Merge pull request #35 from sbryngelson/refac

Author: sbryngelson

.github/workflows/pages.yml

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+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches: ["master"]
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1'
+          bundler-cache: true
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Build with Jekyll
+        run: |
+          gem install bundler
+          bundle init
+          echo 'gem "jekyll", "~> 4.3.2"' >> Gemfile
+          echo 'gem "just-the-docs"' >> Gemfile
+          bundle install
+          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2 

SEARCH_README.md

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+# Search Functionality for Group Syllabus
+
+This document explains how to use and maintain the search functionality for the Georgia Tech Computational Physics Group Syllabus.
+
+## How It Works
+
+The search functionality is implemented using GitHub Pages with the Just the Docs Jekyll theme, which includes built-in search capabilities. This allows students and researchers to quickly find information across all documentation pages.
+
+## Features
+
+- Full-text search across all documentation pages
+- Search by headings, content, and keywords
+- Highlighting of search terms in results
+- Search results ranked by relevance
+
+## Setting Up GitHub Pages
+
+1. **Enable GitHub Pages in your repository settings**:
+   - Go to Settings > Pages
+   - Set the source to "GitHub Actions"
+
+2. **Verify the workflow is running**:
+   - Check the Actions tab to ensure the "Deploy Jekyll site to Pages" workflow is running
+   - The first build may take a few minutes
+
+## Adding New Content
+
+When adding new content to be searchable:
+
+1. Create markdown files in the appropriate collection directory:
+   - `_syllabus/` - For general syllabus content
+   - `_papers/` - For writing and publication guidance
+   - `_details/` - For specific details and resources
+
+2. Add front matter to each markdown file:
+   ```yaml
+   ---
+   layout: page
+   title: Your Page Title
+   nav_order: 1
+   description: "Brief description of the page content"
+   permalink: /collection-name/page-name
+   ---
+   ```
+
+3. Push changes to the repository, and GitHub Actions will automatically rebuild the site with updated search index
+
+## Search Tips for Users
+
+Share these tips with your students:
+
+- Use the search bar in the top navigation to find content
+- Use quotes for exact phrase matching: `"research meeting"`
+- Use multiple terms to narrow results: `funding conference`
+- Results are ranked by relevance
+
+## Maintenance
+
+- The search index is automatically updated when changes are pushed to the repository
+- No manual maintenance is required
+- To modify search behavior, edit the `search` section in `_config.yml`
+
+## Troubleshooting
+
+If search isn't working properly:
+
+1. Check that the GitHub Pages site is properly deployed
+2. Verify that front matter is correctly formatted in all markdown files
+3. Ensure the `search_enabled: true` setting is in `_config.yml`
+4. Check the GitHub Actions logs for any build errors 

_config.yml

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+title: Computational Physics @ GT Group Documentation
+description: Documentation and resources for the Computational Physics research group at Georgia Tech
+theme: just-the-docs
+
+url: https://comp-physics.github.io/group-shb
+
+aux_links:
+  "Group GitHub": 
+    - "https://github.com/comp-physics"
+
+# Enable search
+search_enabled: true
+search:
+  # Split pages into sections that can be searched individually
+  heading_level: 2
+  # Maximum amount of previews per search result
+  previews: 3
+  # Maximum amount of words to display before a matched word in the preview
+  preview_words_before: 5
+  # Maximum amount of words to display after a matched word in the preview
+  preview_words_after: 10
+
+# Footer content
+footer_content: "CC BY-NC 4.0"
+
+# Collections for website structure
+collections:
+  syllabus:
+    permalink: "/:collection/:path/"
+    output: true
+  papers:
+    permalink: "/:collection/:path/"
+    output: true
+  details:
+    permalink: "/:collection/:path/"
+    output: true 

_details/computers.md

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+---
+layout: page
+title: Available Computers
+nav_order: 1
+description: "Information about computing resources available to the group"
+permalink: /details/computers
+---
+
+# Computers
+
+This page provides information about the computing resources available to our research group.
+
+## Georgia Tech
+
+* GT PACE Phoenix
+    * User guide [here](https://docs.pace.gatech.edu/phoenix_cluster/gettingstarted_phnx/)
+    * Login via `ssh <GTusername>@login-phoenix-rh9.pace.gatech.edu` to get the RHEL9 nodes
+    * Purpose: All-purpose campus resource of CPU and GPU jobs with a variety of hardware. 
+    * "Rules": Use the `embers` queue type to use idle nodes at zero cost.
+    * To get access, let Spencer know, and he will fill out [this form](https://gatech.service-now.com/home?id=sc_cat_item&sys_id=61bc5e351b37f994a8622f4b234bcbf0).
+ 
+* GT ICE
+  * [Resources/User guide](https://gatech.service-now.com/home?id=kb_article_view&sysparm_article=KB0042095) (click `Available Resources`, e.g.)
+     * This looks like ~40 V100s, 8 A100s, 4 A40s, 20 RTX6000s, and 4 MI210s.
+  * May need to contact Spencer for access.
+  * __Most GPU nodes sit idle__
+     * On those nodes: `MaxNodes=UNLIMITED MaxTime=18:00:00`
+
+* GT Rogues Gallery 
+    * User guide [here](https://gt-crnch-rg.readthedocs.io/en/main/)
+    * Purpose: Use of brand-new, forward-looking, or weird hardware. At the time of writing, it includes an NV H100 server, GH200 nodes, AMD MI210 GPU server, Bluefield-2/3 SmartNICs, RISC-V and Arm CPUs, etc.
+    * "Rules": There are few rules; just follow the guidelines in the documentation. There are no limitations on hardware access/node hours.
+    * Get access via [this link](https://crnch-rg.cc.gatech.edu/request-rogues-gallery-access/)
+
+* GT Wingtip-gpu3
+    * User guide [here](https://github.gatech.edu/cse-computing/compute-resources/blob/main/docs/systems/wingtip-gpu.md)
+    * Purpose: Small (but possibly very long) GPU jobs, hosts 5x NV A100-80GB PCIe at the moment
+    * "Rules":  Be mindful of others' use of this machine as it does not have a scheduler.
+    * Get access by emailing [Will Powell](mailto:will.powell@cc.gatech.edu), cc me.
+
+## University Clusters
+
+* ACCESS-CI computers
+    * These are a set of university supercomputers listed [here](https://access-ci.org/resource-providers/). Each has its own user guide. At the time of writing, we have access to NCSA Delta (A100 GPUs), PSC Bridges2 (V100 GPUs), Purdue Anvil, and Texas A&M ACES (H100 GPUs), but we can change to others as needed. We primarily use NCSA Delta.
+    * Purpose: All-purpose resources for CPU and GPU simulation. 
+    * "Rules": Be mindful of the available node hours. Queue times might be long.
+    * Our account number:
+       * `PHY240200` (ACCESS-CI Maximize, NCSA Delta only)
+       * `PHY210084` (ACCESS-CI Accelerate; Bridges2, Delta, and so on)
+    * Get access by
+        * Creating an account [here](https://identity.access-ci.org/new-user.html)
+        * Then, message Spencer on Slack with your username
+   * On [NCSA Delta](https://docs.ncsa.illinois.edu/systems/delta/en/latest/)
+      * The account name is `bdiy-delta-gpu` (ACCESS-CI Maximize) or `bbsc-delta-gpu` (ACCESS-CI Accelerate) for GPU resources
+      * Replace `-gpu` with `-cpu` for CPU resources
+
+## DOE Labs
+
+* Oak Ridge National Lab OLCF: Frontier/Wombat/Andes/etc.
+    * Purpose
+        * Frontier: Very large-scale GPU simulation on AMD MI250X GPUs.
+        * Wombat: Testbed for next-gen HPC platforms, including ARM nodes and soon next-generation NVIDIA nodes (GraceHopper).
+        * Andes: For postprocessing
+    * Our account number: `CFD154`
+    * "Rules": Ask Spencer before running any jobs that use a very large number of node hours
+    * Get access by
+        * Create an account by following [these instructions](https://docs.olcf.ornl.gov/accounts/accounts_and_projects.html#applying-for-a-user-account)
+        * The account/allocation number is `CFD154`.
+
+* Sandia National Lab (SNL)
+    * Purpose: Resources for DOE-sponsored/funded research projects are only available to those students working on these projects. You will only have access to non-restricted resources.
+    * "Rules": Usually, there are not many rules aside from the very many that they will impute onto you as you acquire access to these machines.
+    * Login process (Sandia National Lab-specific)
+        * Onto the DaaS
+            * VMware Horizon ([download online](https://customerconnect.vmware.com/en/downloads/info/slug/desktop_end_user_computing/vmware_horizon_clients/horizon_8))
+            * URL: `daas.sandia.gov`
+            * Passcode: `[PIN] + [your yubikey1timepassword]`
+            * Password: `[kerberos pw]`
+            * 3 options
+                * badge update
+                * conference room
+                * daas <- open this one
+            * Can complete training and do other things here, like look at your WebCARS to get `WC_ID` (which you need to submit jobs)
+        * Onto a computer remotely
+            * https://hpc.sandia.gov/access/ssh/
+            * Can do the below with DaaS (using my example username, `[usrname]`)
+                * `ssh [usrname]@srngate.sandia.gov`
+                * Passcode: `[PIN] + [yubikey one time pw]`
+                * Choose a computer: e.g., Skybridge, Attaway, Weaver, etc.
+                * Press `1` - `ssh session`
+                * Default user name (`[usrname]`)
+                * Password is (usually) the Kerberos one
+                * If it asks for token OTP (e.g., on Weaver) then this is `[PIN] + [yubikey1timepassword]`
+
+ * LLNL Livermore Computing: Lassen, Tioga, etc.
+    * Anyone working on a specific LLNL project can use [LLNL CZ](https://lc.llnl.gov/) (non-restricted) resources
+    * Talk to Spencer about getting access to CZ (collaboration zone) if you are working on a LLNL project
+    * "Rules": Usually not many rules aside from the very many that they will impute onto you as you acquire access to these machines.
+    * Login process (Lawrence Livermore National Lab-specific)
+        * Onto LC-idm
+            * URL: `ic-idm.llnl.gov`
+            * Passcode: `[PIN] + [rsa one time password]`
+            * Can use to view user profile and request roles (ask for resources on specific machines)
+        * Onto the LC
+            * URL: `lc.llnl.gov`
+            * Passcode: `[PIN] + [rsa one time password]`
+            * Requires three logins to fully log in
+            * Can be used to access collaboration tools such as Confluence and Gitlab, user documentation, and MyLC for alerts, machine status, and job status
+        * Onto a computer remotely
+            * Can do the below with ssh (using my example username, `[usrname]`, for a specific LLNL machine, `[llnlmachine]`)
+                * `ssh [usrname]@[llnlmachine].llnl.gov`
+                * Passcode: `[PIN] + [rsa one time password]`
+             
+## DOD Labs
+
+* Department of Defense
+    * Anyone working on a DOD project can use [DOD HPCMP](https://www.hpc.mil/) (non-restricted) resources 
+    * The process of getting permissions to the non-restricted systems is a bit tedious but usually worth it
+    * See [here](https://centers.hpc.mil/) for information on the available supercomputers
+        * In particular, it's useful to keep an eye on [upcoming systems](https://centers.hpc.mil/systems/hardware.html#upcoming)
+        * Current unclassified systems are [here](https://centers.hpc.mil/systems/unclassified.html)
+    * Talk to Spencer about getting access to a DOD machine if you are working on a DOD project
+    * Subproject: `ONRDC51242690`, Group: `5124D690`, Project: `5124`
+       * Site: `NAVY`
+          * nautilus 
+          * narwhal
+       * Site: `ERDC`
+          * carpenter
+    * [Docs available here](https://centers.hpc.mil/users/docs/index.html#general) 

_details/hardware.md

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+---
+layout: page
+title: Hardware Ownership
+nav_order: 3
+description: "Information about hardware ownership and policies"
+permalink: /details/hardware
+---
+
+{% include_relative ../group-syllabus/hardware.md %} 

_details/index.md

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+---
+layout: page
+title: Details
+nav_order: 4
+description: "Specific details about resources and policies"
+permalink: /details
+has_children: true
+---
+
+# Details
+
+This section contains specific information about resources, policies, and guidelines for undergraduate researchers and hardware usage.
+
+## Available Documents
+
+* [Undergraduate specifics](/details/undergraduate-specifics) - Information specific to undergraduate researchers
+* [Available computers](/details/computers) - Information about computing resources available to the group
+* [Whose hardware is this, anyway?](/details/hardware) - Information about hardware ownership and policies 

_details/undergraduate-specifics.md

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+---
+layout: page
+title: Undergraduate Specifics
+nav_order: 1
+description: "Information specific to undergraduate researchers"
+permalink: /details/undergraduate-specifics
+---
+
+{% include_relative ../group-syllabus/undergraduate-specifics.md %} 

_papers/figures.md

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+---
+layout: page
+title: Making Figures
+nav_order: 3
+description: "Guidelines for creating effective figures for publications"
+permalink: /papers/figures
+---
+
+{% include_relative ../group-syllabus/figures.md %} 

_papers/formatting.md

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+---
+layout: page
+title: Formatting Your Documents
+nav_order: 2
+description: "Guidelines for formatting academic papers and documents"
+permalink: /papers/formatting
+---
+
+{% include_relative ../group-syllabus/formatting.md %} 

_papers/improving-your-writing.md

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+---
+layout: page
+title: Academic Writing
+nav_order: 1
+description: "Guidelines for improving academic writing skills"
+permalink: /papers/improving-your-writing
+---
+
+{% include_relative ../group-syllabus/improving-your-writing.md %}