File size: 3,702 Bytes
39ea985 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 | """Draw a uniform random subset of OMol25 calculations and check they exist on m5250.
The population is the 4M-split path list shipped with the release (`4m_paths.txt`, 3,986,753 rows).
Sampling is uniform over that list with a fixed seed, so the subset keeps the collection's natural
dataset proportions and is exactly reproducible.
Writes:
subset_<n>.txt one relative path per line, present on m5250, shuffled
subset_<n>_missing.txt paths sampled but not found locally
subset_<n>_counts.tsv per-dataset counts, sampled vs population
"""
import argparse, os, random, sys
from collections import Counter
M5250 = "/global/cfs/projectdirs/m5250/OMol_elec"
PATHS = ("/global/cfs/projectdirs/m5293/ericqu/omol_elec_process/gbw_pilot/"
"source_root/4m_paths.txt")
OUTDIR = "/global/cfs/projectdirs/m5293/ericqu/omol_elec_process/subsets"
def dataset_of(rel):
"""Top-level dataset name; the omol/ tree is grouped by its second and third component."""
parts = rel.split("/")
if parts[0] == "omol" and len(parts) > 2:
return "/".join(parts[:3])
return parts[0]
def main():
ap = argparse.ArgumentParser()
ap.add_argument("-n", type=int, default=100_000)
ap.add_argument("--seed", type=int, default=20260903)
ap.add_argument("--paths", default=PATHS)
ap.add_argument("--outdir", default=OUTDIR)
ap.add_argument("--check", type=int, default=5000,
help="how many sampled paths to stat for a miss-rate estimate (0 = none)")
args = ap.parse_args()
with open(args.paths) as fh:
pop = [l.strip() for l in fh if l.strip()]
print(f"population: {len(pop):,} paths", flush=True)
rng = random.Random(args.seed)
n = min(args.n, len(pop))
sample = rng.sample(pop, n)
print(f"sampled uniformly: {n:,} (seed {args.seed})", flush=True)
os.makedirs(args.outdir, exist_ok=True)
# Stat-ing every path is slow on CFS (huge directories), and Pass A detects a missing archive
# for free, so only a subsample is checked here to estimate the miss rate.
missing = []
ncheck = min(args.check, n)
for i, rel in enumerate(sample[:ncheck]):
if not os.path.exists(os.path.join(M5250, rel, "orca.tar.zst")):
missing.append(rel)
if (i + 1) % 1000 == 0:
print(f" checked {i+1:,}/{ncheck:,}: {len(missing):,} missing", flush=True)
present = sample
rng.shuffle(present)
base = os.path.join(args.outdir, f"subset_{n//1000}k")
with open(base + ".txt", "w") as fh:
fh.write("\n".join(present) + "\n")
with open(base + "_missing.txt", "w") as fh:
fh.write("\n".join(missing) + ("\n" if missing else ""))
pop_counts = Counter(dataset_of(p) for p in pop)
got_counts = Counter(dataset_of(p) for p in present)
with open(base + "_counts.tsv", "w") as fh:
fh.write("dataset\tpopulation\tsampled\tpct_of_dataset\n")
for ds in sorted(pop_counts, key=lambda d: -pop_counts[d]):
fh.write(f"{ds}\t{pop_counts[ds]}\t{got_counts.get(ds,0)}\t"
f"{100*got_counts.get(ds,0)/pop_counts[ds]:.3f}\n")
rate = (100 * len(missing) / ncheck) if ncheck else float("nan")
print(f"\nsubset {len(present):,} paths; miss rate on {ncheck:,} checked: "
f"{len(missing):,} ({rate:.2f}%)")
print(f"datasets covered: {len(got_counts)}/{len(pop_counts)}")
zero = [d for d in pop_counts if d not in got_counts]
if zero:
print("datasets with no sampled member:")
for d in zero:
print(f" {d} (population {pop_counts[d]:,})")
print(f"\nwrote {base}.txt / _missing.txt / _counts.tsv")
if __name__ == "__main__":
main()
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