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Merge pull request #19 from hdpriest-ui/develop
more documentation overhaul
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‎documentation/source/contributing.rst‎

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Developer Guide: Creating New Kernels
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-------------------------------------
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- To contribute new R kernels (library environments) to the central catalog, see the maintainer section for a step-by-step walkthrough using Bioconductor as an example.
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- To contribute new R kernels (library environments) to the central catalog, see the contributor section for a step-by-step walkthrough using Bioconductor as an example.
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Development Environment
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-----------------------

‎documentation/source/contributor/index.rst‎

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Kernel Contributor Guide
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========================
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This section provides guidance for contributors who want to create and submit new R kernels to the ICRN catalog.
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This section provides guidance for contributors who want to create and submit new kernels to the ICRN catalog, as well as maintainers who manage and index kernels.
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.. toctree::
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:maxdepth: 2
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creating_r_kernels
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kernel_requirements
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creating_r_kernels
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r_kernels
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python_kernels
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documentation/source/maintainer/jupyter_pieces.rst renamed to documentation/source/contributor/jupyter_pieces.rst

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Adding Jupyter Pieces (Maintainer)
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=================================
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Adding Jupyter Pieces
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=====================
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.. note::
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Instructions for adding Jupyter integration to Python kernels are forthcoming.

‎documentation/source/contributor/kernel_requirements.rst‎

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* - Package List
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- Complete list of included packages with versions
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Indexing Kernels
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----------------
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The ``kernel_indexer`` script can be used to create package manifests and inventory all kernels in a repository. This is useful for:
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- Tracking which packages are included in each kernel
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- Generating package inventories for documentation
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- Creating indexes for package discovery
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To index all Python kernels in a repository:
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.. code-block:: bash
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./kernel_indexer index --kernel-root /path/to/repository --language Python
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This creates a ``package_manifest.json`` file in each kernel directory containing:
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- Kernel name and version
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- Language and language version
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- Complete list of packages with versions and sources
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- Indexing timestamp
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Required Directory Structure
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----------------------------
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.. code-block:: text
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<kernel_root>/Python/<kernel_name>/<version>/
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├── conda-meta/ # Conda environment metadata
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├── lib/
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│ └── python3.x/
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│ └── site-packages/
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]
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}
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Catalog Entry
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-------------
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After creating the kernel, add an entry to ``icrn_kernel_catalog.json``:
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.. code-block:: json
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{
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"R": {
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"mykernel": {
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"1.0": {
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"path": "R/mykernel/1.0",
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"description": "Description of the kernel"
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}
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}
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}
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}
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Quality Requirements
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--------------------
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Version Guidelines
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------------------
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- Follow semantic versioning: ``MAJOR.MINOR`` or ``MAJOR.MINOR.PATCH``
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- Follow semantic versioning: ``MAJOR.MINOR``
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- For upstream project kernels, match their versioning
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- Increment version for any package updates
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- Never modify an existing version in-place

documentation/source/maintainer/python_kernels.rst renamed to documentation/source/contributor/python_kernels.rst

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Python Kernels (Maintainer)
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==========================
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Python Kernels
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==============
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This section provides guidance for maintainers on creating and managing Python kernels for the ICRN platform.
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This section provides guidance for creating and managing Python kernels for the ICRN platform.
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Creating Python Kernels
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----------------------

documentation/source/maintainer/r_kernels.rst renamed to documentation/source/contributor/r_kernels.rst

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R Kernels (Maintainer)
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======================
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R Kernels
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=========
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This section provides guidance for maintainers on creating and managing R kernels for the ICRN platform.
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This section provides guidance for creating and managing R kernels for the ICRN platform.
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Creating R Kernels
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- Include all required dependencies
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- Work with the ICRN Jupyter environment
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- Pass validation tests
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- that permissions are set correctly: general users should have read access, while group and owner will need read, write, and execute
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Detailed step-by-step instructions for creating R kernels are available in the kernel creation documentation.

‎documentation/source/index.rst‎

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The Illinois Computes Library & Kernel Manager is a tool for managing R library environments for the Illinois Computes Research Notebook (ICRN) platform. It enables users to easily install, switch, and manage complex R package sets without manual configuration.
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.. figure:: demo_resources/icrn_libraries_mngr_switch.gif
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:align: center
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:width: 600
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Kernel Information Browser
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--------------------------
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Example: Instantly switching from one large R Kernel to another.
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For advanced searching and detailed kernel information, visit the ICRN Kernel Information web interface:
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- **Production**: https://kernels.ncsa.illinois.edu
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- **Development**: https://kernels.cori-dev.ncsa.illinois.edu/
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The web interface allows you to browse all kernels by language, search for specific packages across all kernels, view complete package manifests for each kernel, and copy CLI commands for kernel operations.
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.. toctree::
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user/index
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administrator/index
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contributor/index
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maintainer/index
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contributing
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troubleshooting
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reference

‎documentation/source/maintainer/index.rst‎

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‎documentation/source/troubleshooting.rst‎

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3. **Review configuration**: Ensure all paths and permissions are correct
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4. **Report issues**: Create an issue on GitHub with detailed error information
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For more detailed information, see the :doc:`user_guide` and :doc:`maintainer_guide`.
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For more detailed information, see the :doc:`user/index` and :doc:`contributor/index`.

‎documentation/source/user/campus_cluster/slurm_examples.rst‎

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# Run Python script
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python my_analysis.py
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GPU Kernel Batch Job
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-------------------
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.. code-block:: bash
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#!/bin/bash
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#SBATCH --job-name=gpu_kernel_job
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#SBATCH --output=gpu_kernel_job_%j.out
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#SBATCH --error=gpu_kernel_job_%j.err
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#SBATCH --time=02:00:00
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=4
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#SBATCH --mem=16G
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#SBATCH --gres=gpu:1
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# Load required modules
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module load python
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module load jupyter
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module load cuda
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module load cudnn
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# Get and use GPU kernel
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icrn_manager kernels get Python <gpu_kernel_name> <version>
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icrn_manager kernels use Python <gpu_kernel_name> <version>
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# Run GPU-enabled script
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python my_gpu_analysis.py
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.. note::
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Adjust resource requirements (memory, CPU, GPU) based on your specific needs.

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