diff --git a/.jules/bolt.md b/.jules/bolt.md index b140c4a7c..ea7f6386b 100644 --- a/.jules/bolt.md +++ b/.jules/bolt.md @@ -5,3 +5,7 @@ ## 2024-05-19 - Caching YAML Load for Framework Registry **Learning:** `yaml.safe_load` on `frameworks.yml` within `load_framework_registry()` was taking ~2-3 ms per call and it was repeatedly called for every framework entry via `get_framework_config()`. This was a micro-bottleneck, especially when dealing with lists or multiple frameworks. **Action:** Applied the `@lru_cache` and `deepcopy` pattern successfully again to `load_framework_registry()` and `get_framework_config()` to avoid caching a mutable dictionary directly and avoid repeated YAML I/O parsing. + +## 2024-05-20 - Faster pandas iteration +**Learning:** Iterating over pandas DataFrames with `.iterrows()` is a significant performance bottleneck due to series object creation overhead. +**Action:** Replace `.iterrows()` with `.itertuples(index=False, name=None)` for standard tuple returns or `.to_dict("records")` when dictionary/dynamic property access is needed. diff --git a/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py b/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py index d57dac3e0..57f7939f2 100644 --- a/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py +++ b/ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py @@ -301,7 +301,8 @@ def run_elasticity_benchmark( else {} ) atoms_list = [] - for _, row in results.iterrows(): + # ⚡ Bolt: Use to_dict('records') over iterrows for faster iteration. + for row in results.to_dict("records"): struct = row.get("final_structure") if not isinstance(struct, Structure): struct = mock_ref_map.get(row[benchmark.index_name]) diff --git a/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py b/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py index a033fabf2..1f732cae0 100644 --- a/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py +++ b/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py @@ -86,9 +86,10 @@ def get_ref_energies(data_path: Path) -> dict[str, float]: ) ref_energies = {} - for row in df.iterrows(): - label = row[1][0] - ref_energies[label] = float(row[1][2]) * KCAL_TO_EV + # ⚡ Bolt: Use itertuples over iterrows for faster iteration. + for row in df.itertuples(index=False, name=None): + label = row[0] + ref_energies[label] = float(row[2]) * KCAL_TO_EV return ref_energies diff --git a/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py b/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py index be51974af..bc473a412 100644 --- a/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py +++ b/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py @@ -84,9 +84,10 @@ def get_ref_energies(data_path: Path) -> dict[str, float]: ) ref_energies = {} - for row in df.iterrows(): - label = row[1][0] - e_ref = float(row[1][1]) * units.Hartree + # ⚡ Bolt: Use itertuples over iterrows for faster iteration. + for row in df.itertuples(index=False, name=None): + label = row[0] + e_ref = float(row[1]) * units.Hartree ref_energies[label] = e_ref return ref_energies diff --git a/ml_peg/calcs/utils/gscdb138.py b/ml_peg/calcs/utils/gscdb138.py index 0fc26c1e0..0a307c444 100644 --- a/ml_peg/calcs/utils/gscdb138.py +++ b/ml_peg/calcs/utils/gscdb138.py @@ -106,11 +106,14 @@ def run_gscdb138( df_refs["Reference"] *= units.Hartree # Calculate relative energy for each entry. - for _, row in tqdm(df_refs.iterrows(), dataset, total=df_refs.shape[0]): + # ⚡ Bolt: Use itertuples over iterrows for faster iteration. + for row in tqdm( + df_refs.itertuples(index=False), dataset, total=df_refs.shape[0] + ): atoms_list = [] - identifier = row["Reaction"] - reactions = row["Stoichiometry"].split(",") # Parse stoichiometry string. - e_rel_ref = row["Reference"] + identifier = row.Reaction + reactions = row.Stoichiometry.split(",") # Parse stoichiometry string. + e_rel_ref = row.Reference num_species = len(reactions) // 2 # Each species has coefficient and name. e_rel_model = 0