CHANGELOG.md

@@ -4,6 +4,28 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [Unreleased]
+### Changed
+- Increased verbosity of output to make debugging easier.
+- Does not launch template script as login shell anymore to speed up load time.
+
+### Fixed
+- Fix job not ending if forked processes still running.
+
+### Removed
+- Removed support for Anaconda Notebook extensions.
+
+## [1.0.1] - 2018-01-03
+### Changed
+- Updated date in `LICENSE.txt`.
+
+### Fixed
+- Remove ERB from YAML comments to avoid possible crash.
+  [#4](https://github.com/OSC/bc_example_jupyter/issues/4)
+
+## 1.0.0 - 2017-11-15
 ### Added
 - Initial release!
+
+[Unreleased]: https://github.com/OSC/bc_example_jupyter/compare/v1.0.1...HEAD
+[1.0.1]: https://github.com/OSC/bc_example_jupyter/compare/v1.0.0...v1.0.1

LICENSE.txt

-Copyright (c) 2016-2017 Ohio Supercomputer Center
+Copyright (c) 2016-2018 Ohio Supercomputer Center
 
 MIT License
 

README.md

@@ -19,12 +19,8 @@ OnDemand node):
 
 **Optional** software:
 
-- [Anaconda](https://www.continuum.io/anaconda-overview) 4.3.13+ and its
-  [Jupyter Notebook extensions](https://docs.continuum.io/anaconda/user-guide/tasks/use-jupyter-notebook-extensions)
-  that allow users to define custom environment-based kernels from within the
-  Jupyter notebook dashboard.
 - [Lmod](https://www.tacc.utexas.edu/research-development/tacc-projects/lmod)
-  6.0.1+ or any other `module restore` and `module load <modules>` based CLI
+  6.0.1+ or any other `module purge` and `module load <modules>` based CLI
   used to load appropriate environments within the batch job before launching
   the Jupyter Notebook server.
 

form.js

+const table = {
+  "interactive": { "max_cpu": 48, "max_hour": 2, "max_gpu": 0 },
+  "express": { "max_cpu": 48, "max_hour": 2, "max_gpu": 0 },
+  "short": { "max_cpu": 48, "max_hour": 12, "max_gpu": 0 },
+  "pascalnodes": { "max_cpu": 28, "max_hour": 12, "max_gpu": 4 },
+  "pascalnodes-medium": { "max_cpu": 28, "max_hour": 48, "max_gpu": 4 },
+  "medium": { "max_cpu": 48, "max_hour": 50, "max_gpu": 0 },
+  "long": { "max_cpu": 48, "max_hour": 150, "max_gpu": 0 },
+  "intel-dcb": { "max_cpu": 24, "max_hour": 150, "max_gpu": 0 },
+  "amd-hdr100": { "max_cpu": 128, "max_hour": 150, "max_gpu": 0 },
+  "largemem": { "max_cpu": 24, "max_hour": 50, "max_gpu": 0 },
+  "largemem-long": { "max_cpu": 24, "max_hour": 150, "max_gpu": 0 },
+  "amperenodes": { "max_cpu": 128, "max_hour": 12, "max_gpu": 2 },
+  "amperenodes-medium": { "max_cpu": 128, "max_hour": 48, "max_gpu": 2 },
+}
+
+const gpu_part_regex = /pascal|ampere/;
+
+function set_max_value(form_id, value) {
+  const form_element = $(form_id);
+  form_element.attr({'max': value});
+  if (form_element.val() > value)
+    form_element.val(value)
+}
+
+function set_partition_change_handler() {
+  let partition_select = $("#batch_connect_session_context_bc_partition");
+  partition_select.change( function(e) {
+    toggle_gpu_visibility(e);
+  });
+}
+
+function toggle_gpu_visibility(event) {
+  const partition = event.target.value;
+  const cpu_selector = '#batch_connect_session_context_bc_num_slots';
+  const gpu_selector = '#batch_connect_session_context_bc_num_gpus';
+  const hour_selector = '#batch_connect_session_context_bc_num_hours';
+
+  toggle_visibilty_of_form_group(gpu_selector, gpu_part_regex.test(partition));
+  set_max_value(cpu_selector, table[partition]["max_cpu"]);
+  set_max_value(gpu_selector, table[partition]["max_gpu"]);
+  set_max_value(hour_selector, table[partition]["max_hour"]);
+}
+
+function toggle_visibilty_of_form_group(form_id, show) {
+  let form_element = $(form_id);
+  let parent = form_element;
+
+  while (
+    (! parent[0].classList.contains('form-group')) &&
+    (! parent.is('html')) // ensure that we don't loop infinitely
+  ) {
+    parent = parent.parent();
+  }
+
+  // If parent is HTML then something has gone wrong and visibility should not be changed
+  if ( parent.is('html') ) {
+    return;
+  }
+
+  if(show) {
+    parent.show();
+  } else {
+    parent.hide();
+  }
+}
+
+toggle_gpu_visibility(
+  // Fake the event
+  { target: document.querySelector('#batch_connect_session_context_bc_partition') }
+);
+set_partition_change_handler();

form.yml → form.yml.erb

+<%-
+  partitions = OodAppkit.clusters[:SLURM_CLUSTER].custom_config[:partitions]
+-%>
 # Batch Connect app configuration file
 #
 # @note Used to define the submitted cluster, title, description, and
@@ -8,7 +11,7 @@
 # under /etc/ood/config/clusters.d/*.yml
 # @example Use the Owens cluster at Ohio Supercomputer Center
 #     cluster: "owens"
-cluster: ""
+cluster: "SLURM_CLUSTER"
 
 # Title of the app displayed in the Dashboard
 title: "Jupyter Notebook"
@@ -16,7 +19,7 @@ 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 nodes.
+  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
@@ -33,7 +36,16 @@ 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
@@ -49,8 +61,44 @@ attributes:
 
   # 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:
+    widget: "number_field"
+    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_num_gpus:
+    widget: "number_field"
+    label: Number of GPUs
+    value: 1
+    min: 0
+    max: 4
+    step: 1
+
+  bc_partition:
+    widget: select
+    label: Partition
+    options:
+    <%- partitions.each do |p| -%>
+      - [ "<%= p %>", "<%= p %>" ]
+    <%- end -%>
 # 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
 # files
@@ -61,11 +109,12 @@ 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_num_hours
+  - bc_partition
+  - bc_num_gpus
   - bc_num_slots
-  - bc_account
-  - bc_queue
+  - bc_num_mems
   - bc_email_on_started

manifest.yml

 ---
-name: Jupyter
+name: Jupyter Notebook
 category: Interactive Apps
 subcategory: Servers
 role: batch_connect
+description: |
+  This app will launch a Jupyter Notebook server on one or more nodes.

submit.yml.erb

 # Job submission configuration file
 #
+<%-
+  email = ENV['USER']
+  if !email.include? '@'
+    email = email + '@uab.edu'
+  end
+-%>
 ---
+# 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
-#
-
-# Example for Slurm
-#
-# @example Specify nodes with specific features for all jobs
-#script:
-#  native: [ "-N", "<%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>", "-C", "c12" ]
-
-# Examples for PBS/Torque
-#
-# @example Specify the PPN for all jobs
-#script:
-#  native:
-#    resources:
-#      nodes: "<%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>:ppn=28"
+script:
+  job_environment:
+    USER: "<%= ENV['USER'] %>"
+  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" or bc_partition.include? "amperenodes" -%>
+    - "--gres=gpu:<%= bc_num_gpus.blank? ? 1 : bc_num_gpus.to_i %>"
+<%- end -%>
+<%- if bc_email_on_started == "1" -%>
+    - "--mail-type=BEGIN"
+    - "--mail-user=<%= email %>"
+<%- end -%>

template/after.sh

+# Wait for the Jupyter Notebook server to start
+echo "Waiting for Jupyter Notebook server to open port ${port}..."
+echo "TIMING - Starting wait at: $(date)"
+if wait_until_port_used "${host}:${port}" 600; then
+  echo "Discovered Jupyter Notebook server listening on port ${port}!"
+  echo "TIMING - Wait ended at: $(date)"
+else
+  echo "Timed out waiting for Jupyter Notebook server to open port ${port}!"
+  echo "TIMING - Wait ended at: $(date)"
+  pkill -P ${SCRIPT_PID}
+  clean_up 1
+fi
+sleep 2

template/before.sh.erb

@@ -26,6 +26,9 @@
 #   - $password
 #       The plain text password used to authenticate to the web server with
 
+# Export the module function if it exists
+[[ $(type -t module) == "function" ]] && export -f module
+
 # Find available port to run server on
 port=$(find_port)
 
@@ -51,13 +54,5 @@ c.NotebookApp.open_browser = False
 c.NotebookApp.allow_origin = '*'
 c.NotebookApp.notebook_dir = '${HOME}'
 c.NotebookApp.disable_check_xsrf = True
-<%- if context.conda_extensions == "1" -%>
-c.NotebookApp.kernel_spec_manager_class = "nb_conda_kernels.CondaKernelSpecManager"
-c.NotebookApp.nbserver_extensions = {
-  "nb_conda": True,
-  "nb_anacondacloud": True,
-  "nbpresent": True
-}
-<%- end -%>
 EOL
 )

template/script.sh.erb

@@ -2,18 +2,12 @@
 
 # Set working directory to home directory
 cd "${HOME}"
-
+module reset
 #
 # Start Jupyter Notebook Server
 #
-
-<%- unless context.modules.blank? -%>
-# Restore the module environment to avoid conflicts
-module restore
-
-# Load the require modules
-module load <%= context.modules %>
-<%- end -%>
-
+module load Anaconda3
+<%= context.custom_environment.gsub(/\r\n?/, "\n") %>
+unset XDG_RUNTIME_DIR
 # Launch the Jupyter Notebook Server
 jupyter notebook --config="${CONFIG_FILE}" <%= context.extra_jupyter_args %>

view.html.erb

-<p>
-  If you see <code>Failed to connect to ...</code>, then wait a few seconds
-  before trying the <strong>Connect to Jupyter</strong> button again. This
-  warning appeared because the Jupyter Notebook is still starting up.
-</p>
-
 <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>