In FPGAs, high communication latency in multi-die chips has driven the integration of hardened networks-on-chip (NoCs) in commercial devices. However, for programming FPGAs with high-level synthesis (HLS), existing tools only provide low-level cumbersome abstractions, and only work for offloading memory accesses. Furthermore, these abstractions remain inaccessible to programmers due to their reliance on placement knowledge. While automatically leveraging the NoC without manual intervention is ideal, it poses several challenges: 1. Managing the trade-off in resource utilization between the hard NoC and the Programmable Logic (PL). 2. Allocating limited hard NoC resources between different communication in the designs. 3. Aligning hard NoC and PL placement even though the actual PL placement cannot be determined beforehand. We address these challenges by developing NoH, the first HLS flow that automates hard NoC offloading. First, we develop a formal NoC-aware placement algorithm that leverages integer linear programming (ILP) and considers the first two challenges for offloading external memory accesses and latency-insensitive communication between modules. Then, we arrange the ports synergistically with PL modules via a port-affinity model that approximates the PL placement. Finally, NoH is integrated into an end-to-end HLS flow and evaluated on 4 workloads with diverse communication patterns. NoH gains 20% FPGA frequency over AMD tools by leveraging the hard NoC. Compared to AutoBridge [1], a recent high-level physical synthesis technique that optimizes frequency but does not consider the hard NoC, NoH never fails place-and-route by offloading inter-die crossings (AutoBridge fails in 31% of workload configurations tested) and is faster (6%) for the rest.

Implementing HLS accelerators on large-scale multi-die FPGAs presents significant challenges. To address this, researchers have proposed High-Level Physical Synthesis (HLPS), which co-optimizes high-level synthesis and physical design to improve achievable frequency. However, existing HLPS techniques suffer from unstable and inconsistent quality of results (QoRs), largely due to the vast number of parameters that need to be selected by the user in an ad-hoc way. As a result, achieving satisfactory solutions still requires substantial manual effort and expertise in low-level circuit design.We propose a robust and practical design space exploration (DSE) framework that enhances the reliability and QoRs of HLPS by automating the iterative parameter tuning process. Informed by metrics extracted from physical implementation outcomes, the framework applies tailored heuristics to refine HLPS parameters, enabling consistent and automated timing closure. In evaluations with large-scale, real-world designs implemented on representative multi-die devices, our framework achieves an average frequency of 311.06 MHz, reaching 2.42× the frequency of the AMD Vitis/Vivado toolchain (128.48 MHz) and 1.67× that of the leading academic solutions (186.21 MHz).

The increasing complexity of large-scale FPGA accelerators poses significant challenges in achieving high performance while maintaining design productivity. High-level synthesis (HLS) has been adopted as a solution, but the mismatch between the high-level description and the physical layout often leads to suboptimal operating frequency. Although existing proposals for high-level physical synthesis, which use coarse-grained design partitioning, floorplanning, and pipelining to improve frequency, have gained traction, they lack a framework enabling (1) pipelining of real-world designs at arbitrary hierarchical levels, (2) integration of HLS blocks, vendor IPs, and handcrafted RTL designs, (3) portability to emerging new target FPGA devices, and (4) extensibility for the easy implementation of new design optimization tools.

In recent years, the adoption of FPGAs in datacenters has increased, with a growing number of users choosing High-Level Synthesis (HLS) as their preferred programming method. While HLS simplifies FPGA programming, one notable challenge arises when scaling up designs for modern datacenter FPGAs that comprise multiple dies. The extra delays introduced due to die crossings and routing congestion can significantly degrade the frequency of large designs on these FPGA boards. Due to the gap between HLS design and physical design, it is challenging for HLS programmers to analyze and identify the root causes, and fix their HLS design to achieve better timing closure. Recent efforts have aimed to address these issues by employing coarse-grained floorplanning and pipelining strategies on task-parallel HLS designs where multiple tasks run concurrently and communicate through FIFO stream channels. However, many applications are not streaming friendly and many existing accelerator designs heavily rely on buffer channel based communication between tasks. In this work, we take a step further to support a task-parallel programming model where tasks can communicate via both FIFO stream channels and buffer channels. To achieve this goal, we design and implement the PASTA framework, which takes a large task-parallel HLS design as input and automatically generates a high-frequency FPGA accelerator via HLS and physical design co-optimization. Our framework introduces a latency-insensitive buffer channel design, which supports memory partitioning and ping-pong buffering while remaining compatible with vendor HLS tools. On the frontend, we provide an easy-to-use programming model for utilizing the proposed buffer channel; while on the backend, we implement efficient placement and pipelining strategies for the proposed buffer channel. To validate the effectiveness of our framework, we test it on four widely used Rodinia HLS benchmarks and two real-world accelerator designs and show an average frequency improvement of 25%, with peak improvements of up to 89% on AMD/Xilinx Alveo U280 boards compared to Vitis HLS baselines.

In recent years, there has been increasing adoption of FPGAs in datacenters as hardware accelerators, where a large population of end users are software developers. While high-level synthesis (HLS) facilitates software programming, it is still challenging to scale large accelerator designs on modern datacenter FPGAs that often consist of multiple dies and memory banks. More specifically, routing congestion and extra delays on these multi-die FPGAs often cause timing closure issues and severe frequency degradation at the physical design level, which are difficult to digest and optimize for high-level programmers using HLS. One promising approach to mitigate such issues is to develop a high-level task-parallel programming model with HLS and physical design co-optimization. Unfortunately, existing studies only support a programming model where tasks communicate with each other via FIFOs, while many applications are not streaming friendly and many existing accelerator designs heavily rely on buffer based communication between tasks. In this paper, we take a step further to support a task-parallel programming model where tasks can communicate via both FIFOs and buffers. To achieve this goal, we design and implement the PASTA framework, which takes a large task-parallel HLS design as input and automatically generates a high-frequency FPGA accelerator via HLS and physical design co-optimization. First, we design a decoupled latency-insensitive buffer channel that supports memory partitioning and ping-pong buffering, which is compatible with the vendor Vitis HLS compiler. In the frontend, we develop an easy-to-use programming interface to allow end users to use our buffer channel in their applications. In the backend, we provide automatic coarse-grained floorplanning and pipelining for designs that use our proposed buffer channel. We test PASTA on a set of task-parallel HLS designs that use buffers for task communication and show an average of 36% (up to 54%) frequency improvement for large design configurations.

The continued growth in the processing power of FPGAs coupled with high bandwidth memories (HBM), makes systems like the Xilinx U280 credible platforms for linear solvers which often dominate the run time of scientific and engineering applications. In this paper, we present Callipepla, an accelerator for a preconditioned conjugate gradient linear solver (CG). FPGA acceleration of CG faces three challenges: (1) how to support an arbitrary problem and terminate acceleration processing on the fly, (2) how to coordinate long-vector data flow among processing modules, and (3) how to save off-chip memory bandwidth and maintain double (FP64) precision accuracy. To tackle the three challenges, we present (1) a stream-centric instruction set for efficient streaming processing and control, (2) vector streaming reuse (VSR) and decentralized vector flow scheduling to coordinate vector data flow among modules and further reduce off-chip memory access latency with a double memory channel design, and (3) a mixed precision scheme to save bandwidth yet still achieve effective double precision quality solutions. To the best of our knowledge, this is the first work to introduce the concept of VSR for data reusing between on-chip modules to reduce unnecessary off-chip accesses and enable modules working in parallel for FPGA accelerators. We prototype the accelerator on a Xilinx U280 HBM FPGA. Our evaluation shows that compared to the Xilinx HPC product, the XcgSolver, Callipepla achieves a speedup of 3.94x, 3.36x higher throughput, and 2.94x better energy efficiency. Compared to an NVIDIA A100 GPU which has 4x the memory bandwidth of Callipepla, we still achieve 77% of its throughput with 3.34x higher energy efficiency. The code is available at https://github.com/UCLA-VAST/Callipepla.

With reduced data reuse and parallelism, recent convolutional neural networks (CNNs) create new challenges for FPGA acceleration. Systolic arrays (SAs) are efficient, scalable architectures for convolutional layers, but without proper optimizations, their efficiency drops dramatically for reasons: (1) the different dimensions within same-type layers, (2) the different convolution layers especially transposed and dilated convolutions, and (3) CNN’s complex dataflow graph. Furthermore, significant overheads arise when integrating FPGAs into machine learning frameworks. Therefore, we present a flexible, composable architecture called FlexCNN, which delivers high computation efficiency by employing dynamic tiling, layer fusion, and data layout optimizations. Additionally, we implement a novel versatile SA to process normal, transposed, and dilated convolutions efficiently. FlexCNN also uses a fully pipelined software-hardware integration that alleviates the software overheads. Moreover, with an automated compilation flow, FlexCNN takes a CNN in the ONNX 1 representation, performs a design space exploration, and generates an FPGA accelerator. The framework is tested using three complex CNNs: OpenPose, U-Net, and E-Net. The architecture optimizations achieve 2.3× performance improvement. Compared to a standard SA, the versatile SA achieves close-to-ideal speedups, with up to 5.98× and 13.42× for transposed and dilated convolutions, with a 6% average area overhead. The pipelined integration leads to a 5× speedup for OpenPose.

In this article, we propose TAPA, an end-to-end framework that compiles a C++ task-parallel dataflow program into a high-frequency FPGA accelerator. Compared to existing solutions, TAPA has two major advantages. First, TAPA provides a set of convenient APIs that allows users to easily express flexible and complex inter-task communication structures. Second, TAPA adopts a coarse-grained floorplanning step during HLS compilation for accurate pipelining of potential critical paths. In addition, TAPA implements several optimization techniques specifically tailored for modern HBM-based FPGAs. In our experiments with a total of 43 designs, we improve the average frequency from 147 MHz to 297 MHz (a 102% improvement) with no loss of throughput and a negligible change in resource utilization. Notably, in 16 experiments, we make the originally unroutable designs achieve 274 MHz, on average. The framework is available at https://github.com/UCLA-VAST/tapa and the core floorplan module is available at https://github.com/UCLA-VAST/AutoBridge

Field-programmable gate arrays (FPGAs) require a much longer compilation cycle than conventional computing platforms such as CPUs. In this article, we shorten the overall compilation time by co-optimizing the HLS compilation (C-to-RTL) and the back-end physical implementation (RTL-to-bitstream). We propose a split compilation approach based on the pipelining flexibility at the HLS level, which allows us to partition designs for parallel placement and routing. We outline a number of technical challenges and address them by breaking the conventional boundaries between different stages of the traditional FPGA tool flow and reorganizing them to achieve a fast end-to-end compilation. Our research produces RapidStream, a parallelized and physical-integrated compilation framework that takes in a latency-insensitive program in C/C++ and generates a fully placed and routed implementation. We present two approaches. The first approach (RapidStream 1.0) resolves inter-partition routing conflicts at the end when separate partitions are stitched together. When tested on the Xilinx U250 FPGA with a set of realistic HLS designs, RapidStream achieves a 5 to 7× reduction in compile time and up to 1.3× increase in frequency when compared with a commercial off-the-shelf toolchain. In addition, we provide preliminary results using a customized open-source router to reduce the compile time up to an order of magnitude in cases with lower performance requirements. The second approach (RapidStream 2.0) prevents routing conflicts using virtual pins. Testing on Xilinx U280 FPGA, we observed 5 to 7× compile time reduction and 1.3× frequency increase.

The k-nearest neighbors (KNN) algorithm is an essential algorithm in many applications, such as similarity search, image classification, and database query. With the rapid growth in the dataset size and the feature dimension of each data point, processing KNN becomes more compute and memory hungry. Most prior studies focus on accelerating the computation of KNN using the abundant parallel resource on FPGAs. However, they often overlook the memory access optimizations on FPGA platforms and only achieve a marginal speedup over a multi-thread CPU implementation for large datasets. In this article, we design and implement CHIP-KNN: an HLS-based, configurable, and high-performance KNN accelerator. CHIP-KNN optimizes the off-chip memory access on modern HBM-based FPGAs such as the AMD/Xilinx Alveo U280 FPGA board. CHIP-KNN is configurable for all essential parameters used in the algorithm, including the size of the search dataset, the feature dimension and data type representation of each data point, the distance metric, and the number of nearest neighbors - K. In terms of design architecture, we explore and discuss the tradeoffs between two design versions: CHIP-KNNv1 (Ping-Pong buffer based) and CHIP-KNNv2 (streaming-based). Moreover, we investigate the routing congestion issue in our accelerator design, implement hierarchical structures to shorten critical paths, and integrate an open-source floorplanning optimization tool called TAPA/AutoBridge to eliminate the place-and-route issues. To explore the design space and balance the computation and memory access performance, we also build an analytical performance model. Given a user configuration of the KNN parameters, our tool can automatically generate TAPA HLS C code for the optimal accelerator design and the corresponding host code, on the HBM-based FPGA platform. Our experimental results on the Alveo U280 show that, compared to a 48-thread CPU implementation, CHIP-KNNv2 achieves a geomean performance speedup of 15×, with a maximum speedup of 45×. Additionally, we show that CHIP-KNNv2 achieves up to 2.1× performance speedup over CHIP-KNNv1 while increasing configurability. Compared with the state-of-the-art Facebook AI Similarity Search (FAISS) [ 23 ] GPU implementation running on a Nvidia Tesla V100 GPU, CHIP-KNNv2 achieves an average latency reduction of 30.6× while requiring 34.3% of GPU power consumption.

Stencil computation is one of the fundamental computing patterns in many application domains such as scientific computing and image processing. While there are promising studies that accelerate stencils on FPGAs, there lacks an automated acceleration framework to systematically explore both spatial and temporal parallelisms for iterative stencils that could be either computation-bound or memory-bound. In this article, we present SASA, a scalable and automatic stencil acceleration framework on modern HBM-based FPGAs. SASA takes the high-level stencil DSL and FPGA platform as inputs, automatically exploits the best spatial and temporal parallelism configuration based on our accurate analytical model, and generates the optimized FPGA design with the best parallelism configuration in TAPA high-level synthesis C++ as well as its corresponding host code. Compared to state-of-the-art automatic stencil acceleration framework SODA that only exploits temporal parallelism, SASA achieves an average speedup of 3.41× and up to 15.73× speedup on the HBM-based Xilinx Alveo U280 FPGA board for a wide range of stencil kernels.

Sparse matrix-vector multiplication (SpMV) multiplies a sparse matrix with a dense vector. SpMV plays a crucial role in many applications, from graph analytics to deep learning. The random memory accesses of the sparse matrix make accelerator design challenging. However, high bandwidth memory (HBM) based FPGAs are a good fit for designing accelerators for SpMV. In this paper, we present Serpens, an HBM based accelerator for general-purpose SpMV, which features memory-centric processing engines and index coalescing to support the efficient processing of arbitrary SpMVs. From the evaluation of twelve large-size matrices, Serpens is 1.91x and 1.76x better in terms of geomean throughput than the latest accelerators GraphLiLy and Sextans, respectively. We also evaluate 2,519 SuiteSparse matrices, and Serpens achieves 2.10x higher throughput than a K80 GPU. For the energy/bandwidth efficiency, Serpens is 1.71x/1.99x, 1.90x/2.69x, and 6.25x/4.06x better compared with GraphLily, Sextans, and K80, respectively. After scaling up to 24 HBM channels, Serpens achieves up to 60.55 GFLOP/s (30,204 MTEPS) and up to 3.79x over GraphLily. The code is available at https://github.com/UCLA-VAST/Serpens.

The emergence of high-bandwidth memory (HBM) brings new opportunities to boost the performance of sorting acceleration on FPGAs, which was conventionally bounded by the available off-chip memory bandwidth. However, it is nontrivial for designers to fully utilize this immense bandwidth. First, the existing sorter designs cannot be directly scaled at the increasing rate of available off-chip bandwidth, as the required on-chip resource usage grows at a much faster rate and would bound the sorting performance in turn. Second, designers need an in-depth understanding of HBM’s characteristics to effectively utilize the HBM bandwidth. To tackle these challenges, we present TopSort, a novel two-phase sorting solution optimized for HBMbased FPGAs. TopSort can sort up to 4 GB data using all 32 HBM channels, with an overall sorting performance of 15.6 GB/s. TopSort is 6.7× and 2.2× faster than state-of-the-art CPU and FPGA sorters.

The single-source shortest path (SSSP) problem is one of the most important and well-studied graph problems widely used in many application domains, such as road navigation, neural image reconstruction, and social network analysis. Although we have known various SSSP algorithms for decades, implementing one for large-scale power-law graphs efficiently is still highly challenging today, because - a work-efficient SSSP algorithm requires priority-order traversal of graph data, - the priority queue needs to be scalable both in throughput and capacity, and - priority-order traversal requires extensive random memory accesses on graph data. In this paper, we present SPLAG to accelerate SSSP for power-law graphs on FPGAs. SPLAG uses a coarse-grained priority queue (CGPQ) to enable high-throughput priority-order graph traversal with a large frontier. To mitigate the high-volume random accesses, SPLAG employs a customized vertex cache (CVC) to reduce off-chip memory access and improve the throughput to read and update vertex data. Experimental results on various synthetic and real-world datasets show up to a 4.9× speedup over state-of-the-art SSSP accelerators, a 2.6× speedup over 32-thread CPU running at 4.4 GHz, and a 0.9× speedup over an A100 GPU that has 4.1× power budget and 3.4× HBM bandwidth. Such a high performance would place SPLAG in the 14th position of the Graph 500 benchmark for data intensive applications (the highest using a single FPGA) with only a 45 W power budget. SPLAG is written in high-level synthesis C++ and is fully parameterized, which means it can be easily ported to various different FPGAs with different configurations. SPLAG is open-source at https://github.com/UCLA-VAST/splag.

FPGAs require a much longer compilation cycle than conventional computing platforms like CPUs. In this paper, we shorten the overall compilation time by co-optimizing the HLS compilation (C-to-RTL) and the back-end physical implementation (RTL-to-bitstream). We propose a split compilation approach based on the pipelining flexibility at the HLS level, which allows us to partition designs for parallel placement and routing then stitch the separate partitions together. We outline a number of technical challenges and address them by breaking the conventional boundaries between different stages of the traditional FPGA tool flow and reorganizing them to achieve a fast end-to-end compilation. Our research produces RapidStream, a parallelized and physical-integrated compilation framework that takes in an HLS dataflow program in C/C++ and generates a fully placed and routed implementation. When tested on the Xilinx U250 FPGA with a set of realistic HLS designs, RapidStream achieves a 5-7X reduction in compile time and up to 1.3X increase in frequency when compared to a commercial-off-the-shelf toolchain. In addition, we provide preliminary results using a customized open-source router to reduce the compile time up to an order of magnitude in the cases with lower performance requirements. The tool is open-sourced at github.com/Licheng-Guo/RapidStream.

FPGAs have been proven to be powerful computational accelerators across many types of workloads. The mainstream programming approach is high level synthesis (HLS), which maps high-level languages (e.g. C+ #pragmas) to hardware. Unfortunately, HLS leaves a significant programmability gap in terms of reconfigurability, customization and versatility: Although HLS compilation is fast, the downstream physical design takes hours to days; FPGA reconfiguration time limits the time-multiplexing ability of hardware, and tools do not reason about cross-workload flexibility. Overlay architectures mitigate the above by mapping a programmable design (e.g. CPU, GPU, etc.) on top of FPGAs. However, the abstraction gap between overlay and FPGA leads to low efficiency/utilization. Our essential idea is to develop a hardware generation framework targeting a highly-customizable overlay, so that the abstraction gap can be lowered by tuning the design instance to applications of interest. We leverage and extend prior work on customizable spatial architectures, SoC generation, accelerator compilers, and design space explorers to create an end-to-end FPGA acceleration system. Our novel techniques address inefficient networks between on-chip memories and processing elements, as well as improving DSE by reducing the amount of recompilation required. Our framework, OverGen, is highly competitive with fixed-function HLS-based designs, even though the generated designs are programmable with fast reconfiguration. We compared to a state-of-the-art DSE-based HLS framework, AutoDSE. Without kernel-tuning for AutoDSE, OverGen gets 1.2$\times$ geomean performance, and even with manual kernel-tuning for the baseline, OverGen still gets 0.55$\times$ geomean performance--all while providing runtime flexibility across workloads.

C/C++/OpenCL-based high-level synthesis (HLS) becomes more and more popular for field-programmable gate array (FPGA) accelerators in many application domains in recent years, thanks to its competitive quality of results (QoR) and short development cycles compared with the traditional register-transfer level design approach. Yet, limited by the sequential C semantics, it remains challenging to adopt the same highly productive high-level programming approach in many other application domains, where coarse-grained tasks run in parallel and communicate with each other at a fine-grained level. While current HLS tools do support task-parallel programs, the productivity is greatly limited ① in the code development cycle due to the poor programmability, ② in the correctness verification cycle due to restricted software simulation, and ③ in the QoR tuning cycle due to slow code generation. Such limited productivity often defeats the purpose of HLS and hinder programmers from adopting HLS for task-parallel FPGA accelerators. In this paper, we extend the HLS C++ language and present a fully automated framework with programmer-friendly interfaces, unconstrained software simulation, and fast hierarchical code generation to overcome these limitations and demonstrate how task-parallel programs can be productively supported in HLS. Experimental results based on a wide range of real-world task-parallel programs show that, on average, the lines of kernel and host code are reduced by 22% and 51%, respectively, which considerably improves the programmability. The correctness verification and the iterative QoR tuning cycles are both greatly shortened by 3.2× and 6.8×, respectively. Our work is open-source at https://github.com/UCLA-VAST/tapa/.

Large-scale sorting is always an important yet demanding task for data center applications. In addition to powerful processing capability, high-performance sorting system requires efficient utilization of the available bandwidth of various levels in the memory hierarchy. Nowadays, with the explosive data size, the frequent data transfers between the host and the storage device are becoming increasingly a performance bottleneck. Fortunately, the emergence of near-storage computing devices gives us the opportunity to accelerate large-scale sorting by avoiding the back and forth data transfer. Near-storage sorting is promising for extra performance improvement and power reduction. However, it is still an open question of how to achieve the optimal sorting performance on the existing near-storage computing device.In this work, we first perform an in-depth analysis of the sorting performance on the newly released Samsung SmartSSD platform. Contrary to the previous belief, our analysis shows that the end-to-end sorting performance is bound by not only the bandwidth of the flash, but also the main memory bandwidth, the configuration of the sorting kernel and the intermediate sorting status. Based on our modeling, we propose FANS, an FPGA accelerated near-storage sorting system which selects the optimized design configuration and achieves the theoretically maximum end-to-end performance when using a single Samsung SmartSSD device. The experiments demonstrate more than 3× performance speedup over the state-of-art FPGA-accelerated flash storage.

While systolic array architectures have the potential to deliver tremendous performance, it is notoriously challenging to customize an efficient systolic array processor for a target application. Designing systolic arrays requires knowledge for both high-level characteristics of the application and low-level hardware details, thus making it a demanding and inefficient process. To relieve users from the manual iterative trial-and-error process, we present AutoSA, an end-to-end compilation framework for generating systolic arrays on FPGA. AutoSA is based on the polyhedral framework, and further incorporates a set of optimizations on different dimensions to boost performance. An efficient and comprehensive design space exploration is performed to search for high-performance designs. We have demonstrated AutoSA on a wide range of applications, on which AutoSA achieves high performance within a short amount of time. As an example, for matrix multiplication, AutoSA achieves 934 GFLOPs, 3.41 TOPs, and 6.95 TOPs in floating point, 16-bit and 8-bit integer data types on Xilinx Alveo U250.

C/C++/OpenCL-based high-level synthesis (HLS) becomes more and more popular for field-programmable gate array (FPGA) accelerators in many application domains in recent years, thanks to its competitive quality of result (QoR) and short development cycle compared with the traditional register-transfer level (RTL) design approach. Yet, limited by the sequential C semantics, it remains challenging to adopt the same highly productive high-level programming approach in many other application domains, where coarse-grained tasks run in parallel and communicate with each other at a fine-grained level. While current HLS tools support task-parallel programs, the productivity is greatly limited in the code development, correctness verification, and QoR tuning cycles, due to the poor programmability, restricted software simulation, and slow code generation, respectively. Such limited productivity often defeats the purpose of HLS and hinder programmers from adopting HLS for task-parallel FPGA accelerators.

Despite an increasing adoption of high-level synthesis (HLS) for its design productivity advantages, there remains a significant gap in the achievable frequency between an HLS design and a handcrafted RTL one. A key factor that limits the timing quality of the HLS outputs is the difficulty in accurately estimating the interconnect delay at the HLS level. This problem becomes even worse when large HLS designs are implemented on the latest multi-die FPGAs. To tackle this challenge, we propose AutoBridge, an automated framework that couples a coarse-grained floorplanning step with pipelining during HLS compilation. First, our approach provides HLS with a view on the global physical layout of the design, allowing HLS to more easily identify and pipeline the long wires, especially those crossing the die boundaries. Second, by exploiting the flexibility of HLS pipelining, the floorplanner is able to distribute the design logic across multiple dies on the FPGA device without degrading clock frequency. This prevents the placer from aggressively packing the logic on a single die which often results in local routing congestion that eventually degrades timing. Since pipelining may introduce additional latency, we further present analysis and algorithms to ensure the added latency will not compromise the overall throughput. AutoBridge can be integrated into the existing CAD toolflow for Xilinx FPGAs. In our experiments with a total of 43 design configurations, we improve the average frequency from 147 MHz to 297 MHz (a 102% improvement) with no loss of throughput and a negligible change in resource utilization. Notably, in 16 experiments we make the originally unroutable designs achieve 274 MHz on average. The tool is available at https://github.com/Licheng-Guo/AutoBridge.

Designs generated by high-level synthesis (HLS) tools typically achieve a lower frequency compared to manual RTL designs. In this work, we study the timing issues in a diverse set of realistic and complex FPGA HLS designs. (1) We observe that in almost all cases the frequency degradation is caused by the broadcast structures generated by the HLS compiler. (2) We classify three major types of broadcasts in HLS-generated designs, including high-fanout data signals, pipeline flow control signals and synchronization signals for concurrent modules. (3) We reveal a number of limitations of the current HLS tools that result in those broadcast-related timing issues. (4) We propose a set of effective yet easy-to-implement approaches, including broadcast-aware scheduling, synchronization pruning, and skid-buffer-based flow control. Our experimental results show that our methods can improve the maximum frequency of a set of nine representative HLS benchmarks by 53% on average. In some cases, the frequency gain is more than 100 MHz.

Designs generated by high-level synthesis (HLS) tools typically achieve a lower frequency compared to manual RTL designs. We study the timing issues in a diverse set of nine realistic HLS designs and observe that in most cases the frequency degradation is related to the signal broadcast structures. In this work, we classify the common broadcast types in HLS designs, including the data signal broadcast and two types of control signal broadcast: the pipeline control broadcast and the synchronization signal broadcast. We further identify several common limitations of the current HLS tools, which lead to improper handling of the broadcasts. First, the HLS delay model does not consider the extra delay caused by broadcasts, thus the scheduling results will be suboptimal. To solve the issue, we implement a set of comprehensive synthetic designs and benchmark the extra delay to calibrate the HLS delay model. Second, the HLS adopts back-pressure signals for pipeline control, which will lead to large broadcasts. Instead, we propose to use the skid-buffer-based pipeline control, where the back-pressure signal is removed, and an extra skid-buffer is used for flow-control. We use dynamic programming to minimize the area of the extra FIFO. Third, there exist redundant synchronizations among concurrent modules that may lead to huge broadcasts. We propose methods to identify and prune unnecessary synchronization signals. Our solutions boost the frequency of nine real-world HLS benchmarks by 53% on average and with marginal area and latency overhead. In some cases, the gain is more than 100 MHz.

In genome sequencing, it is a crucial but time-consuming task to detect potential overlaps between any pair of the input reads, especially those that are ultra-long. The state-of-the-art overlapping tool Minimap2 outperforms other popular tools in speed and accuracy. It has a single computing hot-spot, chaining, that takes 70% of the time and needs to be accelerated. There are several crucial issues for hardware acceleration because of the nature of chaining. First, the original computation pattern is poorly parallelizable and a direct implementation will result in low utilization of parallel processing units. We propose a method to reorder the operation sequence that transforms the algorithm into a hardware-friendly form. Second, the large but variable sizes of input data make it hard to leverage task-level parallelism. Therefore, we customize a fine-grained task dispatching scheme which could keep parallel PEs busy while satisfying the on-chip memory restriction. Based on these optimizations, we map the algorithm to a fully pipelined streaming architecture on FPGA using HLS, which achieves significant performance improvement. The principles of our acceleration design apply to both FPGA and GPU. Compared to the multi-threading CPU baseline, our GPU accelerator achieves 7x acceleration, while our FPGA accelerator achieves 28x acceleration. We further conduct an architecture study to quantitatively analyze the architectural reason for the performance difference. The summarized insights could serve as a guide on choosing the proper hardware acceleration platform.

The advent of next-generation sequencing has made a great impact on many applications from precision medicine to new drug discovery, leading to an explosion in sequencing of individual genomes. This motivates the research of FPGA acceleration for genome sequencing algorithms to complement the computation capabilities of conventional CPU systems. The recently developed SMEM seeding algorithm, which is based on FMD-index, becomes a time-consuming computation kernel in genome sequencing, but it has not been well studied. The fundamental challenge of accelerating the SMEM algorithm is to handle its large volume of random memory accesses. While the state-of-the-art SMEM accelerator attempts to achieve high memory bandwidth by sacrificing the performance of individual processing elements to maximize the task-level parallelism, this design methodology suffers serious inefficiency of resource utilization and does not scale well for future technology advances. To resolve these impediments, we propose SMEM++, a pipelined and time-multiplexed FPGA accelerator for the SMEM algorithm. SMEM++ features a fully pipelined processing element design that significantly improves the efficiency of FPGA on-chip resource utilization. Moreover, we design a communication interface adapter to make the accelerator compatible to the designated CPU-FPGA platform, increasing its portability. Our experiments on the Intel HARPv2 platform show that SMEM++ outperforms CPU by 24x, and outperforms the state-of-the-art SMEM accelerator design by 6.3x, even with 43% less logic resource consumption.

Next-generation sequencing motivates the researchof FPGA acceleration for genome sequencing algorithms. Therecently developed quadratic-time SMEM seeding algorithmbecomes a time-consuming computation kernel in genomesequencing, but it has not been well studied. The fundamentalchallenge of accelerating the SMEM algorithm is to handle itslarge volume of random memory accesses. While the state-ofthe-art SMEM accelerator attempts sacrifices the performanceof individual processing elements to maximize the task-levelparallelism, this methodology suffers a serious resource underutilizationissue. Therefore, we propose SMEM++, a pipelinedand time-multiplexed FPGA accelerator for SMEM algorithm.SMEM++ adopts the canonical non-blocking pipelinemethodology and implements a fully pipelined acceleratorwith initiation interval equal to one. Moreover, we designa communication interface adapter to make the acceleratorcompatible to the target platform interface and increase itsportability. Experiments on the Intel HARPv2 platform showthat SMEM++ outperforms the original software by 24x, andoutperforms the state-of-the-art SMEM accelerator design by6.3x, with 43% less logic resource usage.