Virtual chunks: On supporting random accesses to scientific data in compressible storage systems

Abstract

Data compression could ameliorate the I/O pressure of scientific applications on high-performance computing systems. Unfortunately, the conventional wisdom of naively applying data compression to the file or block brings the dilemma between efficient random accesses and high compression ratios. Filelevel compression can barely support efficient random accesses to the compressed data: any retrieval request need trigger the decompression from the beginning of the compressed file. Block-level compression provides flexible random accesses to the compressed data, but introduces extra overhead when applying the compressor to each every block that results in a degraded overall compression ratio. This paper introduces a concept called virtual chunks aiming to support efficient random accesses to the compressed scientific data without sacrificing its compression ratio. In essence, virtual chunks are logical blocks identified by appended references without breaking the physical continuity of the file content. These additional references allow the decompression to start from an arbitrary position (efficient random access), and retain the file's physical entirety to achieve high compression ratio on par with file-level compression. One potential concern of virtual chunks lies on its space overhead (from the additional references) that degrades the compression ratio, but our analytic study and experimental results demonstrate that such overhead is negligible. We have implemented virtual chunks in two forms: a middleware to the GPFS parallel file system, and a module in the FusionFS distributed file system. Large-scale evaluations on up to 1,024 cores showed that virtual chunks could help improve the I/O throughput by 2X speedup.