Evaluating kernels on Xeon Phi to accelerate Gysela application

This work describes the challenges presented by porting parts ofthe Gysela code to the Intel Xeon Phi coprocessor, as well as techniques used for optimization, vectorization and tuning that can be applied to other applications. We evaluate the performance of somegeneric micro-benchmark on Phi versus Intel Sandy Bridge. Several interpolation kernels useful for the Gysela application are analyzed and the performance are shown. Some memory-bound and compute-bound kernels are accelerated by a factor 2 on the Phi device compared to Sandy architecture. Nevertheless, it is hard, if not impossible, to reach a large fraction of the peek performance on the Phi device,especially for real-life applications as Gysela. A collateral benefit of this optimization and tuning work is that the execution time of Gysela (using 4D advections) has decreased on a standard architecture such as Intel Sandy Bridge.Comment: submitted to ESAIM proceedings for CEMRACS 2014 summer school version reviewe

Analysis of a benchmark suite to evaluate mixed numeric and symbolic processing

The suite of programs that formed the benchmark for a proposed advanced computer is described and analyzed. The features of the processor and its operating system that are tested by the benchmark are discussed. The computer codes and the supporting data for the analysis are given as appendices

Vector coprocessor sharing techniques for multicores: performance and energy gains

Vector Processors (VPs) created the breakthroughs needed for the emergence of computational science many years ago. All commercial computing architectures on the market today contain some form of vector or SIMD processing. Many high-performance and embedded applications, often dealing with streams of data, cannot efficiently utilize dedicated vector processors for various reasons: limited percentage of sustained vector code due to substantial flow control; inherent small parallelism or the frequent involvement of operating system tasks; varying vector length across applications or within a single application; data dependencies within short sequences of instructions, a problem further exacerbated without loop unrolling or other compiler optimization techniques. Additionally, existing rigid SIMD architectures cannot tolerate efficiently dynamic application environments with many cores that may require the runtime adjustment of assigned vector resources in order to operate at desired energy/performance levels. To simultaneously alleviate these drawbacks of rigid lane-based VP architectures, while also releasing on-chip real estate for other important design choices, the first part of this research proposes three architectural contexts for the implementation of a shared vector coprocessor in multicore processors. Sharing an expensive resource among multiple cores increases the efficiency of the functional units and the overall system throughput. The second part of the dissertation regards the evaluation and characterization of the three proposed shared vector architectures from the performance and power perspectives on an FPGA (Field-Programmable Gate Array) prototype. The third part of this work introduces performance and power estimation models based on observations deduced from the experimental results. The results show the opportunity to adaptively adjust the number of vector lanes assigned to individual cores or processing threads in order to minimize various energy-performance metrics on modern vector- capable multicore processors that run applications with dynamic workloads. Therefore, the fourth part of this research focuses on the development of a fine-to-coarse grain power management technique and a relevant adaptive hardware/software infrastructure which dynamically adjusts the assigned VP resources (number of vector lanes) in order to minimize the energy consumption for applications with dynamic workloads. In order to remove the inherent limitations imposed by FPGA technologies, the fifth part of this work consists of implementing an ASIC (Application Specific Integrated Circuit) version of the shared VP towards precise performance-energy studies involving high- performance vector processing in multicore environments

Hardware implementation of non-bonded forces in molecular dynamics simulations

Molecular Dynamics is a computational method based on classical mechanics to describe the behavior of a molecular system. This method is used in biomolecular simulations, which are intended to contribute to the study and advance of nanotechnology, medicine, chemistry and biology. Software implementations of Molecular Dynamics simulations can spend most of time computing the non-bonded interactions. This work presents the design and implementation of an FPGA-based coprocessor that accelerates MD simulations by computing in parallel the non-bonded interactions, specifically, the van der Waals and the electrostatic interactions. These interactions are modeled as the Lennard-Jones 6-12 potential and the direct-space Ewald summation, respectively. In addition, this work introduces a novel variable transformation of the potential energy functions, and a novel interpolation method with pseudo-floating-point representation to compute the short-range forces. Also, it uses a combination of fixed-point and floating-point arithmetic to obtain the best of both representations. The FPGA coprocessor is a memory-mapped system connected to a host by PCI Express, and is provided with interruption capabilities to improve parallelization. Its main block is based on a single functional pipeline, and is connected via Avalon Bus to other peripherals such as the PCIe Hard-IP and the SG-DMA. It is implemented on an Altera¿s EP2AGX125EF35C4 device, can process 16k particles, and is configured to store up to 16 different types of particles. Simulations in a custom C-application for MD that only computes non-bonded forces become up to 12.5x faster using the FPGA coprocessor when considering 12500 atoms.PregradoINGENIERO(A) EN ELECTRÓNIC

REAL-TIME ADAPTIVE PULSE COMPRESSION ON RECONFIGURABLE, SYSTEM-ON-CHIP (SOC) PLATFORMS

New radar applications need to perform complex algorithms and process a large quantity of data to generate useful information for the users. This situation has motivated the search for better processing solutions that include low-power high-performance processors, efficient algorithms, and high-speed interfaces. In this work, hardware implementation of adaptive pulse compression algorithms for real-time transceiver optimization is presented, and is based on a System-on-Chip architecture for reconfigurable hardware devices. This study also evaluates the performance of dedicated coprocessors as hardware accelerator units to speed up and improve the computation of computing-intensive tasks such matrix multiplication and matrix inversion, which are essential units to solve the covariance matrix. The tradeoffs between latency and hardware utilization are also presented. Moreover, the system architecture takes advantage of the embedded processor, which is interconnected with the logic resources through high-performance buses, to perform floating-point operations, control the processing blocks, and communicate with an external PC through a customized software interface. The overall system functionality is demonstrated and tested for real-time operations using a Ku-band testbed together with a low-cost channel emulator for different types of waveforms