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Storage-compute disaggregation has recently emerged as a novel architecture in modern data centers, particularly in the cloud. By decoupling compute from storage, this new architecture enables independent and elastic scaling of compute and storage resources, potentially increasing resource utilization and reducing overall costs. To best leverage the disaggregated architecture, a new breed of database systems termed storage-disaggregated databases has recently been developed, such as Amazon Aurora, Microsoft Socrates, Google AlloyDB, Alibaba PolarDB, and Huawei Taurus. However, little is known about the effectiveness of the design principles in these databases since they are typically developed by industry giants, and only the overall performance results are presented without detailing the impact of individual design principles. As a result, many critical research questions remain unclear, such as the performance impact of storage-disaggregation, the log-as-the-database design, shared-storage, and various log-replay methods. In this paper, we investigate the performance implications of the design principles that are widely adopted in storage-disaggregated databases for the first time. As these databases were usually not open-sourced, we have made a significant effort to implement a storage-disaggregated database prototype based on PostgreSQL v13.0. By fully controlling and instrumenting the codebase, we are able to selectively enable and disable individual optimizations and techniques to evaluate their impact on performance in various scenarios. Furthermore, we open-source our storage-disaggregated database prototype for use by the broader database research community, fostering collaboration and innovation in this field. 

Cloud functions, exemplified by AWS Lambda and Azure Functions, are emerging as a new computing paradigm in the cloud. They provide elastic, serverless, and low-cost cloud computing, making them highly suitable for bursty and sparse workloads, which are quite common in practice. Thus, there is a new trend in designing data systems that leverage cloud functions. In this paper, we focus on vector databases, which have recently gained significant attention partly due to large language models. In particular, we investigate how to use cloud functions to build high-performance and cost-efficient vector databases. This presents significant challenges in terms of how to perform sharding, how to reduce communication overhead, and how to minimize cold-start times. In this paper, we introduce Vexless, the first vector database system optimized for cloud functions. We present three optimizations to address the challenges. To perform sharding, we propose a global coordinator (orchestrator) that assigns workloads to Cloud function instances based on their available hardware resources. To overcome communication overhead, we propose the use of stateful cloud functions, eliminating the need for costly communications during synchronization. To minimize cold-start overhead, we introduce a workload-aware Cloud function lifetime management strategy. Vexless has been implemented using Azure Functions. Experimental results demonstrate that Vexless can significantly reduce costs, especially on bursty and sparse workloads, compared to cloud VM instances, while achieving similar or higher query performance and accuracy. 

Optimizing LSM-based Key-Value Stores (LSM-KVS) for disaggregated storage is essential to achieve better resource utilization, performance, and flexibility. Most of the existing studies focus on offloading the compaction to the storage nodes to mitigate the performance penalties caused by heavy network traffic between computing and storage. However, several critical issues are not addressed including the strong dependency between offloaded compaction and LSM-KVS, resource load-balancing, compaction scheduling, and complex transient errors. To address the aforementioned issues and limitations, in this paper, we propose CaaS-LSM, a novel disaggregated LSM-KVS with a new idea of Compaction-as-a-Service. CaaS-LSM brings three key contributions. First, CaaS-LSM decouples the compaction from LSM-KVS and achieves stateless execution to ensure high flexibility and avoid coordination overhead with LSM-KVS. Second, CaaS-LSM introduces a performance- and resource-optimized control plane to guarantee better performance and resource utilization via an adaptive run-time scheduling and management strategy. Third, CaaS-LSM addresses different levels of transient and execution errors via sophisticated error-handling logic. We implement the prototype of CaaS-LSM based on RocksDB and evaluate it with different LSM-based distributed databases (Kvrocks and Nebula). In the storage disaggregated setup, CaaS-LSM achieves up to 8X throughput improvement and reduces the P99 latency up to 98% compared with the conventional LSM-KVS, and up to 61% of improvement compared with state-of-the-art LSM-KVS optimized for disaggregated storage. 

Vector databases have recently gained significant attention due to the emergence of large language models that produce vector embeddings for text. Existing vector databases can be broadly categorized into two types: specialized and generalized. Specialized vector databases are explicitly designed and optimized for managing vector data, while generalized ones support vector data management within a general purpose database. While specialized vector databases are interesting, there is a substantial customer base interested in generalized vector databases for various reasons, e.g., a reluctance to move data out of relational databases to reduce data silos and costs, the desire to use SQL, and the need for more sophisticated query processing of vector and non-vector data. However, generalized vector databases face two main challenges: performance and interoperability of vector search with SQL, such as combining vector search with filters, joins, or even fulltext search. In this paper, we present SingleStore-V, a full-fledged generalized vector database integrated into SingleStore, a modern distributed relational database optimized for both OLAP and OLTP workloads. SingleStore-V achieves high performance and interoperability via a suite of optimizations. Experiments on standard vector benchmarks show that SingleStore-V performs comparably to Milvus, a highly-optimized specialized vector database, and significantly outperforms pgvector, a popular generalized vector database in PostgreSQL. We believe this paper will shed light on integrating vector search into relational databases in general, as many design concepts and optimizations apply to other databases. 

Abstract Adding synthetic nucleotides to DNA increases the linear information density of DNA molecules. Here we report that it also can increase the diversity of their three-dimensional folds. Specifically, an additional nucleotide (dZ, with a 5-nitro-6-aminopyridone nucleobase), placed at twelve sites in a 23-nucleotides-long DNA strand, creates a fairly stable unimolecular structure (that is, the folded Z-motif, or fZ-motif) that melts at 66.5 °C at pH 8.5. Spectroscopic, gel and two-dimensional NMR analyses show that the folded Z-motif is held together by six reverse skinny dZ⁻:dZ base pairs, analogous to the crystal structure of the free heterocycle. Fluorescence tagging shows that the dZ⁻:dZ pairs join parallel strands in a four-stranded compact down–up–down–up fold. These have two possible structures: one with intercalated dZ⁻:dZ base pairs, the second without intercalation. The intercalated structure would resemble the i-motif formed by dC:dC⁺-reversed pairing at pH ≤ 6.5. This fZ-motif may therefore help DNA form compact structures needed for binding and catalysis. 

Submitted for Journal Publication Also available as arXiv preprint arXiv:2403.06456, 2024 

While both the database and high-performance computing (HPC) communities utilize lossless compression methods to minimize floating-point data size, a disconnect persists between them. Each community designs and assesses methods in a domain-specific manner, making it unclear if HPC compression techniques can benefit database applications or vice versa. With the HPC community increasingly leaning towards in-situ analysis and visualization, more floating-point data from scientific simulations are being stored in databases like Key-Value Stores and queried using in-memory retrieval paradigms. This trend underscores the urgent need for a collective study of these compression methods' strengths and limitations, not only based on their performance in compressing data from various domains but also on their runtime characteristics. Our study extensively evaluates the performance of eight CPU-based and five GPU-based compression methods developed by both communities, using 33 real-world datasets assembled in the Floating-point Compressor Benchmark (FCBench). Additionally, we utilize the roofline model to profile their runtime bottlenecks. Our goal is to offer insights into these compression methods that could assist researchers in selecting existing methods or developing new ones for integrated database and HPC applications.