Sandbox apps on OOD - Githubissues

uabrc / uabrc.github.io

UAB Research Computing Documentation

https://docs.rc.uab.edu

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Sandbox apps on OOD #428

Open wwarriner opened 1 year ago

wwarriner commented 1 year ago

What would you like to see added?

Add docs on using Sandbox Apps on OOD.

wwarriner commented 1 year ago

Purpose

The purpose of Sandbox apps is to provide an in-browser display for interactive graphical applications installed on Cheaha.

Rather than wait for us to develop interactive apps for you, now you can develop and deploy your own!

Responsibilities

As with all research software, researchers are responsible for maintaining their own custom software and app definitions fall into that category.

What we can support:

Cheaha platform.
Open OnDemand web portal.
Installation and maintenance of certain system-wide software, and software that requires administrator privileges to install.
Facilitation, documentation and guidance for how to use app definitions.
A curated selection of app definitions and templates.

Development

template sandbox app
- manifest.yml: job metadata, what it is
  - name: Display name in list of apps
  - category: Interactive Apps (don't change)
  - subcategory: grouping in list of apps
  - role: batch_connect (don't change)
  - description: long text field here (use pipe char)
- form.yml.erb: job submission form definition
  - custom_environment
  - extra_app_args
  - bc_num_hours
  - bc_num_slots
  - bc_num_mems
  - bc_partition
  - bc_num_gpus
  - form (composes the form from the above definitions)
- submit.yml.erb: how to transform the submission into a job
  - Keep predefined "email" variable definition! Necessary for XIAS.
  - batch_connect:
    - template: Depends on exactly what is needed.
      - "basic" for webserver clients, like Jupyter
      - "vnc" for apps with a locally-served graphical interface, like MATLAB
  - script: lots of flexibility here using Ruby applied to the form fields above
- template/script.sh.erb: what is executed within the job
  - this is the sbatch payload
  - write it like any other job script
  - include context.custom_environment
- template/before.sh.erb
  - things to do before sbatch ...
- template/after.sh.erb
  - things to do after sbatch ...

Deployment

Document the process of deploying a sandbox app on OOD

Check legacy docs at: https://docs.uabgrid.uab.edu/wiki/Open_OnDemand_Sandbox
Check (latter half of) recording at: https://uab.app.box.com/folder/204278671584

Generally:

Make $DATA_USER/ondemand/dev
OOD -> Help -> Restart Web Server
Clone the job repo into it (either through OOD interface or directly into dir)
Go to "My Interactive Sessions" and check the left pane

Examples

From Cheaha:

RStudio Server: https://github.com/uabrc/bc_uab_rstudio_server
SAS: https://github.com/uabrc/bc_uab_sas
MATLAB: https://github.com/uabrc/bc_uab_matlab
JupyterLab: https://github.com/uabrc/bc_uab_jupyterlab
Jupyter Notebook: https://github.com/uabrc/bc_uab_jupyter
ANSYS: https://github.com/uabrc/bc_uab_ansys
IGV: https://github.com/uabrc/bc_uab_igv

Other Examples:

Here is where we can get creative!