feat: Parsl-based simulation orchestration (Issue #16) - #25

Merged

gregorweiss merged 88 commits into

feat/parsl-simulate

Aug 12, 2026

Commits on Jul 23, 2026

initial greenfield implementation
gregorweiss
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29846ac
Auto-detect GROMACS binary (gmx_mpi vs gmx) and add error handling
gregorweiss
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ba109ee
Fix stage functions to support optional prev_future for checkpoint resume
gregorweiss
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d0f77cf
Add checkpoint detection, stage execution, and trajectory validation
gregorweiss
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04e79e2
Add comprehensive test suite (64 tests) for checkpoint and workflow validation
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c85b903
Refactor GROMACS binary detection into testable function
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c2562e4
Update tests to expect dynamic GROMACS binary detection
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67f14fb
Add retries=3 to Parsl config for transient fault recovery
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bf69835
Wire restart_from_cpt into mdrun bash app for -cpi/-append restart support
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8b429d1
Thread checkpoint restart info from detection through stages into mdrun
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d80f7b4
Add stage_overrides field and get_stage_config() to SlurmExecutorConfig
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1ce80e7
Thread per-stage resource config (ntasks, disable_gpu) through stage execution pipeline
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5c417fe
Fix simulate CLI to discover fresh sim dirs without requiring BuildInput YAML or prod.xtc
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33c88fd
Make account optional in BaseSlurmConfig to support clusters without explicit account
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9baa8d3
Support gmx_mpi (pure MPI) builds in mdrun app: use -ntomp instead of -nt/-ntmpi
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bb8cd9c
Normalise bash app exit codes to status dicts in _wait_with_progress
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3881ea7
Add result_transform to _wait_with_progress to decouple bash_app result normalisation from progress UI
gregorweiss
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e83f7de
Update account test to document optional-account contract for cluster-agnostic configs
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ea7076f
Remove run_full_pipeline dead code: bypassed stage_config, restart support and _execute_stage_list
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44e8c1f
Fix MPI comment (single-rank execution) and accept prod.trr alongside prod.xtc in output check
gregorweiss
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bd06d3f
Fix simulate --hash filter; add next-steps hint after build
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7878af4
Handle ValueError from hash filter with clean sys.exit
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a6fead9
Remove stale filter_paths_by_hash import from simulate command
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59e31b0
Fix examples/slurm_gpu.yaml partition (gpu-l40s→gpu) and module; make next-step hint generic
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cfcba15
Fix PME-GPU for EM: pass pme_gpu=False so EM uses -nb gpu -pme cpu
gregorweiss
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719cb13
Add StageSpec/STAGE_REGISTRY and generic run_stage(); stage functions become one-liner wrappers
gregorweiss
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d2ac1f4
Replace six scattered stage dicts with STAGE_BY_NAME lookups; make _detect_needed_stages a thin wrapper; add domain validation to run_simulations
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00613d7
Extract _require_bash_app, _build_grompp_script, _build_mdrun_script as pure/shared helpers; remove hardcoded deffnm comparisons from bash output validation
gregorweiss
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cccb7e8
Extract _get_block_status, _is_running, _poll_future as module-level functions; simplify _wait_with_progress poll loop
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e45db6c
Extract _resolve_analysis_slurm_config and _resolve_sim_paths_for_simulate; simplify simulate_systems; remove duplicated autodiscovery block
gregorweiss
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d80bc20
Update tests to use _build_grompp_script/_build_mdrun_script pure functions directly; add _build_mdrun_script import
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df2dfec
update CONTRIBUTORS.md
gregorweiss
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aa47a90
Promote _find_structure_file to public API; export from orchestration package
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1a9d80d
Document sequential session constraint in parsl_session docstring
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da17c04
Skip simulations for dirs with incomplete builds instead of raising
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bd26a3d
Export OMP_NUM_THREADS=$NTHR in mdrun script to match -ntomp flag
gregorweiss
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395c631

Commits on Jul 24, 2026

Commits on Jul 27, 2026

Commits on Aug 10, 2026

Commits on Aug 11, 2026

Commits on Aug 12, 2026

feat: print resolved gmx commands in dry-run mode
gregorweiss
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378c28d
docs: add Parsl investigation findings write-up
gregorweiss
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aa37bb6
docs: move parsl-findings to developer-guide
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08f6aeb
docs: remove parsl-findings from docs (moved to issue)
gregorweiss
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3c96e9a
refactor: separate EnvironmentConfig from SLURM allocation (#41)
gregorweiss
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7e96242
refactor: clean up simulation orchestration per DESIGN.md
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16168c4
fix: resolve ruff lint and format issues
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46a0626
fix: single Ctrl+C cleanly exits simulation workflow
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df8cbb5
fix: suppress Parsl interchange tracebacks on Ctrl+C
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648fda2
fix: use daemon threads to prevent atexit hang on Ctrl+C
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67dda01
fix: squeue fallback to cancel Parsl jobs missed by DFK tracking
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96e7e56