In recent decades, increasing ultrasound frame rates has been the main motivation behind many novel ultrasound imaging applications [1]-[3]. With this work, we propose an efficient ultrafast FPGA beamformer that applies coherent compounding, through a delay-reuse optimization.

DNA read alignment is an integral part of genome study, which has been revolutionised thanks to the growth of Next Generation Sequencing (NGS) technologies. The inherent computational intensity of string matching algorithms such as Smith-Waterman (SmW) and the vast amount of NGS input data, create a bottleneck in the workflows. Accelerated reconfigurable computing has been extensively leveraged to alleviate this bottleneck, focusing on high-performance albeit standalone implementations. In existing accelerated solutions effective co-design of NGS short-read alignment still remains an open issue, mainly due to narrow view on real integration aspects, such as system wide communication and accelerator call overheads. In this paper, we first propose GANDAFL, a novel Genome AligNment DAta-FLow architecture for SmW Matrix-fill and Traceback stages to perform high throughput short-read alignment on NGS data. We then propose a radical software restructuring to widely-used Bowtie2 aligner that allows read alignment by batches to expose acceleration capabilities. Batch alignment minimizes calling overhead of the accelerators whereas moving both Matrix-fill and Traceback on chip extinguishes the communication data overheads. The standalone solution delivers up to ×116 and ×2 speedup over state-of-the-art software and hardware accelerators respectively and GANDAFL-enhanced Bowtie2 aligner delivers a ×1.9 speedup.

Mathematical models with varying degrees of complexity have been proposed and simulated in an attempt to represent the intricate mechanisms of the human neuron. One of the most biochemically realistic and analytical models, based on the Hodgkin–Huxley (HH) model, has been selected for study in this paper. In order to satisfy the model's computational demands, we present a simulator implemented on Intel Xeon Phi Knights Landing manycore processors. This high-performance platform features an x86-based architecture, allowing our implementation to be portable to other common manycore processing machines. This is reinforced by the fact that Phi adopts the popular OpenMP and MPI programming models. The simulator performance is evaluated when calculating neuronal networks of varying sizes, density and network connectivity maps. The evaluation leads to an analysis of the neuronal synaptic patterns and their impact on performance when tackling this type of workload on a multinode system. It will be shown that the simulator can calculate 100 ms of simulated brain activity for up to 2 millions of biophysically-accurate neurons and 2 billion neuronal synapses within one minute of execution time. This level of performance renders the application an efficient solution for large-scale detailed model simulation.

Emerging cloud applications like machine learning, AI, big data analytics and scientific computing require highperformance computing systems that can sustain the increased amount of data processing without consuming excessive power. To this end, many cloud operators have started deploying hardware accelerators, like GPUs and FPGAs, to increase the performance of computationally intensive tasks. However, increased performance, comes at a higher cost of increased programming complexity for utilizing these accelerators. VINEYARD has developed a versatile framework that allows the seamless deployment and utilization of heterogeneous accelerators in the cloud without increasing the programming complexity while offering the flexibility of software packages. This paper presents the main components that have been developed in the VINEYARD framework and focuses on BrainFrame, the neurocomputing case that demonstrates the new framework's value. BrainFrame not only accelerates neuronal simulations but also has an architecture that allows easy access to neuroscientists, hiding the system complexity, and enabling a modular integration of new accelerated simulators.

Ordinary Differential Equations (ODEs) are widely used in many high-performance computing applications. However, contemporary processors generally provide limited throughput for these kinds of calculations. A high-performance hardware accelerator has been developed for speeding-up the solution of ODEs. The hardware accelerator has been developed both for single and double floating-point precision types and a design-space exploration has been performed in terms of performance and hardware resources. The hardware accelerator has been mapped to an FPGA board and connected through PCIe to a typical processor. The performance evaluation shows that the proposed scheme can achieve up to 14x speedup compared to a reference, single-core CPU solution.

In-vivo and in-vitro experiments are routinely used in neuroscience to unravel brain functionality. Although they are a powerful experimentation tool, they are also time-consuming and, often, restrictive. Computational neuroscience attempts to solve this by using biologically-plausible and biophysically-meaningful neuron models, most prominent among which are the conductance-based models. Their computational complexity calls for accelerator-based computing to mount large-scale or real-time neuroscientific experiments. In this paper, we analyze and draw conclusions on the class of conductance models by using a representative modeling application of the inferior olive (InfOli), an important part of the olivocerebellar brain circuit. We conduct an extensive profiling session to identify the computational and data-transfer requirements of the application under various realistic use cases. The application is, then, ported onto two acceleration nodes, an Intel Xeon Phi and a Maxeler Vectis Data Flow Engine (DFE). We evaluate the performance scalability and resource requirements of the InfOli application on the two target platforms. The analysis of InfOli, which is a real-life neuroscientific application, can serve as a useful guide for porting a wide range of similar workloads on platforms like the Xeon Phi or the Maxeler DFEs. As accelerators are increasingly populating High-Performance Computing (HPC) infrastructure, the current paper provides useful insight on how to optimally use such nodes to run complex and relevant neuron modeling workloads.

Biologically accurate neuron simulations are increasingly important in research related to brain activity. They are computationally intensive and feature data and task parallelism. In this paper, we present a case study for the mapping of a biologically accurate inferior-olive (InfOli), neural cell simulator on an many-core research platform. The Single-Chip Cloud Computer (SCC) is an experimental processor created by Intel Labs. The target neurons provide a major input to the cerebellum and are involved in motor skills and space perception. We exploit task-and data-partitioning, scaling the simulation over more than 40,000 neurons. The voltage-and frequency-scaling capabilities of the chip are explored, achieving more than 20% energy savings with negligible performance degradation. Four platform configurations are evaluated and a mapping with balanced workload and constant voltage and frequency is formally derived as optimal.