sux

A pure Rust implementation of succinct and compressed data structures.

This crate started is part of the Sux project; it contains also code ported from the DSI Utilities and new structures.

Presently, it provides:

• bit vectors and bit-field vectors;
• several structures for rank and selection with different tradeoffs;
• indexed dictionaries, including an implementation of the Elias–Fano representation of monotone sequences and lists of strings compressed by prefix omission.

The focus is on efficiency (in particular, there are unchecked versions of all methods) and on flexible composability (e.g., you can fine-tune your Elias–Fano instance by choosing different types of internal indices, and whether to index zeros or ones).

ε-serde support

All structures in this crate are designed to work well with ε-serde: in particular, once you have created and serialized them, you can easily map them into memory or load them in memory regions with specific mmap() attributes.

MemDbg/MemSize support

All structures in this crate support the MemDbg and MemSize traits from the mem_dbg crate, which provide convenient facilities for inspecting memory usage and debugging memory-related issues. For example, this is the output of mem_dbg() on a large EliasFano instance:

  117_041_232 B 100.00% ⏺: sux::dict::elias_fano::EliasFano<sux::rank_sel::select_zero_adapt_const::SelectZeroAdaptConst<sux::rank_sel::select_adapt_const::SelectAdaptConst>>
           8 B   0.00% ├╴u: usize
           8 B   0.00% ├╴n: usize
           8 B   0.00% ├╴l: usize
  75_000_048 B  64.08% ├╴low_bits: sux::bits::bit_field_vec::BitFieldVec
  75_000_024 B  64.08% │ ├╴data: alloc::vec::Vec<usize>
           8 B   0.00% │ ├╴bit_width: usize
           8 B   0.00% │ ├╴mask: usize
           8 B   0.00% │ ╰╴len: usize
  42_041_160 B  35.92% ╰╴high_bits: sux::rank_sel::select_zero_adapt_const::SelectZeroAdaptConst<sux::rank_sel::select_adapt_const::SelectAdaptConst>
  35_937_608 B  30.71%   ├╴bits: sux::rank_sel::select_adapt_const::SelectAdaptConst
  32_031_296 B  27.37%   │ ├╴bits: sux::bits::bit_vec::CountBitVec
  32_031_280 B  27.37%   │ │ ├╴data: alloc::vec::Vec<usize>
           8 B   0.00%   │ │ ├╴len: usize
           8 B   0.00%   │ │ ╰╴number_of_ones: usize
   3_906_312 B   3.34%   │ ╰╴inventory: alloc::vec::Vec<u64>
   6_103_552 B   5.21%   ╰╴inventory: alloc::vec::Vec<u64>

Composability, functoriality, and performance

The design of this crate tries to satisfy the following principles:

• High performance: all implementations try to be as fast as possible (we try to minimize cache misses, then tests, and then instructions).
• Composability: all structures are designed to be easily composed with each other; structures are built on top of other structures, which can be extracted with the usual into_inner idiom.
• Zero-cost abstraction: all structures forward conditionally all ranking/selection non-implemented methods on the underlying structures.
• Functoriality: whenever possible, there are mapping methods that replace an underlying structure with another one, provided it is compatible.

What this crate does not provide:

• High genericity: all bit vectors are based on the rather concrete trait combination AsRef<[usize]> + BitLength.

Benchmarks

You can run a number of benchmarks on the structures. Try

cargo bench --bench sux --features cli -- --help

to see the available tests. For example, with

cargo bench --bench sux --features cli -- Rank9 -d 0.5 -r 1 -l 100000,1000000,10000000

you can test the Rank9 structure with a density of 0.5, using one test repetition, on a few bit sizes. Afterwards, you can generate an SVG plot and CSV data in the plots directory with

./python/plot_benches.py --benches-path ./target/criterion/ --plot-dir plots

You can then open the plots/plot.svg with a browser to see the results, or inspect the directory csv for CSV data. Note that as you run benchmarks, the results will cumulate in the target/criterion directory, so you can generate plots for multiple runs.

By specifying multiple structures (using also substring matching), you can compare the behavior of different structures. For example,

cargo bench --bench sux --features cli -- SelectSmall SelectAdapt0 -d 0.5 -r 1 -l 100000,1000000,10000000

will test all variants of SelectSmall against a SelectAdapt with one (2⁰) u64 per subinventory. The plot will highlight the differences in performance:

./python/plot_benches.py --benches-path ./target/criterion/ --plot-dir plots

Acknowledgments

This software has been partially supported by project SERICS (PE00000014) under the NRRP MUR program funded by the EU - NGEU, and by project ANR COREGRAPHIE, grant ANR-20-CE23-0002 of the French Agence Nationale de la Recherche. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the Italian MUR. Neither the European Union nor the Italian MUR can be held responsible for them