Workflow Engine Mapper

Workflow Engine Mapper

Goal

Choose the smallest workflow structure that preserves reproducibility, restartability, and provenance for a materials simulation task.

Requirements

• Python 3.10+
• No external dependencies
• Works on Linux, macOS, and Windows

Inputs to Gather

Decision Guidance

• Use one-off scripts for fewer than 5 local exploratory runs (no provenance, no HPC).
• Use jobflow/atomate2 when the workflow is Python-native and Materials Project style input sets are useful.
• Use AiiDA when provenance-critical work is also remote (HPC) or large (>= 50 runs) — i.e. long-lived, database-backed campaigns. For smaller local provenance needs, atomate2 (Materials Project codes, >= 10 runs) or jobflow stores already capture inputs, outputs, code version, and environment, so the mapper recommends those instead of the heavier AiiDA stack.
• Use pyiron when interactive atomistic workflows, notebooks, and job management are the primary user surface (ASE/LAMMPS without strict provenance).

The recommendations are emitted in a fixed precedence so the prose and the implemented thresholds agree: an explicit --preferred engine overrides everything; otherwise one-off (small local, no provenance/HPC) -> AiiDA (provenance AND remote/large) -> atomate2 (VASP/QE/CP2K/force-field, >= 10 runs) -> pyiron (ASE/LAMMPS, no provenance) -> jobflow (fallback).

Script Outputs

scripts/workflow_engine_mapper.py emits:

• recommended_engine
• dag_pattern
• provenance_requirements
• restart_strategy
• storage_layout
• migration_triggers
• notes

Workflow

bashCopy code
python3 skills/simulation-workflow/workflow-engine-mapper/scripts/workflow_engine_mapper.py \
  --task "relax static dos for 200 oxides" \
  --code vasp \
  --runs 200 \
  --needs-provenance \
  --needs-restart \
  --hpc \
  --json

Use the output to scaffold the workflow before writing engine-specific code.

Error Handling

If the task has too few details, choose the conservative pattern and ask for engine, run count, and restart needs before implementation.

Limitations

The skill does not replace the official APIs of atomate2, jobflow, AiiDA, or pyiron; it selects and explains the workflow shape.

Verification checklist

• Recorded the full --json payload from workflow_engine_mapper.py (including inputs) and confirmed the echoed runs, code, needs_provenance, needs_restart, and hpc match the task you actually intend, not a guessed default.
• Confirmed recommended_engine follows the documented precedence for these inputs: --preferred override -> one-off (runs<5, no provenance, no HPC) -> aiida (provenance AND (hpc or runs>=50)) -> atomate2 (code in vasp/qe/cp2k/forcefield AND runs>=10) -> pyiron (ase/lammps, no provenance) -> jobflow fallback; if the result surprises you, re-check which branch the inputs hit rather than overriding blindly.
• Verified dag_pattern reflects the task keywords: branch terms (dos/band/phonon/static) and sweep terms (screen/sweep/campaign/many/batch) compose into the map+branch pattern, and with restart checkpoints is appended only when --needs-restart was passed.
• Checked provenance_requirements and restart_strategy against intent: store_code_version/store_environment, checkpoint_jobs (also auto-true at runs>=20), and resume_by_job_id_or_name (false for one-off) are consistent with how the campaign will actually be audited and resumed.
• Read migration_triggers; for a one-off recommendation, confirmed the forward-looking "migrate once results are compared/published/screened/resumed or runs reach ~5+" entry is present and planned for, rather than treating one-off as permanent.
• Used storage_layout (inputs/, runs/<job-id>/, outputs/, metadata/workflow.json, reports/) as the on-disk scaffold and confirmed it maps onto the chosen engine's native store before writing engine-specific code.
• Confirmed the mapper exit code was 0 (a 2 means input validation rejected the args and no recommendation was produced) before trusting any output.

Common pitfalls & rationalizations

Security

Input Validation

• The script accepts only scalar CLI inputs and boolean flags (--needs-provenance, --needs-restart, --hpc, --json via store_true).
• runs must be a positive integer (rejects booleans, non-integers, and values <= 0) and is capped at MAX_RUNS = 1,000,000; main() also rejects non-finite values via math.isfinite.
• Free-text fields are length-bounded: task <= 2000 characters (MAX_TASK_LEN) and must be non-empty after stripping; code and preferred <= 100 characters each (MAX_FIELD_LEN).
• preferred must be one of the allowed engine names: auto, one-off, jobflow, atomate2, aiida, pyiron.
• The task and code strings are not otherwise restricted by an allowlist; only their length and (for task) emptiness are validated.
• All invalid input raises ValueError, which is printed to stderr and exits with code 2 before any recommendation is computed.

File Access

• The script reads and writes no files; all I/O is CLI args in -> stdout (JSON or two summary lines) out.
• It accepts no path arguments, so there is no path-sandboxing concern; there are no on-disk size limits because nothing is read from disk.

Tool Restrictions

• The frontmatter declares allowed-tools: Read, Bash, Write, Grep, Glob.
• Bash is used only to run the bundled scripts/workflow_engine_mapper.py.
• Read/Grep/Glob are used to inspect the skill's own files and references (e.g. references/workflow_engines.md) and the user's task context; Write is available to scaffold workflow files from the recommended structure.

Safety Measures

• No eval/exec, no subprocess, and no shell invocation inside the script.
• No network access: it does not connect to remote services, submit jobs, or deserialize untrusted data.
• Output is emitted as structured JSON via json.dumps (with --json) or plain text summary lines.
• DoS caps bound resource use: the runs ceiling (1,000,000) and the task/code/preferred length caps prevent unbounded input.

References

• See references/workflow_engines.md for engine selection heuristics.

Version History

• 1.2.2: Add a Verification checklist (evidence tied to the mapper's JSON outputs, precedence, DAG composition, and exit code) and a Common pitfalls & rationalizations table covering one-off permanence, AiiDA over-selection, unread input flags, and forced checkpointing.
• 1.2.0: Strengthen evals with deterministic script_checks that pin the mapper's exact output (recommended_engine, dag_pattern, provenance_requirements, restart_strategy, migration_triggers) so each case discriminates the skill from a from-memory baseline.
• 1.1.0: Compose branch+sweep DAG patterns instead of overwriting; emit a forward-looking migration trigger for one-off runs; document AiiDA gating/precedence; add input-validation safeguards (bounds, length caps) matching the Security section.
• 1.0.0: Initial workflow engine mapping skill.