Experimental research software · Synthetic data · Not for clinical use · Not scientifically validated

Source: docs/orchestration_state.md @ e3d560e · Source SHA-256 3612ab7c649235ae4d95864a77436fd0e7a698eedb94560313f1694b88d57977 · Markdown source

This document is reproduced verbatim. Only sensitive information (server host names, OS user names, file paths, account and billing details, AI usage, internal request IDs, and private repository names) was redacted in 15 places. No other content was changed.

Orchestration state (multi-model engineering log)

Lightweight coordination record. Status vocabulary is strict: PROPOSED < IMPLEMENTED < TESTED < SCIENTIFICALLY VALIDATED. Nothing in this project is scientifically validated against external physiological data.

Current milestone

Phase 1 cardiovascular core: numerical-verification hardening before any reference-model reproduction or renal coupling (see decisions.md).

Verified tool / model configuration (2026-10-31)

Effective tiers: Claude LIGHT/STANDARD/DEEP = haiku/sonnet/opus-5-5. Codex LIGHT = gpt-5.6-terra, STANDARD = gpt-5.6-sol (substitute for unavailable gpt-6.1-sol), DEEP = gpt-6-astra. Note: ~/.codex/config.toml defaults to gpt-6.1-sol, which fails here [redacted: account detail], so always pass -m. [redacted: AI usage detail]

Isolation: this directory is not a git repository. Workers ran in git-baselined scratch copies with their own venvs; the integrator applied reviewed diffs here. Pre-integration snapshot: [redacted: local file path].

Task and routing history

No escalation was needed. No task was retried.

Test evidence (integrated tree)

• Full suite: 101 passed (64 pre-existing + 13 + 24), 5 RDFLib-internal deprecation warnings.
• Default simulate() path unchanged: canonical experiment CSVs regenerated from the integrated code are byte-identical to results/phase1/*.csv.

Findings

• Strict 3-beat 1e-4 mL periodicity verdicts at canonical tolerances depend on solver error control (see physiology.md table); at rtol 1e-11/atol 1e-12/T/400 all three scenarios pass (<= 6.1e-7 mL).
• Solver-integrated SV converges to 1.3e-6 mL under refinement; 400-sample trapezoid SV is biased by ~0.056% (sign scenario-dependent).

Pending / next (PROPOSED)

1. Decide whether the runner should report periodicity_report and cumulative-flow SV in summary.json (changes canonical outputs; needs approval and regenerated results/manifests).
2. Rebuild wheel, reinstall .clean-venv, rerun reproducibility scripts (not done; dist/ wheel and results/ predate these changes).
3. Local parameter sensitivity analysis of final-beat metrics (STANDARD, Codex).
4. Licensed reference-model reproduction (DEEP research). Smith 2004 license resolved 2026-10-31: CC BY 3.0 with attribution (physiology.md). Use only the canonical CellML (evidence/a_smith_2004_canonical.cellml); the workspace-267 capture has no parameter/initial values.
5. Renal coupling remains deferred per decisions.md.

OpenCOR reference run (Hermes, remote research server [redacted: host name])

• 2026-10-31 attempt stopped before download: curl: (6) Could not resolve host: github.com inside the worker CLI sandbox. The host itself resolves github.com, so the block was the sandbox's network policy, not the server.
• Official OpenCOR v0.8.3 OpenCOR-0-8-3-Linux.tar.gz (322,810,313 bytes, GitHub asset SHA-256 513ad729…60ee) is staged at [redacted: server path] (root-owned, read-only to others). Hermes runs as a dedicated service user [redacted: user name and UID], so the first staging under [redacted: server path] was invisible to it (ENOENT); after the move, the archive hash, pythonshell and bin/OpenCOR were checked as that service user. Static ldd with the bundled lib/ and plugins/: core simulation/Python plugins resolve; only GUI, web-view and PMR plugins miss system libraries. Startup not yet tried.
• Reference input switched to the canonical CellML (SHA-256 8cca17e8…3e60); the integrator downloaded and hash-verified it outside the sandbox (2026-10-31 14:25:29 UTC). Simulation status: PROPOSED.
• 2026-11-01 default run (CVODE + KINSOL) loaded the model but simulation.run() failed: std::runtime_error: the maximum number of iterations was reached before convergence. That wording matches KINSOL (septum algebraic equation), not CVODE. Cause not established; a scipy re-implementation (not the reference) points at the discontinuous valve law at Q=0 but that is a hypothesis only.
• 2026-11-01 user-approved solver deviation: OpenCOR's built-in fixed-step fourth-order Runge-Kutta replaces CVODE only. KINSOL, the model, parameters and units are unchanged. Two step sizes (1e-5 s and 5e-6 s) are run for a step-halving comparison. Outputs are labelled "OpenCOR RK4", never as the OpenCOR default-solver result. This does not show why CVODE failed.
• Result of the approved runs: A and B both completed 1.5 s and wrote CSVs; no KINSOL convergence error. The existing comparator rejects the pair because output times differ at floating-point level, so the aggregate status is still failed (comparator condition, not a failed calculation).
• Decision approved by the user (2026-11-01): time stamps count as equal when |dt| <= 1e-9 s, applied to the time axis only. Raw CSVs stay unmodified (no rounding or interpolation). Fixed before looking at value differences. Superseded the same day (user-approved, see decisions.md): 1e-9 s was the assistant's own choice and is replaced by the derived bound |dt| <= N_steps * eps * t_max.
• 2026-11-01 value-comparison basis (PubMed, text read unless noted): Pathmanathan & Gray 2013 (doi 10.3389/fphys.2013.00358), Pathmanathan & Gray 2014 (10.1002/cnm.2615; abstract plus Wiley passages), Erdemir 2020 (10.1186/s12967-020-02540-4), Mulugeta 2018 (10.3389/fninf.2018.00018), Santiago 2022 (10.1371/journal.pcbi.1010141). Abstract only: Smith 2004 (10.1016/j.medengphy.2003.10.001), Hicks 2015 (10.1115/1.4029304). Not read (outside PubMed): Celik 2008, Roache, ASME V&V 20/40, FDA 2023 guidance. User decision: report-only, no pass/fail line.
• User-approved (2026-11-01), run C not yet requested or run: add a third step size, 2.5e-6 s (run C), so an observed order of convergence can be computed (two sizes cannot); expect it below the RK4 order of 4 near valve switches. Quantities of interest fixed beforehand: P_lv, P_ao, Q_av, stroke volume, valve open/close times. The independent scipy re-implementation stays blind until the procedure is fixed. Run C must be requested from Hermes.
• 2026-11-01 Hermes check before run C: A used RK4 step 1e-5 s and B 5e-6 s (settings read back before and after); both CSVs have 0.001 s output spacing and 1,501 rows. The earlier "every 4th C row = A grid" instruction was the assistant's error and was withdrawn. Run C: step 2.5e-6 s, same 0.001 s output, compared by output index; scalar definitions and the decision not to add the negative-flow integral are in decisions.md. Hermes confirmed it will run C once with these rules and add no pass/fail wording. A and B files unchanged.
• 2026-11-01 run C result (Hermes report, report-only; recomputed from the reported numbers, raw CSVs not seen here): C ran 05:48:23-05:48:27 UTC, exit codes 0/0, empty stderr, no NaN/Inf, 1,501 rows, CSV SHA-256 8d0943e5…b427; report ZIP SHA-256 b4ec9e79…2166. Max time difference at the same output index about 7e-18 s (bounds 5.0e-11 to 2.0e-10 s). Max abs difference A-B / B-C: P_lv 0.00712 / 0.00365, P_ao 0.00495 / 0.00254 (labelled kPa), Q_av 1.928 / 0.964 mL/s. Observed order p (max norm) 0.964, 0.960, 1.000; RMS norm gives the same picture. RK4's formal order is 4; the cause of the lower order is not established. Stroke volume per beat (A/B/C, mL): 65.8474 / 65.8479 / 65.8481 (p 2.29, GCI_fine 5.4e-7) and 65.7768 / 65.7769 / 65.7770 (p 1.00, GCI_fine 1.2e-6); this GCI excludes the 1 ms sampling quadrature error, which is common to A, B and C. Aortic valve sample times identical in A, B, C: open 0.247 / 0.997 s, close 0.384 / 1.134 s; p undefined (0/0). The requested check GCI_AB / (2^p x GCI_BC) equals f_C / f_B by construction when p comes from the same three values, so it carries no evidence; asking for it was the assistant's error.
• Blind comparison with the assistant's scipy re-implementation (not a reference, not independent of the assistant), report-only: stroke volume 65.8 mL vs 65.848 mL (beat 1); aortic valve opening 0.247 s vs first positive sample 0.247 s. From the raw C CSV: P_lv -3.2 to 119.0 vs -3.23 to 119.00; P_ao 79.0 to 116.4 vs 78.96 to 116.38; Q_av peak 1110 vs 1110.05. All agree to the precision the scipy values were recorded at.
• 2026-11-01 review of the Hermes report ZIP (SHA-256 matches b4ec9e79… 2166; read, not executed). A/B/C signals.csv hashes match the report; B's rawsignals.csv is byte-identical to its signals.csv. Solver readbacks: KINSOL settings identical in A, B, C; only the RK4 Step differs (1e-5, 5e-6, 2.5e-6); output interval 0.001 s. Comparator (compare_abc.py, report_math.py) implements the approved definitions; undefined orders are labelled, not adjusted. Runner changes limit execution to the single run C and re-hash A/B before and after; the old 1e-9 s grid assertion and the embedded PATH injection were removed. No defect found. An independent recomputation from the raw CSVs (own code, not Hermes's) reproduces every reported number.
• Observation, not an established cause: negative Q_av holds one constant value per closed-valve span, and in the first span it halves exactly with each step halving (-3.856, -1.928, -0.964 mL/s over 0.001-0.246 s); later spans are smaller (A/B/C -0.0095/-0.0049/-0.0003 and -0.0097/-0.0051/ -0.0005) and do not halve cleanly. Flow that scales with the integration step points to a numerical artifact of the fixed-step solution at the valve law's Q=0 switch rather than physiology; Smith 2004 (abstract only read) describes solving with a phase-dependent number of states. This offset dominates the Q_av order (largest B-C difference at t=0.001 s); the largest P_lv/P_ao B-C differences sit at 0.255-0.26 s, just after aortic valve opening. Hermes notes OpenCOR's Step unit (seconds) is owner intent, not confirmed from API documentation.
• Still open: unit labels (kPa labels on values that behave as mmHg) and agreement with the published waveform; both need the Smith 2004 paper.
• Not yet verified: negative Q_av, original-unit plausibility (pressures labelled kPa behave numerically as mmHg), agreement with the published waveform.
• 2026-11-01 update from the Smith 2004 author manuscript (card S6P in docs/evidence_review/evidence_cards.md; quotations only, file not retained): the paper uses mmHg, ml and s throughout and never kPa, but has no parameter table (C1). Its valve law removes Q from the state vector when Q turns negative, whereas the CellML holds dQ/dt = 0, so a negative Q reached in one step is frozen; this is consistent with the run C negative-Q_av observation being an artefact of the CellML encoding (C11). The six CellML initial volumes sum to the paper's 1500 mL stressed volume, and the 0.75 s period matches its 80 beats/min. Agreement with the published waveform (Figure 7) is still not checked.
• 2026-11-01 user decision (decisions.md, "C1 units and the R13 numeric block"): the CellML numerals are read as mmHg-based and existing OpenCOR outputs labelled kPa are read as mmHg, with no conversion factor; no file is edited. Numeric comparison with the CellML is no longer blocked and stays report-only.
• 2026-11-01 C11 check (Hermes [redacted: internal request ID], read-only on the A/B/C CSVs; results in evidence_review.md C11): three Q_av < 0 spans per run, each exactly constant, with P_lv - P_ao < 0 throughout. B/C ratios of the frozen values are 2.0000, 16.27 and 10.50, so only the first span halves with the step; the earlier "halves with the step" wording applies to the first span only. Independent review of the result is not done.
• 2026-11-01 SHACL reproduction (Hermes [redacted: internal request ID]; clean detached worktree of baf499e on the remote server [redacted: host name], new venv from requirements-shacl.txt; Python 3.12.3, pyshacl 0.26.0, rdflib 7.6.0): translate_ws267.py and run_shacl.py exit 0 with the same output as here (controls 0 / 13 / 12; ws267 22 Violations, 7 Warnings, 46 Info). ws267_omex_form.ttl regenerates byte for byte; report_ws267.json differs only in its Python version line (3.11.15 here). The SHACL results therefore do not depend on this Mac's environment. This is a reproduction test, not a check that the shapes are correct. Full command log reviewed (REPORT (2).txt, SHA-256 707e08f1…3cc6, not retained): pip installed from PyPI, so the network was available; the venv was made from the server project's .venv Python. The six dependencies that requirements-shacl.txt did not pin at baf499e resolved to the same versions as the local environment (html5lib 1.1, packaging 26.3, prettytable 3.18.0, six 1.17.0, wcwidth 0.9.4, webencodings 0.6.1; the local Python 3.11 venv also has importlib_metadata 10.1.0 and zipp 4.1.2). Only the four direct packages were pinned, so all of these were then pinned in requirements-shacl.txt (the two 3.11-only ones with pyshacl's own python_version < "3.12" marker). Fresh pip installs from that file on Python 3.11.15 and 3.12.13 here land exactly the pinned set (12 and 10 packages, pip check clean) and reproduce the results; on 3.12 the report differs only in its Python version line. The log does not show the fetch or git worktree add commands; its git rev-parse HEAD confirms baf499e. The server's other worktrees stay at older commits (main tree d19e3bc, smith-c11 4b2e181, smith-prov-runs 63d3ac1).

Open questions

• Whether to exclude cumulative states from error control (not supported by scipy's solve_ivp directly) or accept documented looser volume control.
• gpt-5.6-luna availability (429 only; retry later before routing to it).