| """Write a flat per-calculation index for a store: one row per calculation with its shard, row |
| number and the handful of columns most queries filter on. Lets a consumer find a calculation |
| without opening every shard. |
| |
| python build_index.py --store $PSCRATCH/omol_100k |
| writes <store>/index.tsv |
| """ |
| from __future__ import annotations |
| import argparse, glob, os |
| import numpy as np |
| import zarr |
|
|
|
|
| def p2_shards(store): |
| out = [] |
| for depth in ("*", "*/*/*"): |
| out += glob.glob(os.path.join(store, "p2", depth, "*.zarr")) |
| return sorted(set(out)) |
|
|
|
|
| def main(): |
| ap = argparse.ArgumentParser() |
| ap.add_argument("--store", required=True) |
| args = ap.parse_args() |
| shards = p2_shards(args.store) |
| out = os.path.join(args.store, "index.tsv") |
| n = 0 |
| cols = ["calc_id", "dataset", "shard", "row", "n_atoms", "nbas", "nelec", "charge", "mult", |
| "is_uhf", "has_fock", "scf_converged", "mo_ok", "e_total", "conv_diiserr", "rel_path"] |
| with open(out, "w") as fh: |
| fh.write("\t".join(cols) + "\n") |
| for sp in shards: |
| g = zarr.open_group(sp, mode="r") |
| rel = os.path.relpath(sp, os.path.join(args.store, "p2")) |
| ids, rels, ds = g.attrs["calc_id"], g.attrs["rel_path"], g.attrs["dataset"] |
| si = np.asarray(g["scalar_i"]); ic = {k: j for j, k in enumerate(g.attrs["scalar_i_cols"])} |
| sf = np.asarray(g["scalar_f8"]); fc_ = {k: j for j, k in enumerate(g.attrs["scalar_f8_cols"])} |
| fl = np.asarray(g["flags"]); fc = {k: j for j, k in enumerate(g.attrs["flag_cols"])} |
| if g.attrs.get("has_mo"): |
| cf = np.asarray(g["mo_flags"])[:, g.attrs["mo_flag_cols"].index("mo_ok")] |
| else: |
| cf = np.full(len(ids), -1) |
| for i in range(len(ids)): |
| fh.write("\t".join(map(str, [ |
| ids[i], ds, rel, i, si[i, ic["n_atoms"]], si[i, ic["nbas"]], si[i, ic["nelec"]], |
| si[i, ic["charge"]], si[i, ic["mult"]], int(fl[i, fc["is_uhf"]]), |
| int(fl[i, fc["has_fock"]]), int(fl[i, fc["scf_converged"]]), int(cf[i]), |
| f"{sf[i, fc_['e_total']]:.10f}", f"{sf[i, fc_['conv_diiserr']]:.3e}", rels[i]])) + "\n") |
| n += 1 |
| print(f"wrote {out}: {n:,} rows from {len(shards)} shards") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
