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Use when asked to set up, install, or bootstrap catheter_navigation, or when hitting import\u002FGPU\u002Fslangpy errors.\nlicense: Apache-2.0\nmetadata:\n  author: \"Isaac for Healthcare Team \u003Cisaac-for-healthcare-support@nvidia.com>\"\n  tags:\n    - isaac-for-healthcare\n    - i4h\n    - catheter-navigation\n    - setup\n    - installation\n---\n\n# i4h Catheter Navigation - Setup\n\n## Purpose\n\nVerify host and GPU requirements, confirm the `.\u002Fi4h` CLI sees the workflow, and run CPU smoke tests. Use when asked to set up catheter navigation or when hitting missing imports, GPU, or slangpy errors.\n\n## Base Code\n\nThese steps drive the i4h-workflows base code (the `workflows\u002Fcatheter_navigation\u002F` tree). To reuse an existing checkout, set `I4H_WORKFLOWS` to its path (no clone happens). Otherwise this resolves the current repo, or clones to `~\u002Fi4h-workflows` - pick that default without prompting. Run every command below from the resolved root:\n\n```bash\nROOT=\"${I4H_WORKFLOWS:-$(git rev-parse --show-toplevel 2>\u002Fdev\u002Fnull)}\"\nif [ ! -d \"$ROOT\u002Fworkflows\u002Fcatheter_navigation\" ]; then\n  ROOT=\"${I4H_WORKFLOWS:-$HOME\u002Fi4h-workflows}\"\n  [ -d \"$ROOT\u002Fworkflows\u002Fcatheter_navigation\" ] || git clone https:\u002F\u002Fgithub.com\u002Fisaac-for-healthcare\u002Fi4h-workflows \"$ROOT\"\nfi\nexport I4H_WORKFLOWS=\"$ROOT\"; cd \"$ROOT\"\n```\n\n## Basics\n\n- Catheter navigation registers via `workflows\u002Fcatheter_navigation\u002Fmetadata.json` and runs through `.\u002Fi4h run catheter_navigation \u003Cmode>`.\n- Runtime is package-first: `render_drr` uses installed `fluorosim` (`python -m fluorosim.examples.render_drr`), while `interactive_viewport` is launched from the local workflow script path in `metadata.json`.\n- Docker image: `workflows\u002Fcatheter_navigation\u002Fdocker\u002FDockerfile` (drop `--local` on `.\u002Fi4h run` to use it).\n- GPU modes need slangpy, Warp, and CUDA; CPU smoke tests do not.\n\n## Preflight\n\n```bash\ncommand -v python3\ncommand -v git\nnvidia-smi\ndf -h .\n```\n\nRequired: Linux x86_64 (Ubuntu 22.04\u002F24.04 tested), NVIDIA GPU (CC >= 7.0), driver compatible with CUDA 12.8, >= 16 GB RAM, >= 20 GB disk.\n\nRun the steps below in order. Each step is a separate bash call; variables persist in the local agent's tmux session.\n\n### Step 1 - resolve repo and export paths\n\n```bash\nREPO_ROOT=\"${I4H_WORKFLOWS:-$(git rev-parse --show-toplevel 2>\u002Fdev\u002Fnull)}\"; [ -d \"$REPO_ROOT\u002Fworkflows\u002Fcatheter_navigation\" ] || REPO_ROOT=\"$HOME\u002Fi4h-workflows\"\nWF_ROOT=\"${REPO_ROOT}\u002Fworkflows\u002Fcatheter_navigation\"\nSIM_ROOT=\"${WF_ROOT}\u002Fscripts\u002Fsimulation\"\nexport PYTHONPATH=\"${SIM_ROOT}:${PYTHONPATH:-}\"\nRUN_DIR=\"${WF_ROOT}\u002Fruns\u002Fsetup_$(date +%Y%m%d_%H%M%S)\"\nmkdir -p \"${RUN_DIR}\u002Flogs\"\nln -sfn \"${RUN_DIR}\" \"${WF_ROOT}\u002Fruns\u002F.latest\"\n```\n\n### Step 2 - verify CLI registration\n\n```bash\n\"${REPO_ROOT}\u002Fi4h\" modes catheter_navigation 2>&1 | tee \"${RUN_DIR}\u002Flogs\u002Fmodes.log\"\n```\n\n### Step 3 - CPU smoke tests (no GPU)\n\n```bash\npython3 -m unittest workflows\u002Fcatheter_navigation\u002Ftests\u002Ftest_fluorosim_smoke.py \\\n  2>&1 | tee \"${RUN_DIR}\u002Flogs\u002Fsmoke.log\"\n```\n\nExpected: `Ran 7 tests ... OK`. Parser error lines in stderr from negative test cases are expected.\n\n### Step 4 - optional GPU sanity (synthetic DRR)\n\nSkip if no GPU or slangpy not installed.\n\n```bash\n\"${REPO_ROOT}\u002Fi4h\" run catheter_navigation render_drr --local \\\n  --run-args=\"--output ${RUN_DIR}\u002Fdrr.png\" \\\n  2>&1 | tee \"${RUN_DIR}\u002Flogs\u002Frender_drr.log\"\n```\n\n## Verify\n\n```bash\ntest -f \"${RUN_DIR}\u002Flogs\u002Fsmoke.log\"\ngrep -q \"OK\" \"${RUN_DIR}\u002Flogs\u002Fsmoke.log\"\npython3 -c \"import fluorosim; print('fluorosim', fluorosim.__file__)\"\n```\n\n## Prerequisites\n\n- Repo checkout with `workflows\u002Fcatheter_navigation\u002F` present.\n- Python 3 with numpy; full GPU stack (slangpy, torch CUDA, warp) for render\u002Fviewport modes.\n\n## Limitations\n\n- No dedicated `setup.sh` yet - this skill verifies and documents host requirements; use Docker when host deps are incomplete.\n- Step 4 requires a GPU; Step 3 alone is sufficient for CI-style verification.\n\n## Troubleshooting\n\n- **Error:** `fluorosim` import fails - Cause: PYTHONPATH not set. 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For RTSP\u002Flive streams, use amc-run-rtsp-calibration instead.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1688,1691,1694,1695],{"name":1689,"slug":1690,"type":15},"Automation","automation",{"name":1692,"slug":1693,"type":15},"Imaging","imaging",{"name":9,"slug":8,"type":15},{"name":1696,"slug":1697,"type":15},"Video","video","2026-07-17T05:28:53.905004",{"slug":1700,"name":1700,"fn":1701,"description":1702,"org":1703,"tags":1704,"stars":23,"repoUrl":24,"updatedAt":1713},"amc-setup-calibration-stack","deploy AutoMagicCalib microservice with Docker","Launch AutoMagicCalib microservice and web UI from NGC release images via Docker Compose. Use when user says 'deploy auto calibration', 'launch auto calibration', 'launch AMC', 'start MS+UI', or 'set up auto-magic-calib'. 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Covers the two pin sites (GitHub CI in `docker\u002F.ngc_version.dev` and GitLab CI in `.gitlab\u002Fstages\u002F01.build.yml`), the post-bump CI loop (re-run functional tests, refresh golden values, mark broken tests), and the gotchas that bit PRs",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1769,1772],{"name":1770,"slug":1771,"type":15},"CI\u002FCD","ci-cd",{"name":1649,"slug":1650,"type":15},"2026-07-14T05:25:59.97109",{"slug":1775,"name":1775,"fn":1776,"description":1777,"org":1778,"tags":1779,"stars":1760,"repoUrl":1761,"updatedAt":1785},"mcore-cicd","manage CI\u002FCD pipelines for Megatron-LM","CI\u002FCD reference for Megatron-LM. Covers CI pipeline structure, PR scope labels, triggering internal GitLab CI (which force-pushes the current branch to a pull-request\u002FBRANCH ref — always dry-run and verify the destination first; never run against shared or protected branches), and CI failure investigation.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1780,1781,1782],{"name":1770,"slug":1771,"type":15},{"name":1649,"slug":1650,"type":15},{"name":1783,"slug":1784,"type":15},"GitHub","github","2026-07-27T06:06:12.278222",{"slug":1787,"name":1787,"fn":1788,"description":1789,"org":1790,"tags":1791,"stars":1760,"repoUrl":1761,"updatedAt":1799},"mcore-create-issue","investigate CI failures and create issues","Investigate a failing GitHub Actions run or job and create a GitHub issue for the failure.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1792,1795,1796],{"name":1793,"slug":1794,"type":15},"Debugging","debugging",{"name":1783,"slug":1784,"type":15},{"name":1797,"slug":1798,"type":15},"Triage","triage","2026-07-14T05:25:57.442089",{"slug":1801,"name":1801,"fn":1802,"description":1803,"org":1804,"tags":1805,"stars":1760,"repoUrl":1761,"updatedAt":1812},"mcore-linting-and-formatting","lint and format Megatron-LM code","Linting and formatting for Megatron-LM. Covers running autoformat.sh, tools (ruff, black, isort, pylint, mypy), and code style rules.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1806,1809],{"name":1807,"slug":1808,"type":15},"Best Practices","best-practices",{"name":1810,"slug":1811,"type":15},"Code Analysis","code-analysis","2026-07-14T05:25:56.18433",{"slug":1814,"name":1814,"fn":1815,"description":1816,"org":1817,"tags":1818,"stars":1760,"repoUrl":1761,"updatedAt":1826},"mcore-migrate-gpt-to-hybrid","migrate Megatron-LM models to HybridModel","Migration guide for moving Megatron Core GPTModel checkpoints, model providers, training commands, and layer mappings to HybridModel.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1819,1822,1825],{"name":1820,"slug":1821,"type":15},"Machine Learning","machine-learning",{"name":1823,"slug":1824,"type":15},"Migration","migration",{"name":9,"slug":8,"type":15},"2026-07-17T06:07:11.777011",{"slug":1828,"name":1828,"fn":1829,"description":1830,"org":1831,"tags":1832,"stars":1760,"repoUrl":1761,"updatedAt":1837},"mcore-onboard-gb200-1node-tests","onboard functional tests for GB200","Onboard 1-node GitHub MR functional tests for GB200 from existing mr-scoped 2-node tests.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1833,1836],{"name":1834,"slug":1835,"type":15},"QA","qa",{"name":1679,"slug":1680,"type":15},"2026-07-14T05:25:53.673039",{"slug":1839,"name":1839,"fn":1840,"description":1841,"org":1842,"tags":1843,"stars":1760,"repoUrl":1761,"updatedAt":1846},"mcore-run-on-slurm","launch distributed training jobs on SLURM","How to launch distributed Megatron-LM training jobs on a SLURM cluster. Covers a minimal sbatch skeleton, environment-variable setup for torch.distributed.run, CUDA_DEVICE_MAX_CONNECTIONS rules across hardware and parallelism modes, container conventions, monitoring, and per-rank failure diagnosis.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1844,1845],{"name":1649,"slug":1650,"type":15},{"name":1652,"slug":1653,"type":15},"2026-07-14T05:25:49.362534",{"slug":1848,"name":1848,"fn":1849,"description":1850,"org":1851,"tags":1852,"stars":1760,"repoUrl":1761,"updatedAt":1860},"mcore-split-pr","split pull requests to reduce review load","Split a PR into multiple PRs to reduce the number of required CODEOWNERS reviewer groups.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1853,1856,1857],{"name":1854,"slug":1855,"type":15},"Code Review","code-review",{"name":1783,"slug":1784,"type":15},{"name":1858,"slug":1859,"type":15},"Pull Requests","pull-requests","2026-07-14T05:26:01.226578",{"slug":1862,"name":1862,"fn":1863,"description":1864,"org":1865,"tags":1866,"stars":1760,"repoUrl":1761,"updatedAt":1869},"mcore-testing","run and manage Megatron-LM tests","Test system for Megatron-LM. Covers test layout, recipe YAML structure, adding and running unit and functional tests, golden values, marker filters, and CI parity.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1867,1868],{"name":1834,"slug":1835,"type":15},{"name":1679,"slug":1680,"type":15},"2026-07-14T05:25:54.928983",{"slug":1871,"name":1871,"fn":1872,"description":1873,"org":1874,"tags":1875,"stars":1760,"repoUrl":1761,"updatedAt":1878},"nightly-sync","manage nightly main-to-dev sync workflows","Domain knowledge for the nightly main-to-dev sync workflow. Covers merge strategy, CI architecture, failure investigation, and known issues.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":9},[1876,1877],{"name":1689,"slug":1690,"type":15},{"name":1770,"slug":1771,"type":15},"2026-07-30T05:29:03.275638",496]