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  • High-Level FPGA Accelerator Design for Structured-Mesh-Based Explicit Numerical Solvers

    Kamalakkannan, Kamalavasan; Mudalige, Gihan R.; Reguly, Istvan Z.; Fahmy, Suhaib A. (IEEE, 2021-05-17) [Conference Paper]
    This paper presents a workflow for synthesizing near-optimal FPGA implementations of structured-mesh based stencil applications for explicit solvers. It leverages key characteristics of the application class and its computation-communication pattern and the architectural capabilities of the FPGA to accelerate solvers for high-performance computing applications. Key new features of the workflow are (1) the unification of standard state-of-the-art techniques with a number of highgain optimizations such as batching and spatial blocking/tiling, motivated by increasing throughput for real-world workloads and (2) the development and use of a predictive analytical model to explore the design space, and obtain resource and performance estimates. Three representative applications are implemented using the design workflow on a Xilinx Alveo U280 FPGA, demonstrating near-optimal performance and over 85% predictive model accuracy. These are compared with equivalent highly-optimized implementations of the same applications on modern HPC-grade GPUs (Nvidia V100), analyzing time to solution, bandwidth, and energy consumption. Performance results indicate comparable runtimes with the V100 GPU, with over 2× energy savings for the largest non-trivial application on the FPGA. Our investigation shows the challenges of achieving high performance on current generation FPGAs compared to traditional architectures. We discuss determinants for a given stencil code to be amenable to FPGA implementation, providing insights into the feasibility and profitability of a design and its resulting performance.
  • Runtime Abstraction for Autonomous Adaptive Systems on Reconfigurable Hardware

    Bucknall, Alex R.; Fahmy, Suhaib A. (IEEE, 2021-02-01) [Conference Paper]
    Autonomous systems increasingly rely on on-board computation to avoid the latency overheads of offloading to more powerful remote computing. This requires the integration of hardware accelerators to handle the complex computations demanded by date-intensive sensors. FPGAs offer hardware acceleration with ample flexibility and interfacing capabilities when paired with general purpose processors, with the ability to reconfigure at runtime using partial reconfiguration. Managing dynamic hardware is complex and has been left to designers to address in an ad-hoc manner without first-class integration in autonomous software frameworks. This paper presents an abstracted runtime for managing adaptation of FPGA accelerators, including partial reconfiguration and parametric changes, that presents as a typical interface used in autonomous software systems. We present a demonstration using the Robot Operating System (ROS), showing negligible latency overhead as a result of the abstraction.
  • Symmetry-dependent field-free switching of perpendicular magnetization

    Liu, Liang; Zhou, Chenghang; Shu, Xinyu; Li, Changjian; Zhao, Tieyang; Lin, Weinan; Deng, Jinyu; Xie, Qidong; Chen, Shaohai; Zhou, Jing; Guo, Rui; Wang, Han; Yu, Jihang; Shi, Shu; Yang, Ping; Pennycook, S. J.; Manchon, Aurelien; Chen, Jingsheng (Nature Nanotechnology, Springer Science and Business Media LLC, 2021-01-18) [Article]
    Modern magnetic-memory technology requires all-electric control of perpendicular magnetization with low energy consumption. While spin–orbit torque (SOT) in heavy metal/ferromagnet (HM/FM) heterostructures1,2,3,4,5 holds promise for applications in magnetic random access memory, until today, it has been limited to the in-plane direction. Such in-plane torque can switch perpendicular magnetization only deterministically with the help of additional symmetry breaking, for example, through the application of an external magnetic field2,4, an interlayer/exchange coupling6,7,8,9 or an asymmetric design10,11,12,13,14. Instead, an out-of-plane SOT15 could directly switch perpendicular magnetization. Here we observe an out-of-plane SOT in an HM/FM bilayer of L11-ordered CuPt/CoPt and demonstrate field-free switching of the perpendicular magnetization of the CoPt layer. The low-symmetry point group (3m1) at the CuPt/CoPt interface gives rise to this spin torque, hereinafter referred to as 3m torque, which strongly depends on the relative orientation of the current flow and the crystal symmetry. We observe a three-fold angular dependence in both the field-free switching and the current-induced out-of-plane effective field. Because of the intrinsic nature of the 3m torque, the field-free switching in CuPt/CoPt shows good endurance in cycling experiments. Experiments involving a wide variety of SOT bilayers with low-symmetry point groups16,17 at the interface may reveal further unconventional spin torques in the future.
  • Protein Phosphatase 1 regulates atypical chromosome segregation and cell polarity during mitotic and meiotic division in Plasmodium sexual stages

    Zeeshan, Mohammad; Pandey, Rajan; Subudhi, Amit; Ferguson, David J P; Kaur, Gursimran; Rashpa, Ravish; Nugmanova, Raushan; Brady, Declan; Bottrill, Andrew R.; Vaughan, Sue; Brochet, Mathieu; Bollen, Mathieu; Pain, Arnab; Holder, Anthony A.; Guttery, David; Tewari, Rita (Cold Spring Harbor Laboratory, 2021-01-17) [Preprint]
    AbstractPP1 is a conserved eukaryotic serine/threonine phosphatase that regulates many aspects of mitosis and meiosis, often working in concert with other phosphatases, such as CDC14 and CDC25. The proliferative stages of the parasite life cycle include sexual development within the mosquito vector, with male gamete formation characterized by an atypical rapid mitosis, consisting of three rounds of DNA synthesis, successive spindle formation with clustered kinetochores, and a meiotic stage during zygote to ookinete development following fertilization. It is unclear how PP1 is involved in these unusual processes. Using real-time live-cell and ultrastructural imaging, conditional gene knockdown, RNA-seq and proteomic approaches, we show that Plasmodium PP1 is involved in both chromosome segregation during mitotic exit, and establishment of cell polarity during zygote development in the mosquito midgut, suggesting that small molecule inhibitors of PP1 should be explored for blocking parasite transmission.
  • Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

    Nasser, Badoor Ali Hassan; Saito, Yoshimoto; Alarawi, Mohammed; Humam, Abdulmohsen A; Mineta, Katsuhiko; Gojobori, Takashi (Gene, Elsevier BV, 2021-01-15) [Article]
    Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion (MIC) or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.

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