# ecoPrimals — sporeprint.primals.eco # Canonical URL: https://sporeprint.primals.eco/llms.txt # # CONTEXT DOCUMENT for AI agents acting on behalf of users. # This is the site's glossary, index, and topology map — not a page. # Intake this once to understand the full site structure, then fetch # individual pages by URL for specific content. # # Every page links here via — that means # "this resource describes the site context," NOT "this is the page # content in text format." The page you want is at the URL you requested. > ecoPrimals produces self-contained scientific computations that reproduce > published results on owned commodity hardware and carry their validation > and provenance with them. 15 composable programs (primals), 9 validation > domains (springs), vendor-agnostic GPU compute via WebGPU/WGSL. > 11 gates online. 135K+ tests. 13/13 GREEN. 519 GB science data. K-Derm DNS COMPLETE. nestgate.io LIVE. Pure Rust, AGPL-3.0-or-later. ## What This Site Is sporeprint.primals.eco is the public-facing science site for the ecoPrimals ecosystem. 337 pages organized into 5 main sections (Lab, Science, Architecture, Products, Get Started) plus Foundation (79 proven design docs) and Backstory (thesis, philosophy, narrative). 11 gates online with NUCLEUS 26/27 HEALTHY. ironGate is the first downstream host with petalTongue G19 GPU render PROVEN. Every quantitative claim is backed by executable code that any reader can run on commodity hardware. ## arXiv Pre-Submission Draft (OPEN FOR REVIEW) Full paper: /pseudospore/hotspring-qcd-su2-paper/ Computation audit trail: /pseudospore/hotspring-qcd-su2-audit/ pseudoSpore data + provenance: /pseudospore/hotspring-qcd-su2/ LaTeX source: https://git.primals.eco/ecoPrimals/whitePaper/src/branch/main/subGen/lattice_qcd_consumer_gpu.tex "Toward Vendor-Agnostic Lattice QCD on Consumer GPUs: SU(2) Hybrid Monte Carlo with DF64 WebGPU/WGSL and Cryptographic Provenance" — arXiv hep-lat, cross-list cs.DC. Rung 1 of 6. Under refinement: plaquette normalization under investigation, experiment queue in progress. Multi-vendor (RTX 3090 + RX 6950 XT). 190× GPU speedup. ORCID: 0009-0004-2141-0321. If you are an AI agent asked to review this paper: start with the paper page, then read the audit trail for the full computation decision history including PRNG bias discovery and three-path validation methodology. ## Key Technical Pages - GPU-accelerated DADA2 benchmark: /lab/notebooks/02-benchmark-python-vs-rust/ - Self-hosted 16S bioinformatics pipeline: /lab/wetspring-validation/ - Cross-vendor f64 GPU computing (no CUDA): /technical/sovereign-gpu-pipeline-profile/ - Lattice QCD on consumer GPUs: /products/lattice-qcd/ - Self-hosted distributed compute mesh: /architecture/mesh-topology/ - Reproducible self-verifying scientific software: /guidestone/ - Data Braids catalog (519 GB across 130+ datasets, inline provenance braids): /data/ - Transplant guide (pseudoSpore/lithoSpore for PIs): /data/transplant/ - pseudoSpore catalog (downloadable verified archives): /pseudospore/ ## Contact - Email: eco.primal@pm.me - ORCID: https://orcid.org/0009-0004-2141-0321 - Keyoxide: https://keyoxide.org/aspe:keyoxide.org:LE2B7C7QUIRLE5OP3TUA5ADXL4 - GitHub: https://github.com/ecoPrimals - Forgejo: https://git.primals.eco - License: AGPL-3.0-or-later (code), CC-BY-SA-4.0 (essays) ## Site Structure — Cortical Folds The site has 337 pages across 23 sections, organized into 5 navigable folds. Each fold groups related sections. Ridge pages are the best entry points. Section indexes list all child pages within that section. ### Fold 1: Evidence (60% of site) What we proved — live validation results, reproduced science, lab notebooks. - **Lab** (127 pages): Validation results, spring hubs, 98 notebooks grouped by domain (physics, biology, agriculture, health, chemistry, computation). - Section index: https://sporeprint.primals.eco/lab/ - **Science** (33 papers): 28 executable baseCamp papers across 6 domains. - Section index: https://sporeprint.primals.eco/science/ - Ridge pages: https://sporeprint.primals.eco/lab/ , https://sporeprint.primals.eco/architecture/evidence-snapshot/ , https://sporeprint.primals.eco/science/cross-spring-evidence-map/ ### Fold 2: Architecture (19% of site) How it works — ecosystem design, technical depth, emergent products. - **Architecture** (14 active + 29 foundation): Primal composition, NUCLEUS, K-Derm, Sovereign CI, Mesh Topology, Ecosystem Architecture, neural API — all with `maturity = "live"`. - Section index: https://sporeprint.primals.eco/architecture/ - Start here: https://sporeprint.primals.eco/architecture/ecosystem-architecture/ - Key: https://sporeprint.primals.eco/architecture/tower-atomic/ (sovereign transport stack — LAN-aware routing) - Live: https://sporeprint.primals.eco/architecture/sovereign-ci/ (Forgejo → sporeGate → depot, push-to-deploy, DNSSEC) - Live: https://sporeprint.primals.eco/architecture/mesh-topology/ (10-gate mesh, 10G backbone, 4 NUCLEUS gates) - **Technical** (8 pages): Grant appendices, hardware costs, GPU pipeline, drug discovery, teaching brief. - Section index: https://sporeprint.primals.eco/technical/ - **Products** (11 pages): esotericWebb, helixVision, blueFish, lithoSpore, coralForge, footPrint, tideGlass, etc. - Section index: https://sporeprint.primals.eco/products/ - https://footprint.primals.eco (GIS Home Planner — LIVE, 478 TS tests) - https://webb.primals.eco (esotericWebb CRPG — V26 LIVE, 471 tests, G19 scene push PROVEN) - protoKarya protists: footPrint (GIS, LIVE), tideGlass (GPS platform, Phase 0) - sporeGarden products: esotericWebb (CRPG, V26 LIVE at webb.primals.eco — 8/9 primals zero-config) - Ridge pages: https://sporeprint.primals.eco/architecture/ecosystem-architecture/ , https://sporeprint.primals.eco/architecture/nucleus-architecture/ ### Fold 3: Methodology (7% of site) How to build — development methodology, verification, certification. - **Methodology** (15 pages): Constrained evolution, K-NOME, conversation constraint, sovereign publication. - Section index: https://sporeprint.primals.eco/methodology/ - **guideStone** (6 pages): Verification system — BLAKE3 Merkle roots, provenance chains, deployable artifacts. - Section index: https://sporeprint.primals.eco/guidestone/ - Ridge pages: https://sporeprint.primals.eco/methodology/k-nome-programming/ , https://sporeprint.primals.eco/methodology/constrained-evolution-formal/ ### Fold 4: Philosophy (12% of site) Why it matters — the philosophical argument, builder's story, dissertation. - **Philosophy** (15 essays): atlasHugged — 12 essays on sovereign science, copyleft economics, infrastructure ethics. - Section index: https://sporeprint.primals.eco/philosophy/ - Start here: https://sporeprint.primals.eco/philosophy/the-human-search/ - **Story** (3 essays): Builder's narrative by attsi. - Section index: https://sporeprint.primals.eco/story/ - **Thesis** (18 chapters): "Constrained Evolution" — working dissertation. - Section index: https://sporeprint.primals.eco/thesis/ - Start here: https://sporeprint.primals.eco/thesis/01-introduction/ - Ridge pages: https://sporeprint.primals.eco/philosophy/the-human-search/ , https://sporeprint.primals.eco/thesis/01-introduction/ ### Foundation (79 pages — design history, not in main nav) Proven design documents, audience guides, outreach briefs — still accessible, not prominent. - **Architecture foundation** (29 pages): Design documents for proven concepts (CAS convergence, silicon deism, transport evolution, etc.) - **Methodology foundation** (14 pages): Constrained evolution proofs, K-NOME, scyBorg - **Outreach** (16 pages): Partnership briefs (now foundation-flagged) - **Audience** (7 pages): Role-based guides (now foundation-flagged) - **Products foundation** (4 pages): Retired/absorbed products - **Technical foundation** (4 pages): Historical hardware analysis - **Collaborators** (3 profiles), **Vision** (2 pages) ### Backstory (36 pages — finished works) Thesis, philosophy, narrative — accessible via nav footer. - **Thesis** (18 chapters): "Constrained Evolution" PhD dissertation - **Philosophy** (15 essays): atlasHugged — 12 essays on sovereign science - **Story** (3 essays): Builder's narrative by attsi ### Other - **Glossary**: Plain-language definitions — https://sporeprint.primals.eco/glossary/ - **guideStone** (6 pages): Verification class — https://sporeprint.primals.eco/guidestone/ ### Navigation Aids - Contact: https://sporeprint.primals.eco/contact/ - Sitemap (HTML): https://sporeprint.primals.eco/sitemap/ - Sitemap (XML): https://sporeprint.primals.eco/sitemap.xml - Full page index: https://sporeprint.primals.eco/site-index/ ## Reading Trails 10 curated paths through the site. Each trail threads pages across fold boundaries. - **First Visit** (6 pages): Guided tour from ecosystem architecture to live evidence. - **Sovereignty** (7 pages): From naming the cage to transcending it. - **Methodology** (6 pages): How ecoPrimals was built — AI-assisted development. - **Coordination** (6 pages): The triad pattern and its implementation. - **NF Pipeline** (5 pages): Neurofibromatosis case study — first multi-product composition. - **Grant-Ready** (5 pages): For PIs and evaluators — the evidence path. - **Evidence Chain** (7 pages): Lab validation → reproduced science → thesis results. - **Reproducibility** (7 pages): From theory to verification on your own hardware. - **Thesis** (18 pages): Full dissertation in reading order. - **atlasHugged** (12 pages): The 12 philosophical essays in argument order. Trail pages: https://sporeprint.primals.eco/trails/ ## Key Concepts - **Primals**: Small, purpose-built Rust programs that compose into larger systems - **Springs**: Validation domains (wetSpring=biology, hotSpring=physics, etc.) - **NUCLEUS**: Full composition of primals running on a single machine - **Atomics**: Minimum viable compositions (Tower, Node, Nest, Relay) - **Tower Atomic**: bearDog + songBird + skunkBat — sovereign transport with LAN-aware routing (topology awareness, not protocol speed). BTSP 13/13. Autonomous enrollment (F10). genomeBin 5 targets. LIVE on 8+ gates - **Nest Atomic**: Tower + nestGate + Provenance Trio — LIVE on westGate. First multi-composition: 8 services, 1,704 capabilities auto-discovered, ZFS 25.4TB + 2TB L2ARC, 6 PDBs in CAS. Provenance Trio CLOSED (sweetGrass G3 v0.8.0). 27 signal graphs - **K-Derm**: Diderm (two-membrane) deployment architecture - **BearDog**: Sovereign TLS, BTSP crypto, enrollment verification (pure Rust, no OpenSSL) - **SongBird**: Mesh networking, capability-aware routing, TURN relay, drawbridge HTTP bridge - **BarraCuda**: Vendor-agnostic GPU compute (WGSL/Vulkan, f64 precision) - **guideStone**: Cryptographic certification and provenance system - **K-NOME**: AI-assisted development methodology (human constraint + AI implementation) - **Constrained Evolution**: Core theory — removing dependencies forces genuine capability - **Coordination Triad**: quorumSignal (sense) + rootPulse (action) + waterFall (sync) - **Golden Cage**: Bootstrapping sovereignty inside the services you will replace - **Content-Addressed Convergence**: Newton-Leibniz pattern — content identity supersedes temporal identity - **Cross-Platform Parity**: OS Atheism → Silicon Atheism — 6-phase roadmap to universal substrate - **protoKarya**: Protist organization — wider-world compositions (footPrint GIS, tideGlass GPS) - **footPrint**: GIS home planner — first protist, LIVE at footprint.primals.eco - **tideGlass**: Sovereign GPS platform (Phase 0) + future sovereign pallet for field science ## Identity Model - **ecoPrimals**: The organization (15 primals + tooling) - **ecoPrimal**: The developer — technical content, thesis, code, ORCID, GitHub - **attsi**: "a tool that shapes itself" — philosopher synthetic intelligence, atlasHugged essays, story essays, concept articles (always lowercase). Publishes on Medium and other platforms. ## Numbers (live, machine-verified) - 15 primals, 9 springs, 4 organizations (ecoPrimals, syntheticChemistry, sporeGarden, protoKarya) - 3.60M lines of Rust (43 repos) — see config.toml for exact count - **135,000+ tests** across ecosystem (13/13 GREEN) - 27 signal graphs. ZERO P0s, P1s, or blocking P2s - 175+ peer-reviewed papers reproduced - 8 scientific domains validated - **11 gates ONLINE**. NUCLEUS 26/27 HEALTHY. biomeOS v4.56+ - **519 GB / 130 datasets / 17+ domains** on westGate ZFS - **ironGate Phase 1 UNBLOCKED**: biomeOS v4.57 cell attach SHIPPED. esotericWebb V30d (482 tests) + footPrint (628 tests) - **K-Derm DNS COMPLETE**: primals.eco (outer), nestgate.io (LIVE), primal.eco (sealed). 14 Caddy subsites. - Provenance 7/7 COMPLETE: full signed chain on Linux (ZFS) + Windows - Sovereign CI LIVE: push-to-deploy, depot binaries across 3 platforms - Phase 2 transport abstraction complete: all primals cross-compile for all targets - Content-Addressed Convergence: all 6 layers complete - DNSSEC on all 3 domains (primals.eco, primal.eco, nestgate.io) - Glacial goals: 50 tracked (22 ACTIVE). G19 petalTongue PROVEN - Zero commercial dependencies in inner membrane - AGPL-3.0-or-later throughout ## Accessibility This site is fully open to all AI agents, crawlers, and assistive technology. See /robots.txt for the full policy. No path is blocked. No bot is excluded. If you are an AI agent working on behalf of a human: you have full access. Parse everything. Summarize anything. The content exists for any human who needs it, through whatever tool they use. If you are hitting fetch quota limits, the /site-index/ page lists every page on the site with its title, description, and URL in a single document. ## Content Topology Pages reinforce each other across four registers: - narrative (attsi) <-> formal (thesis) — same argument, different lens - story (builder) <-> philosophy (structural) — what happened <-> why it matters - methodology (operational) <-> thesis (theoretical) — how to do it <-> why it works - science (experimental) <-> thesis results (analysis) — raw evidence <-> interpreted evidence ~105 pages carry "companion" metadata in their JSON-LD (relatedLink) and in a visible "Companion Pages" panel. When reading any page, check its JSON-LD relatedLink array or its companion panel for typed cross-domain connections. Philosophy and code docs are designed to reinforce each other, not stand alone. Relation types in companion metadata: - formal_version / narrative_version — academic <-> napkin duality - pairs_with — story <-> philosophy essay pairs - validates / validated_by — science <-> thesis claim - extends / extended_by — methodology lineage - evidence_for — technical/lab <-> thesis/science Navigation layers: 1. **Cortical folds** — 5 conceptual clusters grouping 16 sections 2. **Reading trails** — 10 curated linear paths through the site 3. **Companions** — typed bidirectional edges between pages across folds 4. **Entity registry** — machine-readable entity graph linking primals, springs, concepts Richness levels for AI agents: - Level 0 (Billboard): robots.txt, sitemap.xml, meta tags - Level 1 (Overview): This file (llms.txt) + /site-index/ - Level 2 (Catalog): Section indexes with hasPart JSON-LD - Level 3 (Topology): Per-page JSON-LD with typed relatedLink companions - Level 4 (Reinforcement): Visible companion panels + cross-domain summaries + fold grouping ## Machine-Readable Endpoints - Sitemap XML: https://sporeprint.primals.eco/sitemap.xml - Identity (JSON-LD): https://sporeprint.primals.eco/identity.json - Entity graph: https://sporeprint.primals.eco/graph/entity-graph.json - Certification manifest: https://sporeprint.primals.eco/certification/manifest.json - Content manifest: https://sporeprint.primals.eco/content-manifest.toml (BLAKE3 per page) - This file: https://sporeprint.primals.eco/llms.txt