Transformations of High-Level Synthesis Codes for High-Performance Computing

Specialized hardware architectures promise a major step in performance and energy efficiency over the traditional load/store devices currently employed in large scale computing systems. The adoption of high-level synthesis (HLS) from languages such as C/C++ and OpenCL has greatly increased programmer productivity when designing for such platforms. While this has enabled a wider audience to target specialized hardware, the optimization principles known from traditional software design are no longer sufficient to implement high-performance codes. Fast and efficient codes for reconfigurable platforms are thus still challenging to design. To alleviate this, we present a set of optimizing transformations for HLS, targeting scalable and efficient architectures for high-performance computing (HPC) applications. Our work provides a toolbox for developers, where we systematically identify classes of transformations, the characteristics of their effect on the HLS code and the resulting hardware (e.g., increases data reuse or resource consumption), and the objectives that each transformation can target (e.g., resolve interface contention, or increase parallelism). We show how these can be used to efficiently exploit pipelining, on-chip distributed fast memory, and on-chip streaming dataflow, allowing for massively parallel architectures. To quantify the effect of our transformations, we use them to optimize a set of throughput-oriented FPGA kernels, demonstrating that our enhancements are sufficient to scale up parallelism within the hardware constraints. With the transformations covered, we hope to establish a common framework for performance engineers, compiler developers, and hardware developers, to tap into the performance potential offered by specialized hardware architectures using HLS

Considerations in using OpenCL on GPUs and FPGAs for throughput-oriented genomics workloads

The recent upsurge in the available amount of health data and the advances in next-generation sequencing are setting the ground for the long-awaited precision medicine. To process this deluge of data, bioinformatics workloads are becoming more complex and more computationally demanding. For this reasons they have been extended to support different computing architectures, such as GPUs and FPGAs, to leverage the form of parallelism typical of each of such architectures. The paper describes how a genomic workload such as k-mer frequency counting that takes advantage of a GPU can be offloaded to one or even more FPGAs. Moreover, it performs a comprehensive analysis of the FPGA acceleration comparing its performance to a non-accelerated configuration and when using a GPU. Lastly, the paper focuses on how, when using accelerators with a throughput-oriented workload, one should also take into consideration both kernel execution time and how well each accelerator board overlaps kernels and PCIe transferred. Results show that acceleration with two FPGAs can improve both time- and energy-to-solution for the entire accelerated part by a factor of 1.32x. Per contra, acceleration with one GPU delivers an improvement of 1.77x in time-to-solution but of a lower 1.49x in energy-to-solution due to persistently higher power consumption. The paper also evaluates how future FPGA boards with components (i.e., off-chip memory and PCIe) on par with those of the GPU board could provide an energy-efficient alternative to GPUs.Peer ReviewedPostprint (published version

FBLAS: Streaming Linear Algebra on FPGA

Spatial computing architectures pose an attractive alternative to mitigate control and data movement overheads typical of load-store architectures. In practice, these devices are rarely considered in the HPC community due to the steep learning curve, low productivity and lack of available libraries for fundamental operations. High-level synthesis (HLS) tools are facilitating hardware programming, but optimizing for these architectures requires factoring in new transformations and resources/performance trade-offs. We present FBLAS, an open-source HLS implementation of BLAS for FPGAs, that enables reusability, portability and easy integration with existing software and hardware codes. FBLAS' implementation allows scaling hardware modules to exploit on-chip resources, and module interfaces are designed to natively support streaming on-chip communications, allowing them to be composed to reduce off-chip communication. With FBLAS, we set a precedent for FPGA library design, and contribute to the toolbox of customizable hardware components necessary for HPC codes to start productively targeting reconfigurable platforms

Large-Scale Pairwise Sequence Alignments on a Large-Scale GPU Cluster

This paper presents design of a GPU kernel for performing pairwise sequence alignments for large-scale short sequence datasets generated by nextgeneration sequencers. This kernel principally performs batch Needleman– Wunsch global alignments. When used with its MPI-based host software, the kernel is scalable and is capable of achieving high throughput alignment when run on a CPU-GPU cluster

Tuning the Computational Effort: An Adaptive Accuracy-aware Approach Across System Layers

This thesis introduces a novel methodology to realize accuracy-aware systems, which will help designers integrate accuracy awareness into their systems. It proposes an adaptive accuracy-aware approach across system layers that addresses current challenges in that domain, combining and tuning accuracy-aware methods on different system layers. To widen the scope of accuracy-aware computing including approximate computing for other domains, this thesis presents innovative accuracy-aware methods and techniques for different system layers. The required tuning of the accuracy-aware methods is integrated into a configuration layer that tunes the available knobs of the accuracy-aware methods integrated into a system

PERFORMANCE ANALYSIS AND FITNESS OF GPGPU AND MULTICORE ARCHITECTURES FOR SCIENTIFIC APPLICATIONS

Recent trends in computing architecture development have focused on exploiting task- and data-level parallelism from applications. Major hardware vendors are experimenting with novel parallel architectures, such as the Many Integrated Core (MIC) from Intel that integrates 50 or more x86 processors on a single chip, the Accelerated Processing Unit from AMD that integrates a multicore x86 processor with a graphical processing unit (GPU), and many other initiatives from other hardware vendors that are underway. Therefore, various types of architectures are available to developers for accelerating an application. A performance model that predicts the suitability of the architecture for accelerating an application would be very helpful prior to implementation. Thus, in this research, a Fitness model that ranks the potential performance of accelerators for an application is proposed. Then the Fitness model is extended using statistical multiple regression to model both the runtime performance of accelerators and the impact of programming models on accelerator performance with high degree of accuracy. We have validated both performance models for all the case studies. The error rate of these models, calculated using the experimental performance data, is tolerable in the high-performance computing field. In this research, to develop and validate the two performance models we have also analyzed the performance of several multicore CPUs and GPGPU architectures and the corresponding programming models using multiple case studies. The first case study used in this research is a matrix-matrix multiplication algorithm. By varying the size of the matrix from a small size to a very large size, the performance of the multicore and GPGPU architectures are studied. The second case study used in this research is a biological spiking neural network (SNN), implemented with four neuron models that have varying requirements for communication and computation making them useful for performance analysis of the hardware platforms. We report and analyze the performance variation of the four popular accelerators (Intel Xeon, AMD Opteron, Nvidia Fermi, and IBM PS3) and four advanced CPU architectures (Intel 32 core, AMD 32 core, IBM 16 core, and SUN 32 core) with problem size (matrix and network size) scaling, available optimization techniques and execution configuration. This thorough analysis provides insight regarding how the performance of an accelerator is affected by problem size, optimization techniques, and accelerator configuration. We have analyzed the performance impact of four popular multicore parallel programming models, POSIX-threading, Open Multi-Processing (OpenMP), Open Computing Language (OpenCL), and Concurrency Runtime on an Intel i7 multicore architecture; and, two GPGPU programming models, Compute Unified Device Architecture (CUDA) and OpenCL, on a NVIDIA GPGPU. With the broad study conducted using a wide range of application complexity, multiple optimizations, and varying problem size, it was found that according to their achievable performance, the programming models for the x86 processor cannot be ranked across all applications, whereas the programming models for GPGPU can be ranked conclusively. We also have qualitatively and quantitatively ranked all the six programming models in terms of their perceived programming effort. The results and analysis in this research indicate and are supported by the proposed performance models that for a given hardware system, the best performance for an application is obtained with a proper match of programming model and architecture

Heterogeneous Acceleration for 5G New Radio Channel Modelling Using FPGAs and GPUs

L'abstract è presente nell'allegato / the abstract is in the attachmen

Efficiently and Transparently Maintaining High SIMD Occupancy in the Presence of Wavefront Irregularity

Demand is increasing for high throughput processing of irregular streaming applications; examples of such applications from scientific and engineering domains include biological sequence alignment, network packet filtering, automated face detection, and big graph algorithms. With wide SIMD, lightweight threads, and low-cost thread-context switching, wide-SIMD architectures such as GPUs allow considerable flexibility in the way application work is assigned to threads. However, irregular applications are challenging to map efficiently onto wide SIMD because data-dependent filtering or replication of items creates an unpredictable data wavefront of items ready for further processing. Straightforward implementations of irregular applications on a wide-SIMD architecture are prone to load imbalance and reduced occupancy, while more sophisticated implementations require advanced use of parallel GPU operations to redistribute work efficiently among threads. This dissertation will present strategies for addressing the performance challenges of wavefront- irregular applications on wide-SIMD architectures. These strategies are embodied in a developer framework called Mercator that (1) allows developers to map irregular applications onto GPUs ac- cording to the streaming paradigm while abstracting from low-level data movement and (2) includes generalized techniques for transparently overcoming the obstacles to high throughput presented by wavefront-irregular applications on a GPU. Mercator forms the centerpiece of this dissertation, and we present its motivation, performance model, implementation, and extensions in this work

Parallel and Distributed Computing

The 14 chapters presented in this book cover a wide variety of representative works ranging from hardware design to application development. Particularly, the topics that are addressed are programmable and reconfigurable devices and systems, dependability of GPUs (General Purpose Units), network topologies, cache coherence protocols, resource allocation, scheduling algorithms, peertopeer networks, largescale network simulation, and parallel routines and algorithms. In this way, the articles included in this book constitute an excellent reference for engineers and researchers who have particular interests in each of these topics in parallel and distributed computing