Genome sequence analysis is fundamental to medical breakthroughs such as developing vaccines, enabling genome editing, and facilitating personalized medicine. The exponentially expanding sequencing datasets and complexity of sequencing algorithms necessitate performance enhancements. While the performance of software solutions is constrained by their underlying hardware platforms, the utility of fixed-function accelerators is restricted to only certain sequencing algorithms.This paper presents QUETZAL, the first general-purpose vector acceleration framework designed for high efficiency and broad applicability across a diverse set of genomics algorithms. While a commercial CPU’s vector datapath is a promising candidate to exploit the data-level parallelism in genomics algorithms, our analysis finds that its performance is often limited due to long-latency scatter/gather memory instructions. QUETZAL introduces a hardware-software co-design comprising an accelerator microarchitecture closely integrated with the CPU’s vector datapath, alongside novel vector instructions to fully capitalize on the proposed hardware. QUETZAL integrates a set of scratchpad-style buffers meticulously designed to minimize latency associated with scatter/gather instructions during the retrieval of input genome sequences data. QUETZAL supports both short and long reads, and different types of sequencing data formats. A combination of hardware and software techniques enables QUETZAL to reduce the latency of memory instructions, perform complex computation using a single instruction, and transform data representations at runtime, resulting in overall efficiency gain. QUETZAL significantly accelerates a vectorized CPU baseline on modern genome sequence analysis algorithms by 5.7×, while incurring a small area overhead of 1.4% post place-and-route at the 7nm technology node compared to an HPC ARM CPU.

Database Management Systems (DBMS) have be-come an essential tool for industry and research and are often a significant component of data centers. There have been many efforts to accelerate DBMS application performance. One of the most explored techniques is the use of vector processing. Unfortunately, conventional vector architectures have not been able to exploit the full potential of DBMS acceleration.In this paper, we present VAQUERO, our Scratchpad-based Vector Accelerator for QUEry pROcessing. VAQUERO improves the efficiency of vector architectures for DBMS operations such as data aggregation and hash joins featuring lookup tables. Lookup tables are significant contributors to the performance bottlenecks in DBMS processing suffering from insufficient ISA support in the form of scatter-gather instructions. VAQUERO introduces a novel Advanced Scratchpad Memory specifically designed with two mapping modes — direct- and associative-mode. These map-ping modes enable VAQUERO to accelerate real-world databases with workload sizes that significantly exceed the scratchpad memory capacity. Additionally, the associative-mode allows to use VAQUERO with DBMS operators that use hashed keys, e.g. hash-join and hash-aggregate. VAQUERO has been designed considering general DBMS algorithm requirements instead of being based on a particular database organization. For this reason, VAQUERO is capable to accelerate DBMS operators for both row- and column-oriented databases.In this paper, we evaluate the efficiency of VAQUERO using two highly optimized popular open-source DBMS, namely the row-based PostgreSQL and column-based MonetDB. We imple-mented VAQUERO at the RTL level and prototype it, by performing Place&Route, at the 7nm technology node. VAQUERO incurs a modest 0.15% area overhead compared with an Intel Ice Lake processor. Our evaluation shows that VAQUERO significantly outperforms PostgreSQL and MonetDB by 2.09× and 3.32× respectively, when processing operators and queries from the TPC-H benchmark.

Sparse matrix operations are critical kernels in multiple application domains such as High Performance Computing, artificial intelligence and big data. Vector processing is widely used to improve performance on mathematical kernels with dense matrices. Unfortunately, existing vector architectures do not cope well with sparse matrix computations, achieving much lower performance in comparison with their dense counterparts.To overcome this limitation, we present the Vector Indexed Architecture (VIA), a novel hardware vector architecture that accelerates applications with irregular memory access patterns such as sparse matrix computations. There are two main bottlenecks when computing with sparse matrices: irregular memory accesses and index matching. VIA addresses these two bottlenecks with a smart scratchpad that is tightly coupled to the Vector Functional Units within the core.Thanks to this structure, VIA improves locality for sparse-dense computations and improves the index matching search process for sparse computations. As a result, VIA achieves significant performance speedup over highly optimized state-of-the-art C++ algebra libraries. On average, VIA outperforms sparse matrix vector multiplication, sparse matrix addition and sparse matrix matrix multiplication kernels by 4.22 ×, 6.14 × and 6.00 ×, respectively, when evaluated over a thousand sparse matrices that arise in real applications. In addition, we prove the generality of VIA by showing that it can accelerate histogram and stencil applications by 4.5 × and 3.5 ×, respectively.