edited Jupyter app template to work with CoD cluster

form.yml

@@ -8,7 +8,15 @@
 # under /etc/ood/config/clusters.d/*.yml
 # @example Use the Owens cluster at Ohio Supercomputer Center
 #     cluster: "owens"
-cluster: ""
+cluster: {{ cluster_name }} 
+
+# Title of the app displayed in the Dashboard
+title: "Jupyter Notebook"
+
+# Description of the app displayed in the Dashboard (can use multi-line string
+# and Markdown syntax)
+description: |
+  This app will launch a Jupyter Notebook server on one or more cores.
 
 # Define attribute values that aren't meant to be modified by the user within
 # the Dashboard form
@@ -25,11 +33,67 @@ attributes:
   #     modules: "python/3.5"
   # @example Using combination of modules
   #     modules: "python/3.5 cuda/8.0.44"
-  modules: "python"
+  custom_environment:
+    widget: text_area
+    label: Environment Setup
+    value: |
+      # The latest version of Anaconda3 with jupyter is loaded by default.
+      # If you would like to load other modules
+      # or use specific version of Anaconda please list below
+      #
+      # format:
+      # module load example_module/VERSION example_module2
+
+  # Whether Conda extensions will be available within the Jupyter notebook
+  # server
+  #
+  # @note Allows the user to use conda environment-based kernels from their
+  #   Jupyter notebook dashboard
+  # @example Do NOT allow Conda extensions to be used
+  #   conda_extensions: "0"
+  # @example Do allow Conda extensions to be used
+  #   conda_extensions: "1"
+  # @see https://docs.continuum.io/anaconda/user-guide/tasks/use-jupyter-notebook-extensions
+  conda_extensions: "1"
 
   # Any extra command line arguments to feed to the `jupyter notebook ...`
   # command that launches the Jupyter notebook within the batch job
-  extra_jupyter_args: ""
+  extra_jupyter_args:
+    widget: text_field
+    label: Extra jupyter arguments
+
+  bc_num_hours:
+    value: 1
+
+  bc_num_slots:
+    label: Number of CPU
+    value: 1
+    min: 1
+    max: 24
+    step: 1
+
+  bc_num_mems:
+    widget: "number_field"
+    label: Memory per CPU (GB)
+    value: 4
+    min: 1
+    max: 128
+    step: 1
+
+  bc_partition:
+    widget: select
+    label: Partition
+    options:
+      - [ "express", "express" ]
+      - [ "short", "short" ]
+      - [ "medium", "medium" ]
+      - [ "long", "long" ]
+      - [ "interactive", "interactive" ]
+      - [ "pascalnodes", "pascalnodes" ]
+      - [ "pascalnodes-medium", "pascalnodes-medium" ]
+      - [ "largemem", "largemem" ]
+      - [ "largemem-long", "largemem-long" ]
+      - [ "amd-hdr100", "amd-hdr100" ]
 
 # All of the attributes that make up the Dashboard form (in respective order),
 # and made available to the submit configuration file and the template ERB
@@ -41,10 +105,11 @@ attributes:
 #   option, then it will not appear in the form page that the user sees in the
 #   Dashboard
 form:
-  - modules
+  - custom_environment
+  - conda_extensions
   - extra_jupyter_args
-  - bc_account
-  - bc_queue
   - bc_num_hours
+  - bc_partition
   - bc_num_slots
+  - bc_num_mems
   - bc_email_on_started

script.sh.erb

+#!/bin/bash -l
+
+# Set working directory to home directory
+cd "${HOME}"
+module reset
+#
+# Start Jupyter Notebook Server
+#
+module load Anaconda3
+<%= context.custom_environment %>
+unset XDG_RUNTIME_DIR
+# Launch the Jupyter Notebook Server
+jupyter notebook --config="${CONFIG_FILE}" <%= context.extra_jupyter_args %>

submit.yml.erb

 # Job submission configuration file
 #
 ---
+# This config comes from below URL
+# https://github.com/OSC/bc_example_jupyter/blob/custom_environment/submit.yml.erb
+# The -C option in the config provided for slurm has been removed because it does 
+# not apply to implementation at UAB. We do not use constraint list to be used with -C. 
 
-#
-# Configure the content of the job script for the batch job here
-# @see http://www.rubydoc.info/gems/ood_core/OodCore/BatchConnect/Template
-#
 batch_connect:
-  # We use the basic web server template for generating the job script
-  #
-  # @note Do not change this unless you know what you are doing!
   template: "basic"
 
-  # You can override the command used to query the hostname of the compute node
-  # here
-  #
-  # @note It is **highly** recommended this be set in the global cluster
-  #   configuration file so that all apps can take advantage of it by default
-  #
-  #set_host: "host=$(hostname -A | awk '{print $2}')"
-
-#
-# Configure the job script submission parameters for the batch job here
-# @see http://www.rubydoc.info/gems/ood_core/OodCore/Job/Script
-#
-#script:
-#  queue_name: "queue1"
-#  accounting_id: "account1"
-#  email_on_started: true
-#  native: # ... array of command line arguments ...
+script:
+  native:
+    - "-N 1"
+    - "-n <%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>"
+    - "--mem-per-cpu=<%= bc_num_mems.blank? ? 4 : bc_num_mems.to_i %>G"
+    - "--partition=<%= bc_partition %>"
+    - "--time=<%= bc_num_hours.blank? ? 1 : bc_num_hours.to_i %>:00:00"
+    - "--job-name=ood-jupyter"
+<%- if bc_partition.include? "pascalnodes" -%>
+    - "--gres=gpu:1"
+<%- end -%>

view.html.erb

 <form action="/node/<%= host %>/<%= port %>/login" method="post" target="_blank">
   <input type="hidden" name="password" value="<%= password %>">
   <button class="btn btn-primary" type="submit">
-    <i class="fa fa-eye"></i> Connect to Jupyter
+    <i class="fas fa-eye"></i> Connect to Jupyter
   </button>
 </form>