osobhandClaude Opus 5.5
b086dc3c2b
gather_storage merged only runs that touch, so a strided selection of a contiguous dataset over a Storage became one range (and one owned Vec) per element: a stride-2 read of 32M f32 through File::open_storage made 16,777,232 read_at calls, took 2.0 s and peaked at 2.09 GB. The selection is now walked twice. The first walk checks the runs and plans spans: runs in increasing order at most 4 KiB apart (GATHER_GAP_BYTES) are read as one span up to 8 MiB (GATHER_SPAN_BYTES; a longer run is split), so nothing is stored per run. The spans are fetched in RAW_BATCH_BYTES batches while the second walk copies each run out of its span. Same checks and errors as before. The same read is now 32 reads and 0.31 s (File::open: 0.08 s). contiguous_read_interop: every h5py-checked selection is also read through File::open_storage and must give libhdf5's bytes; a new test bounds the range reads of strided, blocked, column and point selections (stride 2: at most 1 data read; 563,200 before). Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
clawhdf5
Pure-Rust HDF5 reader/writer — no C dependencies.
Features
- Read and write HDF5 files entirely in Rust
- Memory-mapped I/O for large files (
mmapfeature, enabled by default) - Parallel chunk reads via Rayon (
parallelfeature) - Lazy dataset access for minimal memory usage
- h5py-compatible file output
Usage
use clawhdf5::File;
let file = File::open("data.h5").unwrap();
let dataset = file.dataset("/group/data").unwrap();
let values: Vec<f64> = dataset.read_1d().unwrap();
License
MIT