FPGA Processor In Memory Architectures (PIMs): Overlay or Overhaul ?

The dominance of machine learning and the ending of Moore's law have renewed interests in Processor in Memory (PIM) architectures. This interest has produced several recent proposals to modify an FPGA's BRAM architecture to form a next-generation PIM reconfigurable fabric. PIM architectures can also be realized within today's FPGAs as overlays without the need to modify the underlying FPGA architecture. To date, there has been no study to understand the comparative advantages of the two approaches. In this paper, we present a study that explores the comparative advantages between two proposed custom architectures and a PIM overlay running on a commodity FPGA. We created PiCaSO, a Processor in/near Memory Scalable and Fast Overlay architecture as a representative PIM overlay. The results of this study show that the PiCaSO overlay achieves up to 80% of the peak throughput of the custom designs with 2.56x shorter latency and 25% - 43% better BRAM memory utilization efficiency. We then show how several key features of the PiCaSO overlay can be integrated into the custom PIM designs to further improve their throughput by 18%, latency by 19.5%, and memory efficiency by 6.2%.Comment: Accepted in 2023 33rd International Conference on Field-Programmable Logic and Applications (FPL

Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

<p>Abstract</p> <p>Background</p> <p>In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design.</p> <p>Results</p> <p>RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%.</p> <p>Conclusion</p> <p>To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (<it>ViennaPackage </it>– 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU.</p

Design of Introspective Circuits for Analysis of Cell-Level Dis-orientation in Self-Assembled Cellular Systems

This paper discusses a novel approach to managing complexity in a large self-assembled system, by utilizing the self-assembling components themselves to address the complexity. A particular challenge is discussed – namely the question of how to deal with elements that are assembled in different orientations from each other – and a solution based on the idea ofintrospective circuitry is described. A methodology for using a set of cells to determine a nearby cell’s orientation is given, leading to a slow (O(n)) means of orienting a 2D region of cells. A modified algorithm is then describe to allow parallel analysis of/adaption to dis-oriented cells, thus allowing re-orientation of an entire 2D region of cells with better-than-linear time performance (O(sqrt(n))). The significance of this work is discussed not only in terms of managing arrays of dis-oriented cells but also more importantly as an example of the usefulness of local, distributed self-configuration to create and use introspective circuitry

Intrinsically Evolvable Artificial Neural Networks

Dedicated hardware implementations of neural networks promise to provide faster, lower power operation when compared to software implementations executing on processors. Unfortunately, most custom hardware implementations do not support intrinsic training of these networks on-chip. The training is typically done using offline software simulations and the obtained network is synthesized and targeted to the hardware offline. The FPGA design presented here facilitates on-chip intrinsic training of artificial neural networks. Block-based neural networks (BbNN), the type of artificial neural networks implemented here, are grid-based networks neuron blocks. These networks are trained using genetic algorithms to simultaneously optimize the network structure and the internal synaptic parameters. The design supports online structure and parameter updates, and is an intrinsically evolvable BbNN platform supporting functional-level hardware evolution. Functional-level evolvable hardware (EHW) uses evolutionary algorithms to evolve interconnections and internal parameters of functional modules in reconfigurable computing systems such as FPGAs. Functional modules can be any hardware modules such as multipliers, adders, and trigonometric functions. In the implementation presented, the functional module is a neuron block. The designed platform is suitable for applications in dynamic environments, and can be adapted and retrained online. The online training capability has been demonstrated using a case study. A performance characterization model for RC implementations of BbNNs has also been presented

Reconfigurable acceleration of Recurrent Neural Networks

Recurrent Neural Networks (RNNs) have been successful in a wide range of applications involving temporal sequences such as natural language processing, speech recognition and video analysis. However, RNNs often require a significant amount of memory and computational resources. In addition, the recurrent nature and data dependencies in RNN computations can lead to system stall, resulting in low throughput and high latency. This work describes novel parallel hardware architectures for accelerating RNN inference using Field-Programmable Gate Array (FPGA) technology, which considers the data dependencies and high computational costs of RNNs. The first contribution of this thesis is a latency-hiding architecture that utilizes column-wise matrix-vector multiplication instead of the conventional row-wise operation to eliminate data dependencies and improve the throughput of RNN inference designs. This architecture is further enhanced by a configurable checkerboard tiling strategy which allows large dimensions of weight matrices, while supporting element-based parallelism and vector-based parallelism. The presented reconfigurable RNN designs show significant speedup over CPU, GPU, and other FPGA designs. The second contribution of this thesis is a weight reuse approach for large RNN models with weights stored in off-chip memory, running with a batch size of one. A novel blocking-batching strategy is proposed to optimize the throughput of large RNN designs on FPGAs by reusing the RNN weights. Performance analysis is also introduced to enable FPGA designs to achieve the best trade-off between area, power consumption and performance. Promising power efficiency improvement has been achieved in addition to speeding up over CPU and GPU designs. The third contribution of this thesis is a low latency design for RNNs based on a partially-folded hardware architecture. It also introduces a technique that balances initiation interval of multi-layer RNN inferences to increase hardware efficiency and throughput while reducing latency. The approach is evaluated on a variety of applications, including gravitational wave detection and Bayesian RNN-based ECG anomaly detection. To facilitate the use of this approach, we open source an RNN template which enables the generation of low-latency FPGA designs with efficient resource utilization using high-level synthesis tools.Open Acces