Binsparse: A Specification for Cross-Platform Storage of Sparse Matrices and Tensors

TL;DR

Binsparse introduces a cross-platform, binary storage format for sparse matrices and tensors that significantly reduces file size and improves read/write performance compared to existing ASCII-based formats.

Contribution

It provides a modular, embeddable binary format specification with multiple reference implementations, addressing the lack of a universal binary sparse storage standard.

Findings

File size reduced by up to 7.5x with compression.

Read speed improved by up to 26.5x over Matrix Market.

Write speed increased by up to 31x.

Abstract

Sparse matrices and tensors are ubiquitous throughout multiple subfields of computing. The widespread usage of sparse data has inspired many in-memory and on-disk storage formats, but the only widely adopted storage specifications are the Matrix Market and FROSTT file formats, which both use ASCII text. Due to the inefficiency of text storage, these files typically have larger file sizes and longer parsing times than binary storage formats, which directly store an in-memory representation to disk. This can be a major bottleneck; since sparse computation is often bandwidth-bound, the cost of loading or storing a matrix to disk often exceeds the cost of performing a sparse computation. While it is common practice for practitioners to develop their own, custom, non-portable binary formats for high-performance sparse matrix storage, there is currently no cross-platform binary sparse matrix storage format. We present Binsparse, a cross-platform binary sparse matrix and tensor format specification. Binsparse is a modular, embeddable format, consisting of a JSON descriptor, which describes the matrix or tensor dimensions, type, and format, and a series of binary arrays, which can be stored in all modern binary containers, such as HDF5, Zarr, or NPZ. We provide several reference implementations of Binsparse spanning 5 languages, 5 frameworks, and 4 binary containers. We evaluate our Binsparse format on every matrix in the SuiteSparse Matrix Collection and a selection of tensors from the FROSTT collection. The Binsparse HDF5 CSR format shows file size reductions of 2.4x on average without compression and 7.5x with compression. We evaluate our parser's read/write performance against a state-of-the-art Matrix Market parser, demonstrating warm cache mean read speedups of 26.5x without compression and 2.6x with compression, and write speedups of 31x without compression and 1.4x with compression.