Merge branch 'remove-init-container' into 'main'

Remove init container

See merge request csusb-hpc!13

.gitignore

-values.template2.yaml
+values.template2.yaml
\ No newline at end of file
+.DS_Store

.gitlab-ci.yml

@@ -13,10 +13,13 @@ deploy-helm:
       --install hpchub jupyterhub/jupyterhub
       --namespace csusb-hpc --version=1.2
       --values values.yaml
-      --set-file hub.extraFiles.image_select_idp.binaryData=./select_idp_cilogon.png.b64
-      --set-file hub.extraFiles.custom_spawner_profile.stringData=./my_spawner.html
-      --set-file hub.extraFiles.custom_spawner.stringData=./my_spawner.py 
-  
+      --set-file hub.extraFiles.custom_spawner_profile.stringData=./extraFiles/my_spawner.html
+      --set-file hub.extraFiles.custom_spawner.stringData=./extraFiles/my_spawner.py
+      --set-file hub.extraFiles.image_select_idp.binaryData=./extraFiles/select_idp_cilogon.png.b64
+      --set-file hub.extraFiles.custom_login_html.stringData=./extraFiles/login.html
+      --set-file hub.extraFiles.custom_page_html.stringData=./extraFiles/page.html
+      --set-file hub.extraFiles.custom_spawn_pending_html.stringData=./extraFiles/spawn_pending.html
+
   environment:
   #Check the namespace
     name: csusb-hpc

extraFiles/login.html

+{# https://github.com/jupyterhub/jupyterhub/issues/1385 #}
+{# https://github.com/jupyterhub/jupyterhub/issues/1385#issuecomment-738447175 #}
+{% extends "templates/login.html" %}
+
+<!-- {% set announcement = 'We are testing customized style / The server works the same way as before' %} -->
+{% set csusb_hub_title = 'Welcome to Cal State San Bernardino JupyterHub' %}
+{% set csusb_cilogon = 'The login process (the orange button) uses CSUSB\'s DUO system' %}
+
+{% block login %}
+<div class="container text-center">
+    <h2>{{ csusb_hub_title  }}</h2>
+    <h5>
+        <p>{{ csusb_cilogon | safe }}</p>
+        {# <p>Visit <a href="https://www.csusb.edu/high-performance-computing" target="_blank">CSUSB High Performance Computing Initiative</a> for more information about CSUSB HPCI 
+        </p> #}
+    </h5>
+</div>
+<p> &nbsp </p>
+<p> &nbsp </p>
+<p> &nbsp </p>
+{{ super() }}
+<p> &nbsp </p>
+<div id="login-cilogon-info" class="service-login">
+    <h5>      
+    <p>Be sure to choose <ins>California State University San Bernardino</ins> on the next page instead of <del>ORCID</del>
+    </h5>
+</div>
+<div class="container text-center">
+<details>
+    <summary>Click here for more details</summary>
+    <img id="idp_selector_info" style="width: 70%" src="{{ static_url("select_idp_cilogon.png") }}" alt="CILogon-CSUSB-Select">
+</details>
+</div>
+{% endblock %}
+
+{% block stylesheet %}
+{{ super() }}
+<style>
+#login-main{
+    margin-top: 1%;
+    height: 100%;
+}
+#login-cilogon-info{
+    text-align: center;
+    display: table;
+    vertical-align: middle;
+    margin: 1% auto auto auto;
+    padding-left: 0%;
+    width: 380px;
+}
+#idp_selector_info {
+    max-width:100%;
+    height:auto;
+    max-height:100%;
+}
+p.extra-space {
+    line-height: 0.7;
+}
+</style>
+{% endblock %}
\ No newline at end of file

my_spawner.html → extraFiles/my_spawner.html

 <style>
-<!--
-/* The profile description should not be bold, even though it is inside the <label> tag */
-    font-weight: normal;
-}
--->
-    
 input[type="range"] {
     display: inline;
     width: 40%;

my_spawner.py → extraFiles/my_spawner.py

@@ -110,7 +110,7 @@ class MySpawner(KubeSpawner):
         {
             'display_name': 'Stack SageMath',
             'kubespawner_override': {
-                'image_spec': 'gitlab-registry.nrp-nautilus.io/youngsu_kim/csusb-jupyter-stack/stack-sagemath:b353d66b',
+                'image_spec': 'gitlab-registry.nrp-nautilus.io/youngsu_kim/csusb-jupyter-stack/stack-sagemath',
             }
         },
     ]

extraFiles/page.html

+{% extends "templates/page.html" %}
+
+<!-- {% set announcement = 'Please contact Youngsu Kim at youngsu.kim@csusb.edu for support' %} -->
+
+{% block stylesheet %}
+{{ super() }}
+<style>
+.footer-bottom {
+    position: auto;
+    bottom: 0px;
+    text-align: center;
+    width: 100%;
+    z-index: -1;
+}
+</style>
+{% endblock %}
+
+{% block footer %}
+<p> &nbsp <br> &nbsp </p>
+<p> &nbsp <br> &nbsp </p>
+<div class="footer-bottom">
+    <hr style="width:35%; margin-bottom: 5px;">
+    <p style="font-size: 100%">This JupyterHub is provided by the <a href="https://www.csusb.edu/high-performance-computing" target="_blank">High Performance Computing Initiative </a> at <a href="https://www.csusb.edu/" target="_blank">California State Univeristy San Bernardino</a> and <a href="https://pacificresearchplatform.org/" target="_blank">Pacific Research Platform</a> <br>
+    If you obtain any results by utilizing our resources, please include <a href="https://www.csusb.edu/academic-technologies-innovation/xreal-lab-and-high-performance-computing/high-performance-computing#acknowledgement" target="_blank">acknowledgements of our service</a> in your work e.g., presentations or papers. <br>
+    It will help us maintain the funding for our resources.
+    </p></div>
+{% endblock %}
\ No newline at end of file

extraFiles/spawn_pending.html

+{% extends "templates/spawn_pending.html" %}
+{% block message %}
+{# {{ super() }} #}
+<p>Your server is starting up and it may take several minutes</p>
+<p>Most issues are related to the server upgrade or temporary maintanance</p>
+<p>If it does not start for an extended period of time, please contact the <a href="https://www.csusb.edu/high-performance-computing/#team" target="_blank"> CSUSB HPC team </a></p>
+<p> &nbsp <br> &nbsp </p>
+{% endblock %}
\ No newline at end of file

values.template.yaml

@@ -30,33 +30,12 @@ hub:
         - 003087200@csusb.edu
         - 000030081@csusb.edu
         - dmishin@ucsd.edu
-  initContainers:
-    - name: git-clone-templates
-      image: alpine/git
-      args:
-        - clone
-        - --single-branch
-        - --branch=main
-        - --depth=1
-        - --
-        - https://gitlab.nrp-nautilus.io/csusb-prp/csusb-jupyterhub-templates.git
-        - /etc/jupyterhub/custom
-      securityContext:
-        runAsUser: 0
-      volumeMounts:
-        - name: custom-templates
-          mountPath: /etc/jupyterhub/custom
-  extraVolumes:
-    - name: custom-templates
-      emptyDir: {}
-  extraVolumeMounts:
-    - name: custom-templates
-      mountPath: /etc/jupyterhub/custom
   extraConfig:
     templates: |
       c.JupyterHub.template_paths = ['/etc/jupyterhub/custom']
 
   # https://github.com/jupyterhub/zero-to-jupyterhub-k8s/issues/1990
+  # To use these .gitlab-ci.yml needs to be updated accordingly
   extraFiles:
     image_select_idp:
       mountPath: /usr/local/share/jupyterhub/static/select_idp_cilogon.png
@@ -72,6 +51,47 @@ hub:
     custom_spawner_profile:
       mountPath: /etc/jupyterhub/custom/my_spawner.html
 
+    # Additional custom html files
+    custom_login_html:
+      mountPath: /etc/jupyterhub/custom/login.html
+    custom_page_html:
+      mountPath: /etc/jupyterhub/custom/page.html
+    custom_spawn_pending_html:
+      mountPath: /etc/jupyterhub/custom/spawn_pending.html
+
+
+
+  nodeSelector:
+    topology.kubernetes.io/region: "us-west"
+    kubernetes.io/hostname: "perfsonar.csusb.edu"
+    # env: system
+
+  image:
+    name: jupyterhub/k8s-hub
+    tag: '1.2.0'
+    pullPolicy: ''
+    pullSecrets: []
+
+  livenessProbe:
+    # The livenessProbe's aim to give JupyterHub sufficient time to startup but
+    # be able to restart if it becomes unresponsive for ~5 min.
+    enabled: true
+    initialDelaySeconds: 300
+    periodSeconds: 10
+    failureThreshold: 30
+    timeoutSeconds: 3
+  readinessProbe:
+    # The readinessProbe's aim is to provide a successful startup indication,
+    # but following that never become unready before its livenessProbe fail and
+    # restarts it if needed. To become unready following startup serves no
+    # purpose as there are no other pod to fallback to in our non-HA deployment.
+    enabled: true
+    initialDelaySeconds: 0
+    periodSeconds: 2
+    failureThreshold: 1000
+    timeoutSeconds: 1
+
+
   service:
     type: ClusterIP
     annotations: {}
@@ -131,20 +151,21 @@ singleuser:
       pvcNameTemplate: claim-{username}{servername}
       volumeNameTemplate: volume-{username}{servername}
       storageAccessModes: [ReadWriteOnce]
-    extraVolumes:
-      - name: csusb-hpc-share
-        persistentVolumeClaim:
-          claimName: csusb-hpc-share
-      - name: mkshare-script
-        configMap:
-          name: mkshare-script
-          defaultMode: 0777
-    extraVolumeMounts:
-      - name: csusb-hpc-share
-        mountPath: /home/shared        
-      - name: mkshare-script
-        mountPath: /usr/local/bin/before-notebook.d/mkshare.sh
-        subPath: mkshare.sh  
+    # extraVolumes(Mounts) are overriden by the custom spawner -> extraFiles/my_spawner.py
+    # extraVolumes:
+    #   - name: csusb-hpc-share
+    #     persistentVolumeClaim:
+    #       claimName: csusb-hpc-share
+    #   - name: mkshare-script
+    #     configMap:
+    #       name: mkshare-script
+    #       defaultMode: 0777
+    # extraVolumeMounts:
+    #   - name: csusb-hpc-share
+    #     mountPath: /home/shared        
+    #   - name: mkshare-script
+    #     mountPath: /usr/local/bin/before-notebook.d/mkshare.sh
+    #     subPath: mkshare.sh  
   image:
     name: localhost:30081/prp/jupyter-stack/prp
     tag: latest
@@ -166,50 +187,6 @@ singleuser:
 #     default: true    
 #     kubespawner_override:
 #       image_spec: localhost:30081/prp/jupyter-stack/minimal
-#   - display_name: Stack Minimal + Desktop GUI + Relion
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/relion-desktop
-#   - display_name: Stack All Spark
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/all-spark
-#       extra_resource_limits:
-#         nvidia.com/gpu: "2"
-#   - display_name: Stack Datascience
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/datascience
-#       extra_resource_limits:
-#         nvidia.com/gpu: "2"
-#   - display_name: Stack Tensorflow [2GPUs]
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/prp
-#       extra_resource_limits:
-#         nvidia.com/gpu: "2"
-#   - display_name: Stack Tensorflow [4GPUs]
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/prp
-#       extra_resource_limits:
-#         nvidia.com/gpu: "4"
-#   - display_name: Stack R-Studio [4.1.2]
-#     kubespawner_override:
-#       image_spec: gitlab-registry.nrp-nautilus.io/youngsu_kim/csusb-jupyter-stack/stack-rstudio:sr-r1
-#   - display_name: Stack R-Studio
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/r-studio
-# #      extra_resource_limits:
-# #        nvidia.com/gpu: "1"
-#   - display_name: Stack Pyspark [2GPUs]
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/pyspark
-#       extra_resource_limits:
-#         nvidia.com/gpu: "2"
-#   - display_name: Stack Pyspark [4GPUs]
-#     kubespawner_override:
-#       image_spec: localhost:30081/prp/jupyter-stack/pyspark
-#       extra_resource_limits:
-#         nvidia.com/gpu: "4"
-#   - display_name: Stack SageMath
-#     kubespawner_override:
-#       image_spec: gitlab-registry.nrp-nautilus.io/youngsu_kim/csusb-jupyter-stack/stack-sagemath:b353d66b
 scheduling:
   userScheduler:
     enabled: false