bench: concurrent-read harness against h5py threads and processes
concurrent_read reads one shared File from 1-16 threads: every dataset in full (distinct datasets per thread) and random hyperslabs of one dataset, over a deflate and a contiguous file it generates (or reuses while manifest.json matches). It reports decoded MB/s and scaling efficiency, warm or --cold (posix_fadvise) page cache, sizes the decode pool with --decode-threads, and writes JSON. scripts/concurrent_read_h5py.py runs the same workload on the same files with h5py threads or spawned processes (same splitmix64 data and slab stream, checked at spot elements), and compare_concurrent_read.py prints one table and refuses runs with different workloads. A smoke test runs all three end to end on tiny files (h5py half honours CLAWHDF5_PYTHON / CLAWHDF5_REQUIRE_INTEROP). BENCHMARKS.md gets a "Concurrent reads" section with the commands, marked not yet measured. Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
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#!/usr/bin/env python3
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"""The concurrent_read workload with h5py, on the files concurrent_read wrote.
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libhdf5 serialises every API call under one global lock, and h5py holds its
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own global lock around every call as well, so h5py *threads* cannot decode in
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parallel. h5py users scale with *processes* instead; ``--executor processes``
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measures that (each worker opens the file itself).
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The workload mirrors ``crates/clawhdf5-bench/src/bin/concurrent_read.rs``:
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* ``distinct``: every dataset read in full once per repetition; worker ``t``
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of ``T`` reads datasets ``t, t + T, ...``.
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* ``same``: ``--slabs`` random ``--slab`` x ``--slab`` hyperslabs of ``d00``
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(slab ``j`` to worker ``j % T``), offsets from the same splitmix64 stream.
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Each worker times itself from a start barrier; a repetition spans the earliest
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start to the latest finish (CLOCK_MONOTONIC, comparable across processes).
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Threads share one ``h5py.File`` per repetition; process workers open the file
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inside the timed region (a few ms against reads of many MiB).
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Generate the files first with the Rust harness (it writes ``manifest.json``),
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then, for example::
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python concurrent_read_h5py.py --dir DIR --executor threads --json h5py-threads.json
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python concurrent_read_h5py.py --dir DIR --executor processes --json h5py-procs.json
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"""
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import argparse
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import json
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import multiprocessing as mp
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import os
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import platform
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import socket
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import sys
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import threading
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import time
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import h5py
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import numpy as np
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M64 = (1 << 64) - 1
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def splitmix64(state):
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"""Return (new_state, value); the same stream as the Rust harness."""
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state = (state + 0x9E3779B97F4A7C15) & M64
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z = state
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z = ((z ^ (z >> 30)) * 0xBF58476D1CE4E5B9) & M64
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z = ((z ^ (z >> 27)) * 0x94D049BB133111EB) & M64
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return state, z ^ (z >> 31)
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def value(k, i):
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"""Element i (row-major) of dataset k, exactly as concurrent_read writes it."""
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_, noise = splitmix64(i ^ (k << 40))
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return np.float32((((i >> 6) % 16384) + k) + (noise & 0xFF) / 256.0)
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def slab_offsets(seed, count, rows, cols, slab):
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s = seed
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out = []
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for _ in range(count):
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s, r = splitmix64(s)
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s, c = splitmix64(s)
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out.append((r % (rows - slab + 1), c % (cols - slab + 1)))
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return out
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def now():
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return time.clock_gettime(time.CLOCK_MONOTONIC)
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def work(f, mode, t, threads, m, slabs, slab, verify):
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"""Worker t's share of one repetition on an open h5py.File."""
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n = m["rows"] * m["cols"]
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if mode == "distinct":
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for k in range(t, m["datasets"], threads):
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got = f[f"d{k:02d}"][...]
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assert got.size == n
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if verify:
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flat = got.reshape(-1)
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for i in (0, n // 3, n - 1):
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assert flat[i] == value(k, i), f"d{k:02d}[{i}]"
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else:
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ds = f["d00"]
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cols = m["cols"]
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for r, c in slabs[t::threads]:
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got = ds[r : r + slab, c : c + slab]
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assert got.shape == (slab, slab)
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if verify:
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assert got[0, 0] == value(0, r * cols + c)
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last = (r + slab - 1) * cols + c + slab - 1
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assert got[-1, -1] == value(0, last)
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# ----- process workers ------------------------------------------------------
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_barrier = None
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def _init(barrier):
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global _barrier
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_barrier = barrier
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def _proc_task(task):
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path, mode, t, threads, m, slabs, slab = task
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_barrier.wait()
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start = now()
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with h5py.File(path, "r") as f:
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work(f, mode, t, threads, m, slabs, slab, False)
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return start, now()
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def _noop(_):
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return os.getpid()
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def run_threads(path, mode, threads, m, slabs, slab):
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spans = [None] * threads
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barrier = threading.Barrier(threads)
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with h5py.File(path, "r") as f:
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def body(t):
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barrier.wait()
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start = now()
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work(f, mode, t, threads, m, slabs, slab, False)
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spans[t] = (start, now())
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ts = [threading.Thread(target=body, args=(t,)) for t in range(threads)]
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for th in ts:
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th.start()
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for th in ts:
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th.join()
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return max(e for _, e in spans) - min(s for s, _ in spans)
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def run_processes(pool, path, mode, threads, m, slabs, slab):
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tasks = [(path, mode, t, threads, m, slabs, slab) for t in range(threads)]
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# One task per worker: each blocks in the barrier until all T have
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# started, so no worker can take a second task.
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spans = pool.map(_proc_task, tasks, chunksize=1)
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return max(e for _, e in spans) - min(s for s, _ in spans)
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def warm(path):
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with open(path, "rb") as fh:
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while fh.read(1 << 24):
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pass
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def evict(path):
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fd = os.open(path, os.O_RDONLY)
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try:
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os.posix_fadvise(fd, 0, 0, os.POSIX_FADV_DONTNEED)
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finally:
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os.close(fd)
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def main():
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ap = argparse.ArgumentParser(description=__doc__.split("\n\n")[0])
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ap.add_argument("--dir", default="concurrent-read-data")
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ap.add_argument("--executor", choices=["threads", "processes"], default="threads")
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ap.add_argument("--threads", default="1,2,4,8,16")
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ap.add_argument("--reps", type=int, default=3)
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ap.add_argument("--slab", type=int, default=256)
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ap.add_argument("--slabs", type=int, default=1024)
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ap.add_argument("--seed", type=int, default=42)
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ap.add_argument("--cold", action="store_true")
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ap.add_argument("--modes", default="distinct,same")
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ap.add_argument("--layouts", default="deflate,contiguous")
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ap.add_argument("--json")
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a = ap.parse_args()
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# The Rust harness pins this value (splitmix64_reference).
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assert splitmix64(42)[1] == 0xBDD732262FEB6E95, "splitmix64 port is wrong"
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try:
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with open(os.path.join(a.dir, "manifest.json")) as fh:
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m = json.load(fh)
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except FileNotFoundError:
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sys.exit(f"{a.dir}/manifest.json not found: generate the files with "
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"`cargo run --release -p clawhdf5-bench --bin concurrent_read -- --dir ...` first")
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threads_list = [int(x) for x in a.threads.split(",")]
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modes = a.modes.split(",")
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layouts = a.layouts.split(",")
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if a.slab < 1 or a.slab > min(m["rows"], m["cols"]):
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sys.exit(f"--slab must be 1..={min(m['rows'], m['cols'])}")
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files = dict(m["files"])
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slabs = slab_offsets(a.seed, a.slabs, m["rows"], m["cols"], a.slab)
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dataset_bytes = m["rows"] * m["cols"] * 4
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tool = f"h5py-{a.executor}"
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ctx = mp.get_context("spawn") # never fork a process holding HDF5 state
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pools = {}
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if a.executor == "processes":
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for t in threads_list:
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pool = ctx.Pool(t, initializer=_init, initargs=(ctx.Barrier(t),))
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pool.map(_noop, range(t)) # start the workers outside the timing
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pools[t] = pool
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rows = []
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print("| layout | mode | threads | MB/s | efficiency | median s |")
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print("|---|---|---:|---:|---:|---:|")
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try:
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for layout in layouts:
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path = os.path.join(a.dir, files[layout])
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if not a.cold:
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warm(path)
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for mode in modes:
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with h5py.File(path, "r") as f: # untimed, checked pass
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work(f, mode, 0, 1, m, slabs, a.slab, True)
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nbytes = (dataset_bytes * m["datasets"] if mode == "distinct"
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else a.slab * a.slab * 4 * a.slabs)
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base = None
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for t in threads_list:
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times = []
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for _ in range(a.reps):
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if a.cold:
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evict(path)
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if a.executor == "threads":
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times.append(run_threads(path, mode, t, m, slabs, a.slab))
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else:
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times.append(run_processes(pools[t], path, mode, t, m, slabs, a.slab))
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med = sorted(times)[len(times) // 2]
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mb_s = nbytes / (1 << 20) / med
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if t == 1:
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base = mb_s
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eff = mb_s / (t * base) if base else None
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print(f"| {layout} | {mode} | {t} | {mb_s:.0f} | "
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f"{'-' if eff is None else f'{eff:.2f}'} | {med:.4f} |")
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rows.append({
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"layout": layout, "mode": mode, "threads": t, "bytes": nbytes,
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"times_s": times, "median_s": med, "mb_s": mb_s, "efficiency": eff,
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})
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finally:
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for pool in pools.values():
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pool.terminate()
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if a.json:
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doc = {
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"tool": tool,
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"version": h5py.__version__,
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"hdf5_version": h5py.version.hdf5_version,
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"python": platform.python_version(),
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"host": socket.gethostname(),
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"cpus": os.cpu_count(),
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"unix_time": int(time.time()),
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"cache": ("cold (posix_fadvise DONTNEED before each repetition)"
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if a.cold else "warm"),
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"decode_threads": 1,
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"params": {
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"datasets": m["datasets"], "rows": m["rows"], "cols": m["cols"],
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"chunk": m["chunk"], "deflate_level": m["deflate_level"],
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"mib": dataset_bytes // (1 << 20), "slab": a.slab, "slabs": a.slabs,
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"seed": a.seed, "reps": a.reps, "dir": a.dir,
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},
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"results": rows,
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}
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with open(a.json, "w") as fh:
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json.dump(doc, fh, indent=2)
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if __name__ == "__main__":
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main()
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