Optimising Sparse Matrix Vector multiplication for large scale FEM problems on FPGA

Sparse Matrix Vector multiplication (SpMV) is an important kernel in many scientific applications. In this work we propose an architecture and an automated customisation method to detect and optimise the architecture for block diagonal sparse matrices. We evaluate the proposed approach in the context of the spectral/hp Finite Element Method, using the local matrix assembly approach. This problem leads to a large sparse system of linear equations with block diagonal matrix which is typically solved using an iterative method such as the Preconditioned Conjugate Gradient. The efficiency of the proposed architecture combined with the effectiveness of the proposed customisation method reduces BRAM resource utilisation by as much as 10 times, while achieving identical throughput with existing state of the art designs and requiring minimal development effort from the end user. In the context of the Finite Element Method, our approach enables the solution of larger problems than previously possible, enabling the applicability of FPGAs to more interesting HPC problems

Parallel cryptanalysis

Most of today’s cryptographic primitives are based on computations that are hard to perform for a potential attacker but easy to perform for somebody who is in possession of some secret information, the key, that opens a back door in these hard computations and allows them to be solved in a small amount of time. To estimate the strength of a cryptographic primitive it is important to know how hard it is to perform the computation without knowledge of the secret back door and to get an understanding of how much money or time the attacker has to spend. Usually a cryptographic primitive allows the cryptographer to choose parameters that make an attack harder at the cost of making the computations using the secret key harder as well. Therefore designing a cryptographic primitive imposes the dilemma of choosing the parameters strong enough to resist an attack up to a certain cost while choosing them small enough to allow usage of the primitive in the real world, e.g. on small computing devices like smart phones. This thesis investigates three different attacks on particular cryptographic systems: Wagner’s generalized birthday attack is applied to the compression function of the hash function FSB. Pollard’s rho algorithm is used for attacking Certicom’s ECC Challenge ECC2K-130. The implementation of the XL algorithm has not been specialized for an attack on a specific cryptographic primitive but can be used for attacking some cryptographic primitives by solving multivariate quadratic systems. All three attacks are general attacks, i.e. they apply to various cryptographic systems; the implementations of Wagner’s generalized birthday attack and Pollard’s rho algorithm can be adapted for attacking other primitives than those given in this thesis. The three attacks have been implemented on different parallel architectures. XL has been parallelized using the Block Wiedemann algorithm on a NUMA system using OpenMP and on an Infiniband cluster using MPI. Wagner’s attack was performed on a distributed system of 8 multi-core nodes connected by an Ethernet network. The work on Pollard’s Rho algorithm is part of a large research collaboration with several research groups; the computations are embarrassingly parallel and are executed in a distributed fashion in several facilities with almost negligible communication cost. This dissertation presents implementations of the iteration function of Pollard’s Rho algorithm on Graphics Processing Units and on the Cell Broadband Engine

Architecture--Performance Interrelationship Analysis In Single/Multiple Cpu/Gpu Computing Systems: Application To Composite Process Flow Modeling

Current developments in computing have shown the advantage of using one or more Graphic Processing Units (GPU) to boost the performance of many computationally intensive applications but there are still limits to these GPU-enhanced systems. The major factors that contribute to the limitations of GPU(s) for High Performance Computing (HPC) can be categorized as hardware and software oriented in nature. Understanding how these factors affect performance is essential to develop efficient and robust applications codes that employ one or more GPU devices as powerful co-processors for HPC computational modeling. The present work analyzes and understands the intrinsic interrelationship of both hardware and software categories on computational performance for single and multiple GPU-enhanced systems using a computationally intensive application that is representative of a large portion of challenges confronting modern HPC. The representative application uses unstructured finite element computations for transient composite resin infusion process flow modeling as the computational core, characteristics and results of which reflect many other HPC applications via the sparse matrix system used for the solution of linear system of equations. This work describes these various software and hardware factors and how they interact to affect performance of computationally intensive applications enabling more efficient development and porting of High Performance Computing applications that includes current, legacy, and future large scale computational modeling applications in various engineering and scientific disciplines

PatDNN: Achieving Real-Time DNN Execution on Mobile Devices with Pattern-based Weight Pruning

With the emergence of a spectrum of high-end mobile devices, many applications that formerly required desktop-level computation capability are being transferred to these devices. However, executing the inference of Deep Neural Networks (DNNs) is still challenging considering high computation and storage demands, specifically, if real-time performance with high accuracy is needed. Weight pruning of DNNs is proposed, but existing schemes represent two extremes in the design space: non-structured pruning is fine-grained, accurate, but not hardware friendly; structured pruning is coarse-grained, hardware-efficient, but with higher accuracy loss. In this paper, we introduce a new dimension, fine-grained pruning patterns inside the coarse-grained structures, revealing a previously unknown point in design space. With the higher accuracy enabled by fine-grained pruning patterns, the unique insight is to use the compiler to re-gain and guarantee high hardware efficiency. In other words, our method achieves the best of both worlds, and is desirable across theory/algorithm, compiler, and hardware levels. The proposed PatDNN is an end-to-end framework to efficiently execute DNN on mobile devices with the help of a novel model compression technique (pattern-based pruning based on extended ADMM solution framework) and a set of thorough architecture-aware compiler- and code generation-based optimizations (filter kernel reordering, compressed weight storage, register load redundancy elimination, and parameter auto-tuning). Evaluation results demonstrate that PatDNN outperforms three state-of-the-art end-to-end DNN frameworks, TensorFlow Lite, TVM, and Alibaba Mobile Neural Network with speedup up to 44.5x, 11.4x, and 7.1x, respectively, with no accuracy compromise. Real-time inference of representative large-scale DNNs (e.g., VGG-16, ResNet-50) can be achieved using mobile devices.Comment: To be published in the Proceedings of Twenty-Fifth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 20

A semi-Lagrangian Vlasov solver in tensor train format

In this article, we derive a semi-Lagrangian scheme for the solution of the Vlasov equation represented as a low-parametric tensor. Grid-based methods for the Vlasov equation have been shown to give accurate results but their use has mostly been limited to simulations in two dimensional phase space due to extensive memory requirements in higher dimensions. Compression of the solution via high-order singular value decomposition can help in reducing the storage requirements and the tensor train (TT) format provides efficient basic linear algebra routines for low-rank representations of tensors. In this paper, we develop interpolation formulas for a semi-Lagrangian solver in TT format. In order to efficiently implement the method, we propose a compression of the matrix representing the interpolation step and an efficient implementation of the Hadamard product. We show numerical simulations for standard test cases in two, four and six dimensional phase space. Depending on the test case, the memory requirements reduce by a factor $10^2-10^3$ in four and a factor $10^5-10^6$ in six dimensions compared to the full-grid method

GPU Acceleration of ADMM for Large-Scale Quadratic Programming

The alternating direction method of multipliers (ADMM) is a powerful operator splitting technique for solving structured convex optimization problems. Due to its relatively low per-iteration computational cost and ability to exploit sparsity in the problem data, it is particularly suitable for large-scale optimization. However, the method may still take prohibitively long to compute solutions to very large problem instances. Although ADMM is known to be parallelizable, this feature is rarely exploited in real implementations. In this paper we exploit the parallel computing architecture of a graphics processing unit (GPU) to accelerate ADMM. We build our solver on top of OSQP, a state-of-the-art implementation of ADMM for quadratic programming. Our open-source CUDA C implementation has been tested on many large-scale problems and was shown to be up to two orders of magnitude faster than the CPU implementation

Doctor of Philosophy

dissertationMemory access irregularities are a major bottleneck for bandwidth limited problems on Graphics Processing Unit (GPU) architectures. GPU memory systems are designed to allow consecutive memory accesses to be coalesced into a single memory access. Noncontiguous accesses within a parallel group of threads working in lock step may cause serialized memory transfers. Irregular algorithms may have data-dependent control flow and memory access, which requires runtime information to be evaluated. Compile time methods for evaluating parallelism, such as static dependence graphs, are not capable of evaluating irregular algorithms. The goals of this dissertation are to study irregularities within the context of unstructured mesh and sparse matrix problems, analyze the impact of vectorization widths on irregularities, and present data-centric methods that improve control flow and memory access irregularity within those contexts. Reordering associative operations has often been exploited for performance gains in parallel algorithms. This dissertation presents a method for associative reordering of stencil computations over unstructured meshes that increases data reuse through caching. This novel parallelization scheme offers considerable speedups over standard methods. Vectorization widths can have significant impact on performance in vectorized computations. Although the hardware vector width is generally fixed, the logical vector width used within a computation can range from one up to the width of the computation. Significant performance differences can occur due to thread scheduling and resource limitations. This dissertation analyzes the impact of vectorization widths on dense numerical computations such as 3D dG postprocessing. It is difficult to efficiently perform dynamic updates on traditional sparse matrix formats. Explicitly controlling memory segmentation allows for in-place dynamic updates in sparse matrices. Dynamically updating the matrix without rebuilding or sorting greatly improves processing time and overall throughput. This dissertation presents a new sparse matrix format, dynamic compressed sparse row (DCSR), which allows for dynamic streaming updates to a sparse matrix. A new method for parallel sparse matrix-matrix multiplication (SpMM) that uses dynamic updates is also presented

Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest