Redesign simulation data model around cases and executions

[Copilot]

Description

Introduces a Case model to group simulations by case name (from timing files), replaces per-case canonical folding with per-execution Simulation records, and restructures the API so Case is the aggregate root. Each archive subdirectory (<jobID>.<timestamp>) becomes its own Simulation row linked to a Case via case_id. The first successful run per case is the canonical baseline; subsequent runs store a config diff dict against it.

Data Model

• New Case table: name (unique), case_group (nullable, indexed — from CASE_GROUP in env_case.xml), canonical_simulation_id FK
• Simulation changes: adds case_id FK, execution_id (unique), run_config_deltas (JSONB dict); drops case_name, name, group_name
• CASE_HASH evaluated but intentionally not used — case grouping is directory-name based

Ingestion

• Every successful run creates its own Simulation; first per case → canonical (run_config_deltas = NULL)
• Non-canonical runs store dict[field, {"canonical": ..., "current": ...}] deltas
• Deduplication by execution_id; incomplete runs skipped with warning
• _get_or_create_case() resolves by case_name; CASE_GROUP stored on Case with conflict-safe upsert

API

• GET /cases, GET /cases/{id} → CaseOut with nested SimulationSummaryOut[] via selectinload
• GET /simulations → flat browser with Case metadata joined (case_name, case_group)
• GET /simulations/{id} → full SimulationOut with derived is_canonical, change_count
• SimulationCreate/SimulationOut drop name, groupName; use caseId + executionId

Frontend

• Case name/group filter dropdowns on SimulationsPage
• All name/groupName references replaced with caseName/executionId/caseGroup
• Upload form uses caseId + executionId

Config delta format

{
  "compiler": { "canonical": "gcc-11", "current": "gcc-12" },
  "grid_resolution": { "canonical": "0.9x1.25", "current": "1.9x2.5" }
}

Checklist

• Code follows project style guidelines
• Self-reviewed code
• No new warnings
• Tests added or updated (if needed)
• All tests pass (locally and CI/CD)
• Documentation/comments updated (if needed)
• Breaking change noted (if applicable)

Breaking changes: SimulationCreate replaces caseName with caseId (UUID) + executionId (string), drops name/groupName. SimulationOut adds caseName, caseGroup, isCanonical, changeCount; drops name/groupName. CaseOut includes caseGroup and nested simulations: SimulationSummaryOut[]. run_config_deltas type changes from list[dict] to dict | None. env_case.xml required for ingestion.

Deployment Notes (if any)

Single squashed Alembic migration 20260304_400000 (revises 20260219_000000):

• Creates cases table, backfills from existing case_name values
• Adds case_id, execution_id to simulations; derives execution_id from UUID for existing rows
• Sets canonical per case (earliest simulation)
• Converts legacy list-format run_config_deltas to dict
• Backfills case_group from existing group_name
• Drops case_name, name, group_name columns and old constraints

Full downgrade is not allowed as it involves destructive changes to data to work.

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>[Enhancement]: Formalize performance_archive semantics and implement canonical run ingestion</issue_title>
<issue_description>## Is your feature request related to a problem?

There is ambiguity in how directories under performance_archive and case subdirectories (<jobID>.<timestamp>) should be interpreted.

This impacts:

• SimBoard’s data model (Case vs. Run)
• Canonical run selection
• Incremental update behavior
• Ingestion logic (e.g., main_parser())

Current assumptions may incorrectly treat all archive entries as completed production runs or treat job subdirectories as independent experiments rather than successive executions of the same case.

Describe the solution you'd like

Document and formalize conventions for how performance_archive should be interpreted and ingested, and update the data model and ingestion logic accordingly.

1. performance_archive Semantics

• The archive can include incomplete or failed runs.
• Some directories may contain build provenance only, with no run provenance (e.g., job never executed or crashed).
• Ingestion must not assume all entries are completed production runs.
• A run is considered successful only if all required run metadata is present.
• Incomplete runs should be detected and either skipped or classified explicitly.

2. Case Directory Structure

Example:

ac.golaz/v3.LR.historical_0121
├── 1081156.251218-200923
├── 1081290.251218-211543
└── 1129347.260120-133246

Subdirectories (<jobID>.<timestamp>)

• These represent multiple executions of the same case, not separate experiments.
• Long simulations (e.g., 100-year runs) require multiple job submissions.
• Each submission appears separately in performance_archive.
• Timing may vary across runs due to machine load.
• All subdirectories are logically grouped under the same casename.

3. Canonical Run Strategy

Recommended ingestion semantics:

• Treat the casename (experiment name) as the primary entity.
• Identify and store the first successful run as the canonical baseline.
  • “Successful” = all required metadata fields are present.
• For subsequent successful runs:
  • Compare against the canonical baseline.
  • Record only configuration differences (e.g., changed namelist values).
  • Do not ingest timing data (handled by PACE).
• Expect certain values to differ across runs (e.g., total days run, starting day).

4. Handling New Runs (Incremental Updates)

When a new <jobID>.<timestamp> directory appears under an existing casename:

• Do not replace existing data.
• Read the new run.
• If successful:
  • Compare it to the stored canonical baseline.
  • Record any configuration differences.
• Maintain grouping under the casename.

Runs are successive executions of the same case whose configuration deltas are tracked over time.

Required Changes

Data Model

• Explicitly model Case (casename) as the primary entity.
• Model Run as a child entity representing individual executions.
• Preserve the existing unique constraint on simulations:
  • (case_name, machine_id, simulation_start_date)
• Ensure ingestion respects this constraint to maintain idempotency.

Ingestion (main_parser())

Update logic to:

• Detect and classify incomplete/failed runs.
• Group <jobID>.<timestamp> directories under a single casename.
• Identify the first successful run (all required metadata present) as canonical.
• Compare subsequent runs against the canonical baseline.
• Support idempotent ingestion using the existing uniqueness constraint.
• Support incremental updates without overwriting prior data.

Initial DB Population Rules

Define and document whether:

• All successful runs are stored (baseline + deltas), or
• Only canonical baseline runs are fully stored, with others stored as diffs.

Deliverables

• Update data model definitions (if needed).
• Modify main_parser() to implement the semantics described above.
• Add or update tests covering:
  • Incomplete runs
  • Multiple runs under one casename
  • Canonical selection behavior
  • Incremental ingestion
• Update relevant documentation.

Describe alternatives you've considered

No response

Additional context

Follow up to:
#88 (comment)

Rob answer:
#88 (comment)</issue_description>

<agent_instructions>You are implementing the semantics defined in this issue.

Scope constraints:

• Do not introduce unrelated architectural refactors.
• Limit changes to:
  • Data model (if required)
  • main_parser() and directly related ingestion utilities
  • Tests
  • Documentation updates tied to this behavior

Implementation requirements:

1. Canonical Selection
   • A run is "successful" only if all required metadata fields are pre...

• Fixes [Enhancement]: Formalize performance_archive semantics and implement canonical run ingestion #104

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[tomvothecoder]

@copilot Fix recent CI/CD issues

[rljacob]

No the CASE_HASH should be the same in different submissions. Where are those simulation directories?

[tomvothecoder]

No the CASE_HASH should be the same in different submissions. Where are those simulation directories?

/lcrc/group/e3sm/PERF_Chrysalis/performance_archive/ac.golaz/v3.LR.historical_0121

[Copilot]

Pull request overview

Copilot reviewed 31 out of 32 changed files in this pull request and generated 4 comments.