"""Verify a Pass A Zarr store: structural checks on every shard, plus a full re-parse comparison for a random sample of calculations. This is the gate before scaling to the full run. """ from __future__ import annotations import argparse, glob, os, random, sys import numpy as np import zarr sys.path.insert(0, os.path.dirname(os.path.abspath(__file__))) from omol_parse import parse_archive from omol_store import (read_calc, inflate_fock, frontier, SCALARS_F8, SCALARS_I, FLAGS, ATOM_1D, ATOM_SHELL, PAIRS) M5250 = "/global/cfs/projectdirs/m5250/OMol_elec" def shard_paths(root, side): out = [] for depth in ("*", "*/*/*"): out += glob.glob(os.path.join(root, side, depth, "*.zarr")) return sorted(set(out)) def close(a, b, tol=0.0): if a is None or b is None: return a is None and b is None a = np.asarray(a, dtype=float) b = np.asarray(b, dtype=float) if a.shape != b.shape: return False return bool(np.all((np.isnan(a) & np.isnan(b)) | (np.abs(a - b) <= tol))) def main(): ap = argparse.ArgumentParser() ap.add_argument("--store", required=True) ap.add_argument("--sample", type=int, default=30) ap.add_argument("--seed", type=int, default=7) args = ap.parse_args() p1 = shard_paths(args.store, "p1") p2 = shard_paths(args.store, "p2") print(f"shards: p1 {len(p1)}, p2 {len(p2)}") if len(p1) != len(p2): print(" ERROR: p1 and p2 shard counts differ") total = 0 problems = [] nbas_all, natm_all, uhf_n, nofock = [], [], 0, 0 for sp in p2: g = zarr.open_group(sp, mode="r") n = int(g.attrs["n_calc"]) total += n si = np.asarray(g["scalar_i"]) icol = {k: j for j, k in enumerate(g.attrs["scalar_i_cols"])} nbas = si[:, icol["nbas"]] natm = si[:, icol["n_atoms"]] nbas_all.append(nbas) natm_all.append(natm) for nm, key in (("atom", "atom_offsets"), ("fock_a", "fock_a_offsets"), ("fock_b", "fock_b_offsets"), ("eps_a", "eps_a_offsets")): o = np.asarray(g[key]) if len(o) != n + 1 or o[0] != 0 or np.any(np.diff(o) < 0): problems.append(f"{os.path.basename(sp)}: bad {nm} offsets") if not np.array_equal(np.diff(np.asarray(g["atom_offsets"])), natm): problems.append(f"{os.path.basename(sp)}: atom offsets != n_atoms") want = nbas.astype("i8") * (nbas.astype("i8") + 1) // 2 flags = np.asarray(g["flags"]) fcol = {k: j for j, k in enumerate(g.attrs["flag_cols"])} is_uhf = flags[:, fcol["is_uhf"]].astype(bool) has_f = flags[:, fcol["has_fock"]].astype(bool) uhf_n += int(is_uhf.sum()) nofock += int((~has_f).sum()) fa = np.diff(np.asarray(g["fock_a_offsets"])) if not np.array_equal(fa[has_f], want[has_f]): problems.append(f"{os.path.basename(sp)}: fock_a length != nbas(nbas+1)/2") if np.any(fa[~has_f] != 0): problems.append(f"{os.path.basename(sp)}: fock_a stored where has_fock is false") fb = np.diff(np.asarray(g["fock_b_offsets"])) if np.any((fb > 0) != (is_uhf & has_f)): problems.append(f"{os.path.basename(sp)}: beta Fock presence != is_uhf & has_fock") if not np.array_equal(fb[is_uhf & has_f], want[is_uhf & has_f]): problems.append(f"{os.path.basename(sp)}: beta Fock length wrong") if len(g.attrs["calc_id"]) != n or len(g.attrs["rel_path"]) != n: problems.append(f"{os.path.basename(sp)}: attrs length != n_calc") if np.any(~np.asarray(g["flags"])[:, fcol["terminated_normally"]].astype(bool)): problems.append(f"{os.path.basename(sp)}: some runs not terminated normally") nbas_all = np.concatenate(nbas_all) if nbas_all else np.zeros(0) natm_all = np.concatenate(natm_all) if natm_all else np.zeros(0) print(f"calculations: {total:,} ({uhf_n:,} UHF, {total-uhf_n:,} RHF, " f"{nofock:,} without a Fock matrix)") if total: print(f" nbas min {nbas_all.min()} median {int(np.median(nbas_all))} max {nbas_all.max()}") print(f" atoms min {natm_all.min()} median {int(np.median(natm_all))} max {natm_all.max()}") for p in problems[:12]: print(" STRUCT ERROR:", p) if not problems: print(" structural checks passed on every shard") rng = random.Random(args.seed) picks = [] for sp in p2: g = zarr.open_group(sp, mode="r") n = int(g.attrs["n_calc"]) if n: picks.append((sp, rng.randrange(n))) rng.shuffle(picks) picks = picks[:args.sample] print(f"\nre-parse comparison on {len(picks)} calculations:") nbad = 0 for sp, i in picks: g = zarr.open_group(sp, mode="r") stored = read_calc(g, i) rel = stored["rel_path"] fresh = parse_archive(os.path.join(M5250, rel, "orca.tar.zst")) fresh["n_atoms"] = len(fresh["elements"]) fresh["homo_a"], fresh["lumo_a"], fresh["gap_a"] = frontier(fresh["eps_a"], fresh["occ_a"]) fresh["homo_b"], fresh["lumo_b"], fresh["gap_b"] = frontier(fresh["eps_b"], fresh["occ_b"]) bad = [] for k in SCALARS_F8: a, b = stored[k], fresh.get(k) if b is None: continue if not close(a, b, tol=abs(float(b)) * 1e-12 + 1e-12): bad.append(f"{k}: {a} vs {b}") for k in SCALARS_I: b = fresh.get(k) if b is not None and stored[k] != int(b): bad.append(f"{k}: {stored[k]} vs {b}") for k in ("scf_converged", "terminated_normally", "nbo_available", "npa_available"): if stored[k] != bool(fresh.get(k)): bad.append(f"{k}: {stored[k]} vs {fresh.get(k)}") if stored["is_uhf"] != (fresh["hftyp"] == "UHF"): bad.append("is_uhf mismatch") if not close(stored["coords"], fresh["coords"], 1e-9): bad.append("coords differ") if fresh["forces"] is not None and not close(stored["forces"], fresh["forces"], 1e-12): bad.append("forces differ") if fresh["atomic_numbers"] is not None and not np.array_equal( stored["atomic_numbers"], fresh["atomic_numbers"]): bad.append("atomic numbers differ") for k in ATOM_1D: if fresh.get(k) is not None and not close(stored[k], fresh[k], 1e-9): bad.append(f"{k} differs") for k in ATOM_SHELL: if fresh.get(k) is not None and not close(stored[k], fresh[k], 2e-5): bad.append(f"{k} differs") for k in PAIRS: idx, val = stored[k] ref = fresh.get(k) or [] if len(val) != len(ref): bad.append(f"{k} count {len(val)} vs {len(ref)}") elif ref: if (not np.array_equal(idx, np.array([[a, b] for a, b, _ in ref])) or not close(val, np.array([v for _, _, v in ref]), 1e-4)): bad.append(f"{k} content differs") if fresh["fock_a"] is None: if stored["has_fock"] or len(stored["fock_a"]): bad.append("fock_a stored but source has none") elif not np.array_equal(stored["fock_a"], fresh["fock_a"]): bad.append("fock_a differs") fb = fresh.get("fock_b") if fb is None: if len(stored["fock_b"]): bad.append("fock_b present but should be absent") elif not np.array_equal(stored["fock_b"], fb): bad.append("fock_b differs") if not close(stored["eps_a"], fresh["eps_a"], 1e-12): bad.append("eps_a differs") if stored["has_fock"]: F = inflate_fock(stored["fock_a"], stored["nbas"]) if np.abs(F - F.T).max() != 0: bad.append("inflated Fock not symmetric") if bad: nbad += 1 print(f" MISMATCH {rel}") for b in bad[:6]: print(f" {b}") else: print(f" ok {rel[:76]}") print(f"\n{len(picks)-nbad}/{len(picks)} exact, {len(problems)} structural problems") def du(p): return sum(os.path.getsize(os.path.join(r, f)) for r, _, fs in os.walk(p) for f in fs) b1 = sum(du(p) for p in p1) b2 = sum(du(p) for p in p2) print(f"\nsize: p1 {b1/1e9:.3f} GB ({b1/max(total,1)/1e3:.1f} kB/calc), " f"p2 {b2/1e9:.3f} GB ({b2/max(total,1)/1e6:.3f} MB/calc)") if total: print(f"extrapolated to 3.73 M: p1 {b1/total*3.73e6/1e12:.2f} TB, " f"p2 {b2/total*3.73e6/1e12:.2f} TB") if __name__ == "__main__": main()