osobhandClaude Opus 5.5
78c769f179
A full read of a contiguous dataset is one memcpy from the mapped file, yet ran at a quarter of h5py's speed on one thread: the fresh output Vec took a page fault and a kernel page clear for every 4 KiB page written, 16384 per 64 MiB, costing several times the copy (the benchmark spent 6.2 s of 8 s in the kernel, 4.3M minor faults). numpy, so h5py, madvises MADV_HUGEPAGE on allocations of 4 MiB or more; the typed readers' output, the raw contiguous read and the chunk assembly buffer now do the same (Linux only, libc as a Linux-only dependency; no-op otherwise). New h5py comparison tests cover full and selection reads of contiguous data for every 1-8-byte integer and float type, both byte orders, ranks 1-4, empty selections, and datasets past the 4 MiB threshold. Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
86 lines
3.3 KiB
TOML
86 lines
3.3 KiB
TOML
[package]
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name = "clawhdf5-format"
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version = "2.7.0"
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edition = "2024"
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rust-version.workspace = true
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description = "Pure-Rust HDF5 binary format parsing and writing — no C dependencies"
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license = "MIT"
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repository = "https://git.redclaw.dev/quantumclaw/clawhdf5"
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readme = "README.md"
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keywords = ["hdf5", "science", "data", "binary", "no-std"]
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categories = ["parser-implementations", "science", "encoding", "no-std"]
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[dependencies]
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byteorder = { version = "1", default-features = false }
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portable-atomic = { version = "1" }
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flate2 = { version = "1", default-features = false, features = ["rust_backend"], optional = true }
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sha2 = { version = "0.10", default-features = false, optional = true }
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rayon = { version = "1", optional = true }
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crc32fast = { version = "1", optional = true }
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lz4_flex = { version = "0.11", optional = true }
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zstd = { version = "0.13", optional = true }
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blake3 = { version = "1", optional = true }
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libaec-sys = { path = "../libaec-sys", version = "0.1", optional = true }
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pco = { version = "1.0", optional = true }
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# Pure-Rust Zstandard, for the plugin filters that embed zstd (bitshuffle,
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# blosc). The `zstd` feature (filter 32015) links libzstd instead.
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ruzstd = { version = "0.9", optional = true }
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# bzip2 with its default backend, libbz2-rs-sys: a pure-Rust port of
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# libbzip2 (no C is compiled, despite the -sys name).
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bzip2 = { version = "0.6", optional = true }
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snap = { version = "1", optional = true }
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[target.'cfg(target_os = "linux")'.dependencies]
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# madvise(MADV_HUGEPAGE) for large read buffers (see src/bulk_alloc.rs).
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libc = { version = "0.2", default-features = false }
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[dev-dependencies]
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half = { workspace = true }
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serde_json = "1"
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criterion = { workspace = true }
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clawhdf5-derive = { path = "../clawhdf5-derive", version = "2.7.0" }
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[[bench]]
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name = "bench"
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harness = false
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[features]
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# Deflate backend: `zlib-rs` (pure Rust) by default. `fast-deflate` selects
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# zlib-ng instead (C, built with cmake); flate2 prefers a C zlib whenever one
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# is enabled, so turning it on anywhere in the build overrides the default.
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default = ["std", "checksum", "deflate", "provenance", "zlib-rs", "system-zlib-decompress", "lzf"]
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std = []
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checksum = []
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deflate = ["flate2"]
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provenance = ["sha2"]
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parallel = ["rayon", "std"]
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fast-checksum = ["crc32fast"]
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fast-deflate = ["flate2/zlib-ng"]
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system-zlib = ["flate2/zlib-default"]
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system-zlib-decompress = []
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# `runtime_detection` gives zlib-rs `std`, which it needs to detect and use
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# SIMD at runtime. flate2 enables it by default, but we build flate2 with
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# default-features = false, and without it zlib-rs inflates 3.5x slower.
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zlib-rs = ["flate2/zlib-rs", "flate2/runtime_detection"]
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lz4 = ["lz4_flex"]
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zstd = ["dep:zstd"]
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blake3_hash = ["blake3"]
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szip = ["libaec-sys"]
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pcodec = ["dep:pco"]
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# Plugin filters, pure Rust. LZF (32000) is h5py's built-in compression; it
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# has no dependencies, so it is on by default.
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lzf = []
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# Bitshuffle (32008), with its LZ4 and Zstandard modes.
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bitshuffle = ["lz4_flex", "ruzstd"]
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# bzip2 (307).
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bzip2 = ["dep:bzip2", "std"]
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# Blosc 1 (32001) with its BloscLZ, LZ4, Snappy, Zlib and Zstandard codecs.
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blosc = ["lz4_flex", "ruzstd", "snap", "deflate", "std"]
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# Every plugin filter above.
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plugin-filters = ["lzf", "bitshuffle", "bzip2", "blosc"]
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[[bench]]
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name = "parallel_decompress_bench"
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harness = false
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required-features = ["parallel"]
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