init bc_jupyter template

Author: joshuaguy22

README.md

@@ -1,2 +1,8 @@
-# bc_jupyter
-Jupyter Interative App for BioHive Portal (Open OnDemand)
+# Batch Connect - Jupyter
+
+![GitHub Release](https://img.shields.io/github/release/osc/bc_osc_jupyter.svg)
+[![GitHub License](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/licenses/MIT)
+
+An interactive app template designed for the BioHive Portal that launches a Jupyter
+server.
+

form.yml.erb

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+<%-
+  groups = OodSupport::User.new.groups.sort_by(&:id).tap { |groups|
+    groups.unshift(groups.delete(OodSupport::Process.group))
+  }.map(&:name).grep(/^P./)
+-%>
+---
+cluster:
+  - "slurm"
+form:
+  - bc_queue
+  - mode
+  - cuda_version
+  - version
+  - bc_num_hours
+  - num_cores
+  - memory
+  - modules
+  - extra_jupyter_args
+  - bc_account
+  - bc_num_slots
+  - classroom 
+attributes:
+  cluster: "slurm"   
+  modules: "python"
+  cuda_version: "cuda11.8/toolkit/11.8.0"
+  classroom: 0
+  version: "3.1"
+  bc_account: null
+  bc_num_slots: null
+  bc_queue:
+    label: Slurm Partition
+    widget: select
+    options:
+      - ["batch", "batch"]
+      - ["interactive", "interactive"]
+      - ["mem", "mem"]
+  extra_jupyter_args: ""
+  bc_num_hours:
+    widget: "number_field"
+    label: "Number of Hours"
+    value: 1
+    min: 1
+    max: 24
+    required: true
+    help: "Specify the number of hours. Min: 1hr, Max: 24hrs"
+  num_cores:
+    widget: "number_field"
+    label: "Number of Cores"
+    value: 1
+    min: 1
+    max: 16
+    required: true
+    help: "Specify the number of cores for the job. Max: 16"
+  memory:
+    widget: "number_field"
+    label: "Memory (GB)"
+    value: 2
+    min: 1
+    max: 32
+    required: true
+    help: "Specify the amount of memory in MB. Min: 1GB - Max: 32GB"
+  mode:
+    widget: "radio"
+    value: "1"
+    options:
+      - ["Jupyter Lab", "1"]
+      - ["Jupyter Notebook", "0"]
+  

icon.png

@@ -0,0 +1,14 @@
+---
+name: Jupyter
+category: Interactive Apps
+subcategory: Servers
+role: batch_connect
+description: |
+  This app will launch a [Jupyter] server using [Python] on the [Ascend], [Owens] or
+  [Pitzer] clusters.
+
+  [Jupyter]: https://jupyter.org/
+  [Python]: https://www.python.org/
+  [Owens]: https://www.osc.edu/resources/technical_support/supercomputers/owens
+  [Pitzer]: https://www.osc.edu/resources/technical_support/supercomputers/pitzer
+  [Ascend]: https://www.osc.edu/vocabulary/systems/ascend

info.md.erb

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+# Disable debuginfo as it causes issues with bundled gems that build libraries
+%global debug_package %{nil}
+%global repo_name bc_osc_jupyter
+%global app_name bc_osc_jupyter
+%{!?package_version: %define package_version %{major}.%{minor}.%{patch}}
+%{!?package_release: %define package_release 1}
+%{!?git_tag: %define git_tag v%{package_version}}
+%define git_tag_minus_v %(echo %{git_tag} | sed -r 's/^v//')
+
+Name:     ondemand-%{app_name}
+Version:  %{package_version}
+Release:  %{package_release}%{?dist}
+Summary:  Batch Connect - OSC Jupyter Notebook
+
+Group:    System Environment/Daemons
+License:  MIT
+URL:      https://github.com/OSC/%{repo_name}
+Source0:  https://github.com/OSC/%{repo_name}/archive/%{git_tag}.tar.gz
+
+Requires: ondemand
+
+# Disable automatic dependencies as it causes issues with bundled gems and
+# node.js packages used in the apps
+AutoReqProv: no
+
+%description
+An interactive app designed for OSC OnDemand that launches a Jupyter Notebook server within an Owens batch job.
+
+
+%prep
+%setup -q -n %{repo_name}-%{git_tag_minus_v}
+
+
+%build
+
+
+%install
+%__mkdir_p %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}
+%__cp -a ./. %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}/
+echo v%{version} > %{buildroot}%{_localstatedir}/www/ood/apps/sys/%{app_name}/VERSION
+
+
+%files
+%defattr(-,root,root)
+%{_localstatedir}/www/ood/apps/sys/%{app_name}
+%{_localstatedir}/www/ood/apps/sys/%{app_name}/manifest.yml
+
+
+%changelog
+* Thu Sep 20 2018 Morgan Rodgers <mrodgers@osc.edu> 0.9.0-1
+- Update Jupyter to v0.9.0 (mrodgers@osc.edu)
+
+* Fri Aug 24 2018 Morgan Rodgers <mrodgers@osc.edu> 0.8.0-1
+- Add IJulia kernel for Julia 0.6.4 (mrodgers@osc.edu)
+
+* Tue Aug 14 2018 Morgan Rodgers <mrodgers@osc.edu> 0.7.0-1
+- Added support for Julia 1.0 kernel (mrodgers@osc.edu)
+
+* Fri Apr 27 2018 Jeremy Nicklas <jnicklas@osc.edu> 0.6.2-1
+- Bump bc_osc_jupyter to 0.6.2 (jnicklas@osc.edu)
+
+* Thu Apr 26 2018 Jeremy Nicklas <jnicklas@osc.edu> 0.6.1-1
+- Bump bc_osc_jupyter to 0.6.1 (jnicklas@osc.edu)
+
+* Tue Apr 17 2018 Jeremy Nicklas <jnicklas@osc.edu> 0.6.0-1
+- Bump bc_osc_jupyter to 0.6.0 (jnicklas@osc.edu)
+
+* Wed Mar 28 2018 Jeremy Nicklas <jnicklas@osc.edu> 0.5.0-1
+- Bump bc_osc_jupyter to 0.5.0 (jnicklas@osc.edu)
+
+* Tue Mar 06 2018 Jeremy Nicklas <jnicklas@osc.edu> 0.4.1-1
+- Bump bc_osc_jupyter to 0.4.1 (jnicklas@osc.edu)
+
+* Tue Mar 06 2018 Jeremy Nicklas <jnicklas@osc.edu>
+- Bump bc_osc_jupyter to 0.4.1 (jnicklas@osc.edu)
+
+* Tue Feb 13 2018 Trey Dockendorf <tdockendorf@osc.edu> 0.3.0-1
+- new package built with tito
+

manifest.yml

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+---
+script:
+  native:
+  - "--mem=<%= memory.blank? ? 2 : memory.to_i %>G"
+  - "--cpus-per-task=<%= num_cores.blank? ? 1 : num_cores.to_i %>"
+
+batch_connect:
+  template: "basic"

packaging/ondemand-bc_osc_jupyter.spec

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+<% if context.cluster !~ /kubernetes/ -%>
+# Wait for the Jupyter server to start
+echo "Waiting for Jupyter server to open port ${port}..."
+if wait_until_port_used "${host}:${port}" 600; then
+  echo "Discovered Jupyter server listening on port ${port}!"
+else
+  echo "Timed out waiting for Jupyter server to open port ${port}!"
+  clean_up 1
+fi
+sleep 2
+<% end -%>

submit.yml.erb

@@ -0,0 +1 @@
+python

template/after.sh.erb

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+# Export the module function if it exists
+<% if context.cluster.match?(/kubernetes/) -%>
+exec &> >(tee -a "pod.log")
+
+source /etc/profile.d/lmod.sh
+
+source /bin/find_host_port
+source /bin/save_passwd_as_secret
+source /bin/create_salt_and_sha1
+<% else -%>
+[[ $(type -t module) == "function" ]] && export -f module
+
+# Find available port to run server on
+port=$(find_port ${host})
+
+# Generate SHA1 encrypted password (requires OpenSSL installed)
+SALT="$(create_passwd 16)"
+password="$(create_passwd 16)"
+PASSWORD_SHA1="$(echo -n "${password}${SALT}" | openssl dgst -sha1 | awk '{print $NF}')"
+<% end -%>
+
+# The `$CONFIG_FILE` environment variable is exported as it is used in the main
+# `script.sh.erb` file when launching the Jupyter server.
+export CONFIG_FILE="${PWD}/config.py"
+
+# Safari users hit this error https://github.com/jupyterlab/jupyterlab/issues/5486
+# so let's make a new workspace dir that's this job's PWD and copy the defult /lab
+# workspace over there so folks can update it.
+WORKSPACE_DIR="$HOME/.jupyter/lab/workspaces"
+FILES=$(ls $WORKSPACE_DIR)
+
+for FILE in ${FILES[@]}
+do
+  ID=$(jq -r '.metadata.id' $WORKSPACE_DIR/$FILE)
+
+  if [[ $ID == "/lab" ]]; then
+    WORKSPACE_FILE="$WORKSPACE_DIR/$FILE"
+    break
+  fi
+done
+
+if [[ ${WORKSPACE_FILE+x} ]]; then
+  cp $WORKSPACE_FILE .
+fi
+
+JUPYTER_API="<%= context.mode == "1" ? "lab" : "tree" %>"
+
+<%- if context.classroom == "1" -%>
+module purge
+module load <%= context.version %>
+
+# Prepare the class environment if the module has set the appropriate variables set.
+# OSC_CLASS_FILES is the instructor's project directory we need to copy from.
+# OSC_CLASS_ID is the name of the class (eg. BIOCHEM5721).
+#
+# Note we make the directory even if there's nothing to copy
+mkdir -p "$HOME/osc_classes/$OSC_CLASS_ID"
+touch "$HOME/osc_classes/$OSC_CLASS_ID/0_${OSC_CLASS_ID:-osc_class}.md"
+NOTEBOOK_ROOT="$HOME/osc_classes/$OSC_CLASS_ID"
+
+if [[ -n "$OSC_CLASS_FILES" ]]; then
+  # Copy over classroom materials
+  set -x
+  rsync -avz --ignore-existing "$OSC_CLASS_FILES" "$HOME/osc_classes/$OSC_CLASS_ID"
+  { set +x; } 2>/dev/null
+fi
+
+# Now set FACLs so that instructors & teaching assistants can copy the
+# students' directories and grade their notebooks.
+# But first remove any old FACLS we may have set previously if applicable.
+RM_ACL_FILE="/users/PZS0645/support/classes/$OSC_CLASS_ID/class.acl.remove"
+if [[ -r "$RM_ACL_FILE" ]]; then
+  nfs4_setfacl -X - "$HOME" "$HOME/osc_classes" "$HOME/osc_classes/$OSC_CLASS_ID" < "$RM_ACL_FILE"
+fi
+
+ACL_FILE="/users/PZS0645/support/classes/$OSC_CLASS_ID/class.acl"
+if [[ -r $ACL_FILE ]]; then
+  echo 'setting facl'
+  nfs4_setfacl -A - "$HOME" "$HOME/osc_classes" "$HOME/osc_classes/$OSC_CLASS_ID" < "$ACL_FILE"
+fi
+
+module purge
+<%- end -%>
+
+export JUPYTERLAB_WORKSPACES_DIR=$PWD
+export jupyter_api="$JUPYTER_API"
+
+# Notebook root directory
+export NOTEBOOK_ROOT="${NOTEBOOK_ROOT:-${HOME}}"
+
+# Generate Jupyter configuration file with secure file permissions
+(
+umask 077
+cat > "${CONFIG_FILE}" << EOL
+c.KernelSpecManager.ensure_native_kernel = False
+c.NotebookApp.ip = '*'
+<% if context.cluster.match?(/kubernetes/) -%>
+c.NotebookApp.port = 8080
+c.NotebookApp.base_url = '/node/${HOST_CFG}/${PORT_CFG}/'
+c.NotebookApp.terminado_settings = {'shell_command': ['/bin/bash', '--login', '-i']}
+<% else -%>
+c.NotebookApp.port = ${port}
+c.NotebookApp.base_url = '/node/${host}/${port}/'
+<% end -%>
+c.NotebookApp.port_retries = 0
+c.NotebookApp.password = u'sha1:${SALT}:${PASSWORD_SHA1}'
+c.NotebookApp.open_browser = False
+c.NotebookApp.allow_origin = '*'
+c.NotebookApp.notebook_dir = '${NOTEBOOK_ROOT}'
+c.NotebookApp.disable_check_xsrf = True
+EOL
+)

template/assets/julia/logo-32x32.png

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+#!/usr/bin/env bash
+<%-
+  require 'pathname'
+-%>
+
+echo "Starting main script..."
+echo "TTT - $(date)"
+
+#
+# Start Jupyter server
+#
+
+# Clean the environment
+module purge
+
+# Required modules
+module load xalt/latest
+<%- unless context.cuda_version.empty? || context.cuda_version == 'none' -%>
+module load <%= context.cuda_version %>
+<%- end -%>
+
+# Set working directory to notebook root directory
+cd "${NOTEBOOK_ROOT}"
+
+# Setup Jupyter environment
+module load project/ondemand <%= context.version %>
+
+module list
+export JUPYTER_PATH="${PWD}/share/jupyter:${OSC_JUPYTER_PATH}"
+
+echo "TTT - $(date)"
+
+# List available kernels for debugging purposes
+set -x
+jupyter kernelspec list
+{ set +x; } 2>/dev/null
+echo "TTT - $(date)"
+
+# Launch the Jupyter server
+set -x
+/cm/local/apps/python3/bin/jupyter <%= context.mode == "1" ? "lab" : "notebook" %> --config="${CONFIG_FILE}"

template/assets/julia/logo-64x64.png

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+<%-
+  base_url  = "/node/#{host}/#{port}"
+  login_url = "#{base_url}/login"
+  next_url  = "#{base_url}/#{jupyter_api}"
+
+  full_url="#{login_url}?next=#{CGI.escape(next_url)}"
+  form_id = "juypyter_form#{login_url.gsub('/', '_')}"
+%>
+
+<!-- Zoom on iPad doesn't like opening in a new tab. It won't foward the form parameters. -->
+<script type="text/javascript">
+  function changeTarget() {
+    const agent = navigator.userAgent;
+    if (/Mozilla\/5\.0 \(Macintosh; Intel Mac OS X \d+_\d+_\d+\) AppleWebKit\/\d+\.\d+\.\d+ \(KHTML, like Gecko\)/.test(agent)) {
+      document.getElementById("<%= form_id %>").target = "_self";
+    }
+  }
+</script>
+
+<form id="<%= form_id %>" action="<%= full_url %>" method="post" target="_blank" onsubmit="changeTarget()" >
+  <input type="hidden" name="password" value="<%= password %>">
+  <button class="btn btn-primary" type="submit">
+    <i class="fa fa-cogs"></i> Connect to Jupyter
+  </button>
+</form>