Chunked reads beat an h5py process pool; unlimited writer B-trees; Blosc2; 599/697 conformance #16

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osobh merged 48 commits from feat/p2b-scale into main 2026-09-26 17:42:16 +00:00
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#!/usr/bin/env python3
"""Inventory of whole-file `&[u8]` parameters in the clawhdf5 workspace.
Used by docs/design/range-reads.md. Run from the repository root:
python3 docs/design/tools/inventory.py # per-file table
python3 docs/design/tools/inventory.py --list # every signature
python3 docs/design/tools/inventory.py --patterns # read patterns per crate
A function counts as taking "the whole file" when it has a parameter named
`file_data: &[u8]` (the repository convention), or a `data` / `file` / `buf` /
`bytes` / `mmap` parameter of type `&[u8]` *together with* a parameter whose
name says it is a file address (`*address*`, `*addr*`, `*offset*` of an
integer type). The second rule is a heuristic; `--list` prints every match so
it can be checked by eye. Code after the first `#[cfg(test)] mod ... {` in a
file is excluded (the repository keeps unit tests at the end of each file),
as are the tests/ and benches/ directories.
"""
import os
import re
import sys
from collections import defaultdict
ROOT = os.getcwd()
FN_RE = re.compile(r"\bfn\s+([A-Za-z_][A-Za-z0-9_]*)\s*(<[^()]*?>)?\s*\(", re.S)
PARAM_RE = re.compile(r"([A-Za-z_][A-Za-z0-9_]*)\s*:\s*&(?:'[a-z_]+\s+)?\[u8\]")
ADDR_RE = re.compile(r"\b([a-z_]*(?:address|addr|offset)[a-z_]*)\s*:\s*(?:u64|usize|u32)")
WHOLE_NAMES = {"data", "file", "buf", "bytes", "file_bytes", "mmap"}
def signature(src, start):
depth, i = 0, start
while i < len(src):
c = src[i]
if c == "(":
depth += 1
elif c == ")":
depth -= 1
if depth == 0:
return src[start + 1 : i]
i += 1
return ""
def non_test_source(src):
m = re.search(r"#\[cfg\(test\)\]\s*mod\s+\w+\s*\{", src)
return src[: m.start()] if m else src
PATTERNS = [
("`file_data` passed on (call sites)", re.compile(r"[(,]\s*&?file_data\s*[,)]")),
("`file_data[..]` slicing", re.compile(r"\bfile_data\s*\[")),
("open-ended `file_data[x..]`", re.compile(r"\bfile_data\s*\[[^\]]*\.\.\s*\]")),
("`file_data.get(..)`", re.compile(r"\bfile_data\s*\.\s*get\s*\(")),
("`file_data.len()`", re.compile(r"\bfile_data\s*\.\s*len\s*\(\)")),
("address/offset `as usize` casts", re.compile(r"\b[a-z_]*(?:addr|address|offset)[a-z_]*\s+as\s+usize")),
("`ObjectHeader::parse(` calls", re.compile(r"ObjectHeader::parse\s*\(")),
("`.as_bytes()` on a file/reader", re.compile(r"\b(?:file|reader|data|self\.file|self\.data|self\.file\.data|root\.file)\s*\.\s*as_bytes\s*\(\)")),
]
def patterns():
"""Per-crate counts of the read patterns (non-test code only)."""
per_crate = defaultdict(lambda: [0] * len(PATTERNS))
for crate in sorted(os.listdir(os.path.join(ROOT, "crates"))):
srcdir = os.path.join(ROOT, "crates", crate, "src")
for dp, _, fns in os.walk(srcdir):
for fn in fns:
if not fn.endswith(".rs"):
continue
with open(os.path.join(dp, fn), encoding="utf-8") as fh:
src = non_test_source(fh.read())
for i, (_, rx) in enumerate(PATTERNS):
per_crate[crate][i] += len(rx.findall(src))
print("| crate | " + " | ".join(n for n, _ in PATTERNS) + " |")
print("|---|" + "---:|" * len(PATTERNS))
tot = [0] * len(PATTERNS)
for c, v in sorted(per_crate.items()):
if any(v):
print("| %s | %s |" % (c, " | ".join(str(x) for x in v)))
tot = [a + b for a, b in zip(tot, v)]
print("| **total** | %s |" % " | ".join("**%d**" % x for x in tot))
def main():
if "--patterns" in sys.argv:
patterns()
return
per_file = defaultdict(lambda: [0, 0, 0]) # [file_data, heuristic, pub]
rows = []
for crate in sorted(os.listdir(os.path.join(ROOT, "crates"))):
srcdir = os.path.join(ROOT, "crates", crate, "src")
for dp, _, fns in os.walk(srcdir):
for fn in sorted(fns):
if not fn.endswith(".rs"):
continue
path = os.path.join(dp, fn)
with open(path, encoding="utf-8") as fh:
src = non_test_source(fh.read())
for m in FN_RE.finditer(src):
sig = signature(src, m.end() - 1)
params = PARAM_RE.findall(sig)
kind = None
if "file_data" in params:
kind = "file_data"
elif any(p in WHOLE_NAMES for p in params) and ADDR_RE.search(sig):
kind = "heuristic"
if not kind:
continue
rel = os.path.relpath(path, ROOT)
line_start = src.rfind("\n", 0, m.start()) + 1
is_pub = src[line_start : m.start()].strip().startswith("pub")
per_file[rel][0 if kind == "file_data" else 1] += 1
per_file[rel][2] += int(is_pub)
line = src.count("\n", 0, m.start()) + 1
rows.append((rel, line, m.group(1), kind, is_pub))
if "--list" in sys.argv:
for r in rows:
print("%s:%d %s [%s%s]" % (r[0], r[1], r[2], r[3], ", pub" if r[4] else ""))
return
print("| file | `file_data` fns | other whole-slice fns (heuristic) | of which `pub` |")
print("|---|---:|---:|---:|")
tot = [0, 0, 0]
for f, (a, b, p) in sorted(per_file.items(), key=lambda kv: (-(kv[1][0] + kv[1][1]), kv[0])):
print("| %s | %d | %d | %d |" % (f, a, b, p))
tot = [tot[0] + a, tot[1] + b, tot[2] + p]
print("| **total** | **%d** | **%d** | **%d** |" % tuple(tot))
if __name__ == "__main__":
main()
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#!/usr/bin/env python3
"""The libhdf5 side of the range-read measurement (docs/design/range-reads.md).
libhdf5_reads.py FILE DATASET # count libhdf5's reads
libhdf5_reads.py FILE DATASET --extents # print DATASET's stored extents
Counting: the file is opened through h5py's `fileobj` driver with a Python
file-like object that logs every `readinto`/`read` libhdf5 makes (this is how
h5py + fsspec reads remote files: each call becomes a range request unless
fsspec's own block cache absorbs it). The phases mirror range-trace: open,
list (visit every object; shape and dtype of every dataset), read (the whole
dataset). Default h5py settings (libhdf5's metadata cache, 64 KiB sieve
buffer, 1 MiB raw chunk cache) apply.
--extents prints `offset size` lines for the dataset's stored data (the
contiguous block, or every allocated chunk), the input range-trace uses to
split its read phase into metadata and raw data.
"""
import sys
import h5py
class LoggingFile:
def __init__(self, path):
self.f = open(path, "rb")
self.pos = 0
self.log = []
def seek(self, off, whence=0):
self.pos = self.f.seek(off, whence)
return self.pos
def tell(self):
return self.pos
def readinto(self, b):
n = self.f.readinto(b)
self.log.append((self.pos, n))
self.pos += n
return n
def read(self, size=-1):
data = self.f.read(size)
self.log.append((self.pos, len(data)))
self.pos += len(data)
return data
def extents(path, name):
with h5py.File(path, "r") as f:
ds = f[name]
if ds.chunks is None:
off = ds.id.get_offset()
if off is not None:
print(off, ds.id.get_storage_size())
return
for i in range(ds.id.get_num_chunks()):
info = ds.id.get_chunk_info(i)
print(info.byte_offset, info.size)
def summarise(label, log):
n = len(log)
total = sum(s for _, s in log)
distinct = len(set(log))
print("| %s | %d | %d | %d |" % (label, n, distinct, total))
def count(path, name):
lf = LoggingFile(path)
f = h5py.File(lf, "r")
opened = list(lf.log)
lf.log.clear()
def visit(_n, obj):
if isinstance(obj, h5py.Dataset):
obj.shape, obj.dtype
f.visititems(visit)
listed = list(lf.log)
lf.log.clear()
f[name][()]
readlog = list(lf.log)
f.close()
print("| phase | read calls | distinct (offset, len) | bytes |")
print("|---|---:|---:|---:|")
summarise("open", opened)
summarise("list", listed)
summarise("read", readlog)
summarise("open+list+read", opened + listed + readlog)
if __name__ == "__main__":
if len(sys.argv) >= 4 and sys.argv[3] == "--extents":
extents(sys.argv[1], sys.argv[2])
else:
count(sys.argv[1], sys.argv[2])
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[package]
name = "range-trace"
version = "0.1.0"
edition = "2024"
rust-version = "1.92"
publish = false
description = "Records which byte ranges of an HDF5 file the clawhdf5 facade reads (docs/design/range-reads.md)"
# Outside the main workspace on purpose: a measurement tool for a design
# document, never built by `cargo test --workspace`. x86-64 Linux only.
[workspace]
[dependencies]
# Default features minus nothing: `parallel` is off by default, and the tracer
# relies on every read happening on the main thread.
clawhdf5 = { path = "../../../../crates/clawhdf5" }
libc = "0.2"
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//! range-trace: which bytes of an HDF5 file does clawhdf5 read?
//!
//! Measurement tool for `docs/design/range-reads.md` (x86-64 Linux only).
//!
//! The file is loaded into a page-aligned buffer and handed to
//! `clawhdf5::File::from_bytes`, so the library parses it exactly as it does
//! today. The buffer is then `mprotect`ed to `PROT_NONE`. Every load from it
//! faults; the SIGSEGV handler logs the exact faulting address, makes that
//! page readable and sets the x86 trap flag, so the CPU single-steps the one
//! instruction and the SIGTRAP handler re-protects the page. Every load
//! instruction that touches the file is therefore recorded (with its first
//! byte; widths are not decoded, see `ACCESS_WIDTH`).
//!
//! Bulk copies (raw data) would fault once per load; a page that faults more
//! than `BULK_THRESHOLD` times in one phase is left readable for the rest of
//! that phase and counted as wholly read ("bulk page").
//!
//! Phases: `open` (superblock), `list` (walk every group; for every dataset
//! its shape and dtype, i.e. what `h5ls -r -v` or a tree view needs), and
//! `read` (read the named dataset in full through `read_selection(All)`).
//!
//! Usage: range-trace FILE DATASET_PATH [RAW_EXTENTS]
//!
//! RAW_EXTENTS (optional) lists the dataset's stored data as `offset size`
//! lines (absolute file offsets; `libhdf5_reads.py --extents` writes it from
//! h5py). With it the `read` phase is split into `read (metadata)`, the
//! loads outside those extents, and `read (raw data)`, the loads inside.
//!
//! Every read must happen on this thread: build without the facade's
//! `parallel` feature (off by default).
use std::alloc::{Layout, alloc_zeroed};
use std::collections::BTreeSet;
use std::sync::atomic::{AtomicPtr, AtomicUsize, Ordering};
use clawhdf5::{File, Group, Selection};
const PAGE: usize = 4096;
const BULK_THRESHOLD: u32 = 4096;
/// Bytes assumed read by one logged load (the widest scalar load the parsers
/// issue; SIMD copies are bulk anyway).
const ACCESS_WIDTH: u64 = 8;
/// Two accesses closer than this belong to the same structure, i.e. would be
/// one range request.
const MERGE_GAP: u64 = 64;
const LOG_CAP: usize = 64 << 20;
static BUF_START: AtomicUsize = AtomicUsize::new(0);
static BUF_LEN: AtomicUsize = AtomicUsize::new(0);
static LOG: AtomicPtr<u64> = AtomicPtr::new(std::ptr::null_mut());
static LOG_LEN: AtomicUsize = AtomicUsize::new(0);
static HITS: AtomicPtr<u32> = AtomicPtr::new(std::ptr::null_mut());
static BULK: AtomicPtr<u8> = AtomicPtr::new(std::ptr::null_mut());
static PENDING: [AtomicUsize; 8] = [const { AtomicUsize::new(0) }; 8];
static PENDING_N: AtomicUsize = AtomicUsize::new(0);
const TF: i64 = 0x100;
extern "C" fn on_segv(_sig: libc::c_int, info: *mut libc::siginfo_t, ctx: *mut libc::c_void) {
unsafe {
let addr = (*info).si_addr() as usize;
let start = BUF_START.load(Ordering::Relaxed);
let len = BUF_LEN.load(Ordering::Relaxed);
if addr < start || addr >= start + len {
// A genuine crash: restore the default action and re-fault.
libc::signal(libc::SIGSEGV, libc::SIG_DFL);
return;
}
let off = addr - start;
let n = LOG_LEN.load(Ordering::Relaxed);
if n < LOG_CAP {
*LOG.load(Ordering::Relaxed).add(n) = off as u64;
LOG_LEN.store(n + 1, Ordering::Relaxed);
}
let page = off / PAGE;
let hits = HITS.load(Ordering::Relaxed).add(page);
*hits += 1;
libc::mprotect(
(start + page * PAGE) as *mut libc::c_void,
PAGE,
libc::PROT_READ | libc::PROT_WRITE,
);
if *hits >= BULK_THRESHOLD {
*BULK.load(Ordering::Relaxed).add(page) = 1;
} else {
let p = PENDING_N.load(Ordering::Relaxed);
if p < PENDING.len() {
PENDING[p].store(page, Ordering::Relaxed);
PENDING_N.store(p + 1, Ordering::Relaxed);
}
}
let uc = ctx as *mut libc::ucontext_t;
(*uc).uc_mcontext.gregs[libc::REG_EFL as usize] |= TF;
}
}
extern "C" fn on_trap(_sig: libc::c_int, _info: *mut libc::siginfo_t, ctx: *mut libc::c_void) {
unsafe {
let start = BUF_START.load(Ordering::Relaxed);
let n = PENDING_N.load(Ordering::Relaxed);
for p in PENDING.iter().take(n) {
let page = p.load(Ordering::Relaxed);
libc::mprotect(
(start + page * PAGE) as *mut libc::c_void,
PAGE,
libc::PROT_NONE,
);
}
PENDING_N.store(0, Ordering::Relaxed);
let uc = ctx as *mut libc::ucontext_t;
(*uc).uc_mcontext.gregs[libc::REG_EFL as usize] &= !TF;
}
}
fn install(
sig: libc::c_int,
h: extern "C" fn(libc::c_int, *mut libc::siginfo_t, *mut libc::c_void),
) {
unsafe {
let mut sa: libc::sigaction = std::mem::zeroed();
sa.sa_sigaction = h as usize;
sa.sa_flags = libc::SA_SIGINFO | libc::SA_NODEFER;
libc::sigemptyset(&mut sa.sa_mask);
assert_eq!(libc::sigaction(sig, &sa, std::ptr::null_mut()), 0);
}
}
fn protect(prot: libc::c_int) {
let start = BUF_START.load(Ordering::Relaxed);
let len = BUF_LEN.load(Ordering::Relaxed);
unsafe {
assert_eq!(libc::mprotect(start as *mut libc::c_void, len, prot), 0);
}
}
struct Phase {
name: &'static str,
log: Vec<u64>,
bulk_pages: Vec<u64>,
}
/// Start a phase: clear the per-page state and protect the buffer.
fn begin() {
let pages = BUF_LEN.load(Ordering::Relaxed) / PAGE;
unsafe {
std::ptr::write_bytes(HITS.load(Ordering::Relaxed), 0, pages);
std::ptr::write_bytes(BULK.load(Ordering::Relaxed), 0, pages);
}
LOG_LEN.store(0, Ordering::Relaxed);
protect(libc::PROT_NONE);
}
fn end(name: &'static str) -> Phase {
protect(libc::PROT_READ | libc::PROT_WRITE);
let n = LOG_LEN.load(Ordering::Relaxed);
let log = unsafe { std::slice::from_raw_parts(LOG.load(Ordering::Relaxed), n) }.to_vec();
let pages = BUF_LEN.load(Ordering::Relaxed) / PAGE;
let bulk = unsafe { std::slice::from_raw_parts(BULK.load(Ordering::Relaxed), pages) };
let bulk_pages = (0..pages)
.filter(|&p| bulk[p] != 0)
.map(|p| p as u64)
.collect();
if n == LOG_CAP {
eprintln!("warning: access log full in phase {name}");
}
Phase {
name,
log,
bulk_pages,
}
}
/// Byte intervals [lo, hi) read in a phase, merged when closer than `gap`.
fn ranges(ph: &[&Phase], gap: u64) -> Vec<(u64, u64)> {
let mut iv: Vec<(u64, u64)> = Vec::new();
for p in ph {
iv.extend(p.log.iter().map(|&o| (o, o + ACCESS_WIDTH)));
iv.extend(
p.bulk_pages
.iter()
.map(|&pg| (pg * PAGE as u64, (pg + 1) * PAGE as u64)),
);
}
iv.sort_unstable();
let mut out: Vec<(u64, u64)> = Vec::new();
for (lo, hi) in iv {
match out.last_mut() {
Some(last) if lo <= last.1 + gap => last.1 = last.1.max(hi),
_ => out.push((lo, hi)),
}
}
out
}
/// Requests a reader with no cache at all would make: a new request each
/// time the access stream leaves the neighbourhood of the current run.
fn uncached_requests(p: &Phase) -> usize {
let mut n = 0;
let (mut lo, mut hi) = (u64::MAX, 0u64);
for &o in &p.log {
if lo != u64::MAX && o + MERGE_GAP >= lo && o <= hi + MERGE_GAP {
lo = lo.min(o);
hi = hi.max(o + ACCESS_WIDTH);
} else {
n += 1;
lo = o;
hi = o + ACCESS_WIDTH;
}
}
n + p.bulk_pages.len()
}
fn blocks(ph: &[&Phase], block: u64) -> usize {
let mut set = BTreeSet::new();
for (lo, hi) in ranges(ph, 0) {
for b in lo / block..=(hi - 1) / block {
set.insert(b);
}
}
set.len()
}
fn read_extents(path: &str) -> Vec<(u64, u64)> {
let text = std::fs::read_to_string(path).expect("read extents");
let mut v: Vec<(u64, u64)> = text
.lines()
.filter_map(|l| {
let mut it = l.split_whitespace().map(|t| t.parse::<u64>());
match (it.next(), it.next()) {
(Some(Ok(o)), Some(Ok(n))) => Some((o, o + n)),
_ => None,
}
})
.collect();
v.sort_unstable();
v
}
fn in_extents(ext: &[(u64, u64)], lo: u64, hi: u64) -> bool {
let i = ext.partition_point(|e| e.1 <= lo);
i < ext.len() && ext[i].0 < hi
}
/// Split a phase into loads outside and inside the raw-data extents. A bulk
/// page counts as raw data when it overlaps an extent.
fn split_raw(p: &Phase, ext: &[(u64, u64)]) -> (Phase, Phase) {
let (mut m, mut r) = (Vec::new(), Vec::new());
for &o in &p.log {
if in_extents(ext, o, o + 1) {
r.push(o)
} else {
m.push(o)
}
}
let pg = PAGE as u64;
let (bm, br): (Vec<u64>, Vec<u64>) = p
.bulk_pages
.iter()
.partition(|&&b| !in_extents(ext, b * pg, (b + 1) * pg));
(
Phase {
name: "read (metadata)",
log: m,
bulk_pages: bm,
},
Phase {
name: "read (raw data)",
log: r,
bulk_pages: br,
},
)
}
fn walk(g: &Group<'_>, path: &str, objs: &mut usize) {
for name in g.datasets().unwrap_or_default() {
*objs += 1;
if let Ok(ds) = g.dataset(&name) {
let _ = ds.shape();
let _ = ds.dtype();
}
}
for name in g.groups().unwrap_or_default() {
*objs += 1;
if let Ok(sub) = g.group(&name) {
walk(&sub, &format!("{path}/{name}"), objs);
}
}
}
fn main() {
let args: Vec<String> = std::env::args().collect();
if args.len() != 3 && args.len() != 4 {
eprintln!("usage: range-trace FILE DATASET_PATH [RAW_EXTENTS]");
std::process::exit(2);
}
let bytes = std::fs::read(&args[1]).expect("read file");
let len = bytes.len();
let cap = len.div_ceil(PAGE).max(1) * PAGE;
let pages = cap / PAGE;
// Page-aligned buffer so that protection covers exactly the file. The
// Vec is never dropped (its layout differs from Vec's own), see the end.
let ptr = unsafe { alloc_zeroed(Layout::from_size_align(cap, PAGE).unwrap()) };
unsafe { std::ptr::copy_nonoverlapping(bytes.as_ptr(), ptr, len) };
drop(bytes);
let buf = unsafe { Vec::from_raw_parts(ptr, len, cap) };
BUF_START.store(ptr as usize, Ordering::Relaxed);
BUF_LEN.store(cap, Ordering::Relaxed);
let mut log = vec![0u64; LOG_CAP];
LOG.store(log.as_mut_ptr(), Ordering::Relaxed);
let mut hits = vec![0u32; pages];
HITS.store(hits.as_mut_ptr(), Ordering::Relaxed);
let mut bulk = vec![0u8; pages];
BULK.store(bulk.as_mut_ptr(), Ordering::Relaxed);
install(libc::SIGSEGV, on_segv);
install(libc::SIGTRAP, on_trap);
begin();
let file = File::from_bytes(buf).expect("open");
let p_open = end("open");
begin();
let mut objs = 0;
walk(&file.root(), "", &mut objs);
let p_list = end("list");
begin();
let out = file
.dataset(&args[2])
.and_then(|d| d.read_selection(&Selection::All))
.expect("read dataset");
let p_read = end("read");
println!("file: {} ({} bytes), objects listed: {objs}", args[1], len);
println!("dataset: {} ({} bytes decoded)", args[2], out.len());
println!(
"| phase | loads logged | bulk 4K pages | uncached requests | distinct ranges (gap<{MERGE_GAP}B) | bytes in ranges | 4 KiB blocks | 64 KiB blocks | 1 MiB blocks |"
);
println!("|---|---:|---:|---:|---:|---:|---:|---:|---:|");
let row = |label: String, ph: &[&Phase], uncached: usize| {
let r = ranges(ph, MERGE_GAP);
let bytes: u64 = r.iter().map(|(a, b)| b - a).sum();
let loads: usize = ph.iter().map(|p| p.log.len()).sum();
let bulk: usize = ph.iter().map(|p| p.bulk_pages.len()).sum();
println!(
"| {label} | {loads} | {bulk} | {uncached} | {} | {bytes} | {} | {} | {} |",
r.len(),
blocks(ph, 4 << 10),
blocks(ph, 64 << 10),
blocks(ph, 1 << 20)
);
};
for p in [&p_open, &p_list, &p_read] {
row(p.name.to_string(), &[p], uncached_requests(p));
}
if let Some(path) = args.get(3) {
let (meta, raw) = split_raw(&p_read, &read_extents(path));
for p in [&meta, &raw] {
row(p.name.to_string(), &[p], uncached_requests(p));
}
let all = [&p_open, &p_list, &meta];
let unc: usize = all.iter().map(|p| uncached_requests(p)).sum();
row("all metadata".into(), &all, unc);
}
let all = [&p_open, &p_list, &p_read];
let unc: usize = all.iter().map(|p| uncached_requests(p)).sum();
row("open+list+read".into(), &all, unc);
let meta = [&p_open, &p_list];
let unc: usize = meta.iter().map(|p| uncached_requests(p)).sum();
row("open+list".into(), &meta, unc);
// The File owns a buffer whose layout Vec does not know; never drop it.
std::mem::forget(file);
std::mem::forget(log);
std::mem::forget(hits);
std::mem::forget(bulk);
}