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phase0-design

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UpdatedJuly 7, 2026 at 07:52

Run Phase 0 (DESIGN) of the A2MC calibration workflow as the offline agent — the human-in-the-loop analog of the orchestrator's `_run_design()`. Sample the parameter space (Morris/Sobol/LHS), materialize one FATES parameter file per case, generate + build + submit the ensemble, and arm monitoring. Use when the user says "design a new round", "set up the ensemble", "sample the parameters", "submit the Morris ensemble", "start a calibration round", "expand the parameter space (redesign)".

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SKILL.md

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name	phase0-design
description	Run Phase 0 (DESIGN) of the A2MC calibration workflow as the offline agent — the human-in-the-loop analog of the orchestrator's `_run_design()`. Sample the parameter space (Morris/Sobol/LHS), materialize one FATES parameter file per case, generate + build + submit the ensemble, and arm monitoring. Use when the user says "design a new round", "set up the ensemble", "sample the parameters", "submit the Morris ensemble", "start a calibration round", "expand the parameter space (redesign)".
modes	{"requires_fates":false,"nutrient_pathway":"any","scope":["calibration"],"summary":"Offline analog of online Phase 0 (design/sample/submit the ensemble). Applies in every calibration mode."}

Phase 0: Design & Submit (offline agent)

The offline analog of the orchestrator's _run_design(). Online this is deterministic sampling + submission; offline you own the design decisions the online loop takes from config — scheme, trajectory count, which parameters vary, bounds, and whether this is a fresh round or a redesign/replay. The underlying scripts are the same the online agent drives.

Floor, not ceiling. This skill is the minimum to stand up a round the way the online agent would. As the offline agent you can do more: reconsider the parameter list itself, add or widen bounds a redesign implies, sanity-check the sampling against prior-round μ* before spending compute, or design a targeted sub-ensemble the fixed loop would never propose. Match the discipline (verify param existence, don't clobber the committed matrix, validate before submit), then exercise judgment about what to sample.

Deliverable: simulation jobs queued (ADSP→RGSP→TRANS dependency chains), submission_manifest.json written, monitoring armed.

Step 1 — sample the parameter space (parameter-file prep — no simulations)

phases/phase0_design/create_parameter_sample.py --method {morris|sobol|lhs} reads $A2MC_PARAM_LIST_FILE (name + bounds) and writes the ensemble matrix ($A2MC_ENSEMBLE_MATRIX_FILE) and SALib problem ($A2MC_SALIB_PROBLEM_FILE). Morris: --trajectories T (N = T×(P+1)).

Footgun — matrix overwrite. $A2MC_ENSEMBLE_MATRIX_FILE for Kougarok points at the committed, byte-stable 4890-set matrix the manuscript depends on. To regenerate without clobbering it, write to a scratch path (--output-matrix) or repoint the env var to a fresh round file first.

Redesign / replay (reuse a prior round's NC dir instead of fresh sampling): apply_param_override.py (global override, e.g. R5's prescribed_puptake=1.0 onto R3's NCs) or create_subset_replay.py (top-N replay preserving source case numbers).

Step 2 — materialize per-case parameter files (parameter-file prep — no simulations)

phases/phase0_design/generate_parameter_files.py reads the X matrix + $A2MC_BASE_PARAM_FILE and writes one parameter file per row into $A2MC_PARAM_DIR (pattern $A2MC_PARAM_PATTERN, {N} placeholder). It is method- and format-agnostic (JSON at api-43+, NetCDF at api-31 and earlier) and dispatches to tools/modify_fates_parameters.py for the per-parameter edits. Verify file count = N_sets.

Footgun — column↔parameter mapping + file format. The X-matrix column order must match the site parameter list; build_param_lookup() in tools/modify_fates_parameters.py maps each shorthand → FATES name + PFT + organ. Confirm tools/describe_mode.py shows the milestone you expect so the right parameter-file format (JSON vs NetCDF) is written. Never assume a column's meaning.

Step 3 — generate scripts, build, submit the simulations

phases/phase0_design/submit_phase0.py --start 1 --end N --dry-run first (preview), then --submit. It (3a) writes per-case scripts via tools/create_case.sh --write-script, (3b) auto-validates via tools/validate_submission_plan.py, (3c.1) builds ONE case fresh (~30 min), (3c.2) runs the rest in --batch-size parallel batches reusing the build's bld/. Non-sequential rounds: --cases-file.

Footgun — build-case reuse. All cases share the build case's bld/. If the build case fails, every dependent case is orphaned — confirm it completed before the batch. Restart it separately, then --skip-build-case --build-case N.

Step 4 — arm monitoring, don't idle-wait

Launch tools/ensemble_auto_monitor.sh (queue polling + auto extraction kick + milestone plots), then hand monitoring setup to arm-hpc-monitoring (CLAUDE.md Rule #6). Point-in-time completion: tools/diagnose_ensemble_status.py --cases 1-N (writes completed/incomplete lists + a validated restart script). Infrastructure failures → restart-failed-jobs; model failures need a fix first.

Step 5 — log it and hand off

Log via calibration-log (phase log → PhaseLogger.log_design): scheme, N cases, param dir, manifest hash, any redesign rationale. Hand off to phase1-exploration once TRANS is >95% complete. (Arrived here from Phase 6 with all candidates pinned at bounds? That's the 6→0 redesign — widen bounds / add parameters and start a new calibration_round.)

Related skills / next phase

Monitoring the in-flight ensemble → arm-hpc-monitoring. Failed jobs → restart-failed-jobs.
Rebuilding a new site/model's knowledge base first → build-rag-from-scratch.
Next: phase1-exploration (extract Y matrix + Morris sensitivity).

Changelog

2026-07-02: Created — offline Phase 0 routine mirroring _run_design(); drives create_parameter_sample → generate_parameter_files → submit_phase0, delegates monitoring/restart, hands off to phase1-exploration.

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name	phase0-design
description	Run Phase 0 (DESIGN) of the A2MC calibration workflow as the offline agent — the human-in-the-loop analog of the orchestrator's `_run_design()`. Sample the parameter space (Morris/Sobol/LHS), materialize one FATES parameter file per case, generate + build + submit the ensemble, and arm monitoring. Use when the user says "design a new round", "set up the ensemble", "sample the parameters", "submit the Morris ensemble", "start a calibration round", "expand the parameter space (redesign)".
modes	{"requires_fates":false,"nutrient_pathway":"any","scope":["calibration"],"summary":"Offline analog of online Phase 0 (design/sample/submit the ensemble). Applies in every calibration mode."}

Phase 0: Design & Submit (offline agent)

Floor, not ceiling. This skill is the minimum to stand up a round the way the online agent would. As the offline agent you can do more: reconsider the parameter list itself, add or widen bounds a redesign implies, sanity-check the sampling against prior-round μ* before spending compute, or design a targeted sub-ensemble the fixed loop would never propose. Match the discipline (verify param existence, don't clobber the committed matrix, validate before submit), then exercise judgment about what to sample.

Deliverable: simulation jobs queued (ADSP→RGSP→TRANS dependency chains), submission_manifest.json written, monitoring armed.

Step 1 — sample the parameter space (parameter-file prep — no simulations)

Footgun — matrix overwrite. $A2MC_ENSEMBLE_MATRIX_FILE for Kougarok points at the committed, byte-stable 4890-set matrix the manuscript depends on. To regenerate without clobbering it, write to a scratch path (--output-matrix) or repoint the env var to a fresh round file first.

Step 2 — materialize per-case parameter files (parameter-file prep — no simulations)

Footgun — column↔parameter mapping + file format. The X-matrix column order must match the site parameter list; build_param_lookup() in tools/modify_fates_parameters.py maps each shorthand → FATES name + PFT + organ. Confirm tools/describe_mode.py shows the milestone you expect so the right parameter-file format (JSON vs NetCDF) is written. Never assume a column's meaning.

Step 3 — generate scripts, build, submit the simulations

Footgun — build-case reuse. All cases share the build case's bld/. If the build case fails, every dependent case is orphaned — confirm it completed before the batch. Restart it separately, then --skip-build-case --build-case N.

Step 4 — arm monitoring, don't idle-wait

Step 5 — log it and hand off

Related skills / next phase

Monitoring the in-flight ensemble → arm-hpc-monitoring. Failed jobs → restart-failed-jobs.
Rebuilding a new site/model's knowledge base first → build-rag-from-scratch.
Next: phase1-exploration (extract Y matrix + Morris sensitivity).

Changelog

2026-07-02: Created — offline Phase 0 routine mirroring _run_design(); drives create_parameter_sample → generate_parameter_files → submit_phase0, delegates monitoring/restart, hands off to phase1-exploration.