TRUE
+  temp_file_cleanup_time: 30
+  node_communication_timeout: 30000
+
+workers: 2