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Merge pull request #75 from ericfranz/jupyter_tut_summary
Jupyter tut summary
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‎ondemand/README.md‎

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# Open OnDemand Tutorial
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- [Jupyter App Tutorial Summary](#jupyter-app-tutorial-summary)
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- [Jupyter App Tutorial](#jupyter-app-tutorial)
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- [Passenger App Tutorial](#passenger-app-tutorial)
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- [XDMoD Integration Tutorial](#xdmod-integration-tutorial)
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* [Online Documentation](https://osc.github.io/ood-documentation/master/)
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* [Jupyter Install Tutorial](https://osc.github.io/ood-documentation/master/app-development/tutorials-interactive-apps/add-jupyter.html)
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## Jupyter App Tutorial
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## Jupyter App Tutorial Summary
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This section provides a few snippets helpful for following along with the live tutorial.
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Login to OnDemand as hpcadmin to https://localhost:3443
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### Get the app working
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1. Develop => My Sandbox Apps
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2. Click New App
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3. Click Clone Existing App: `jupyter` and `/var/git/bc_example_jupyter`
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Fix environment: `source /usr/local/jupyter/2.1.4/bin/activate`
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### Modify the Partition field
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form.yml changes:
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```
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attributes:
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custom_queue:
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widget: "select"
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label: "Partition"
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options:
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- ["Compute", "compute"]
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- ["Debug", "debug"]
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form:
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- custom_queue
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# - bc_queue
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```
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- `custom_queue` is used instead of `partition` because of 1.8 bug that will be fixed prior to release
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script.yml.erb changes:
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```yaml
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script:
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queue_name: "<%= custom_queue %>"
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```
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- the constructor for the Ruby object https://osc.github.io/ood_core/0.11.4/OodCore/Job/Script.html shows all the options you can set in the script.yml above (https://www.rubydoc.info/gems/ood_core/OodCore/Job/Script typically shows the latest - but sometimes this service is unavailable)
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### Deploy to production
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Edit manifest:
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```
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---
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# change the name, this is what shows up in the menu
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name: HPC Tutorial Jupyter
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# change the category just to differentiate from the system installed
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# deskop application
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category: Tutorial Apps
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# change the subcategory
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subcategory: Machine Learning
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role: batch_connect
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# change the description, this shows up when you hover over the menu item on the interactive sessions page
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description: |
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This app will launch a Jupyter Lab or Notebootk on one or more nodes.
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```
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Deployment steps on ondemand host via Shell:
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sudo mv /var/www/ood/apps/sys/jupyter /var/www/ood/apps/sys/jupyter.old
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sudo cp -r jupyter /var/www/ood/apps/sys/jupyter
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- app directory names with periods in them do not display in the navbar, which is why we can rename the old app to jupyter.old
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### Set the memory for the job
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form.yml changes:
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```
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attributes:
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memory:
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widget: "number_field"
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max: 1000
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min: 200
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step: 200
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value: 600
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label: "Memory (MB)"
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help: "RSS Memory"
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form:
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- memory
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```
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- widget specifies the type of widget to be a number
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- max the maximum value, ~1 GB in this case
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- min the minimum value, 200 MB
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- step the step size when users increase or decrease the value
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- value the default value of 600 MB
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- label the for UIs label
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- help a help message
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- See https://osc.github.io/ood-documentation/master/app-development/interactive/form.html#customizing-attributes for more details about what you can set in each "attribute"
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script.yml.erb modifications:
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```
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script:
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native:
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- "--mem"
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- "<%= memory %>M"
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```
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- script.native attributes are way for us to specify scheduler specific argument to sbatch or qsub or bsub
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- this lets you set arguments that OnDemand doesn't provide an abstraction for
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### Limit number of cores
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form.yml:
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```yaml
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attributes:
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bc_num_slots:
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max: 2
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```
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### Add checkbox to start JupyterLab
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form.yml:
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```
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attributes:
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jupyterlab_switch:
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widget: "check_box"
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label: "Use JupyterLab instead of Jupyter Notebook?"
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help: |
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JupyterLab is the next generation of Jupyter, and is completely compatible with existing Jupyter Notebooks.
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form:
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- jupyterlab_switch
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```
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template script.sh:
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```
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jupyter <%= context.jupyterlab_switch == "1" ? "lab" : "notebook" %> --config="${CONFIG_FILE}" <%= context.extra_jupyter_args %>
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```
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## Jupyter App Detailed Tutorial
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This tutorial will be using the the `hpcadmin` credentials listed in
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[Accessing the Applications](../docs/applications.md).
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They're given here in full if you want to copy/paste them. And remember to [save your spot](#save-your-spot)!
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```yaml
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# script.erb.yml
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# script.yml.erb
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script:
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queue_name: "<%= custom_queue %>"
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```
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it in the `submit.yml.erb`. This is where `script.native` attributes come in.
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```yaml
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# script.erb.yml
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# script.yml.erb
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script:
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native:
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- "--mem"
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They're given here in full if you want to copy/paste them. And remember to [save your spot](#save-your-spot)!
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```yaml
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# script.erb.yml
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# script.yml.erb
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---
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script:
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queue_name: "<%= custom_queue %>"

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