With the increased interest in energy efficiency, a lot of application domains experiment with Field Programmable Gate Arrays (FPGAs), which promise customized hardware accelerators with high-performance and low power consumption. These experiments possible due to the development of High-Level Languages (HLLs) for FPGAs, which permit non-experts in hardware design languages (HDLs) to program reconfigurable hardware for general purpose computing. However, some of the expert knowledge remains difficult to integrate in HLLs, eventually leading to performance loss for HLL-based applications. One example of such a missing feature is the efficient exploitation of the local memories on FPGAs. A solution to address this challenge is PolyMem, an easy-to-use polymorphic parallel memory that uses BRAMs. In this work, we present HLS-PolyMem, the first complete implementation and in-depth evaluation of PolyMem optimized for the Xilinx Design Suite. Our evaluation demonstrates that HLS-PolyMem is a viable alternative to HLS memory partitioning, the current approach for memory parallelism in Vivado HLS. Specifically, we show that PolyMem offers the same performance as HLS partitioning for simple access patterns, and outperforms partitioning as much as 13x when combining multiple access patterns for the same data structure. We further demonstrate the use of PolyMem for two different case studies, highlighting the superior capabilities of HLS-PolyMem in terms of performance, resource utilization, flexibility, and usability. Based on all the evidence provided in this work, we conclude that HLS-PolyMem enables the efficient use of BRAMs as parallel memories, without compromising the HLS level or the achievable performance.

The question 'Can big data and HPC infrastructure converge?' has important implications for many operators and clients of modern computing. However, answering it is challenging. The hardware is currently different, and fast evolving: big data uses machines with modest numbers of fat cores per socket, large caches, and much memory, whereas HPC uses machines with larger numbers of (thinner) cores, non-trivial NUMA architectures, and fast interconnects. In this work, we investigate the convergence of big data and HPC infrastructure for one of the most challenging application domains, the highly irregular graph processing. We contrast through a systematic, experimental study of over 300,000 core-hours the performance of a modern multicore, Intel Knights Landing (KNL) and of traditional big data hardware, in processing representative graph workloads using state-of-the-art graph analytics platforms. The experimental results indicate KNL is convergence-ready, performance-wise, but only after extensive and expert-level tuning of software and hardware parameters.

Background Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. Results The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. Conclusions pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

To handle the stringent performance requirements of future exascale-class applications, High Performance Computing (HPC) systems need ultra-efficient heterogeneous compute nodes. To reduce power and increase performance, such compute nodes will require hardware accelerators with a high degree of specialization. Ideally, dynamic reconfiguration will be an intrinsic feature, so that specific HPC application features can be optimally accelerated, even if they regularly change over time. In the EXTRA project, we create a new and flexible exploration platform for developing reconfigurable architectures, design tools and HPC applications with run-time reconfiguration built-in as a core fundamental feature instead of an add-on. EXTRA covers the entire stack from architecture up to the application, focusing on the fundamental building blocks for run-time reconfigurable exascale HPC systems: new chip architectures with very low reconfiguration overhead, new tools that truly take reconfiguration as a central design concept, and applications that are tuned to maximally benefit from the proposed run-time reconfiguration techniques. Ultimately, this open platform will improve Europe's competitive advantage and leadership in the field.