Notebook PGE

Refer to the NISAR JupyterHub User Guide for details on using the notebooks in this repository to execute a notebook at scale within the SDS.

Below is the 'standard' README.md file that is auto-generated upon executing notebook-pge-wrapper create.

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Generating a base Notebook PGE project

$ notebook-pge-wrapper create <project_name>

The following project structure will be generated

<project_name>
├── README.md
├── docker/
│   └── Dockerfile
└── notebook_pges/

• Dockerfile will go through container-builder to build the docker image
  • Will later be used to execute the notebook in a PGE setting
• Place all your .ipynb files in notebook_pges/

Papermill

Your notebooks will leverage papermill to execute notebooks

• Papermill Project
• Papermill parameters documentation
• Can set parameter types 2 ways
  • Adding a comment, ie. x = 34 # type: int
  • Python type hinting (introduced in python 3.5)

HySDS job specs generation

• Tag the top notebook cell with parameters
  • To add tags in your notebook, go to the toolbar: View -> Cell Toolbar -> Tags
• prepend any hysds specification fields with hysds_ and extract_hysds_specs will populate hysds-io and job_specs with it's specified values
  • If not found it will set to default values (ie. time_limit: 3600)

# job_specs
hysds_time_limit -> time_limit
hysds_soft_time_limit -> soft_time_limit
hysds_disk_usage -> disk_usage
hysds_required_queue -> required_queue

# hysds-ios
hysds_submission_type -> submission_type
hysds_label -> label

Example:

# parameters
from typing import List

a = 100 # type: int
b = "jfksl" # type: str
c = 10.2553 # type: float
d = [1,2,3,4,5] # type: List
e: List[str] = ['a', 'b', 'c']
f = "fjskl"
g: List[str] = ["a", "b", "c"]

# hysds specs
hysds_time_limit = 57389
hysds_soft_time_limit = 4738
hysds_disk_usage = "10GB"
hysds_submission_type = "iteration"
hysds_required_queue = "test_queue-worker"
hysds_label = "TEST LABEL FOR HYSDS_IOS"

Use the notebook-pge-wrapper cli to generate the spec files

• notebook-pge-wrapper specs all to iterate generate spec files for all notebooks in notebook_pges/
• notebook-pge-wrapper specs <notebook path> to generate spec files for a notebook

$ notebook-pge-wrapper specs --help
Usage: notebook-pge-wrapper specs [OPTIONS] NOTEBOOK_PATH

  Generates the hysdsio and job specs for json files (in the docker
  directory) for a notebook

  enter "all" to generate all spec files in notebook_pges/

  ie. notebook-pge-wrapper specs <notebook_path or all>

  :param notebook_path: str :return: None