Max-plus matrix multiplication library for GPUs - MPMML

2019 Spring.Includes bibliographical references.Max-Plus algebra finds its applications in discrete event simulations, dynamic programming, biological sequence comparisons etc. Although there exist highly tuned libraries like CUDA Linear Algebra Subprograms (CuBLAS) [1] for matrix operations, they implement the standard matrix-multiplication (multiply-add) for floating points. We found no standard library for Max- Plus-Matrix-Multiplication (MPMM) on integers. Hence,we developed a highly tuned parallelized MPMM library kernel. We chose GPUs as hardware platform for this work because of their significantly more parallelism and arithmetic functional units as compared to CPUs. We designed this kernel to be portable across three successive Nvidia GPU architectures and it achieves performance in the range 3065 GOPs/S - 3631 GOPs/S on all of these architectures. We closely followed the benchmarking approach described by Volkov et al. [2] when they contributed to cuBLAS. This MPMM kernel can be part of a max-plus algebra library for GPUs and can help speed up Biological Sequence comparison applications like BPMax

Adaptive heterogeneous parallelism for semi-empirical lattice dynamics in computational materials science.

With the variability in performance of the multitude of parallel environments available today, the conceptual overhead created by the need to anticipate runtime information to make design-time decisions has become overwhelming. Performance-critical applications and libraries carry implicit assumptions based on incidental metrics that are not portable to emerging computational platforms or even alternative contemporary architectures. Furthermore, the significance of runtime concerns such as makespan, energy efficiency and fault tolerance depends on the situational context. This thesis presents a case study in the application of both Mattsons prescriptive pattern-oriented approach and the more principled structured parallelism formalism to the computational simulation of inelastic neutron scattering spectra on hybrid CPU/GPU platforms. The original ad hoc implementation as well as new patternbased and structured implementations are evaluated for relative performance and scalability. Two new structural abstractions are introduced to facilitate adaptation by lazy optimisation and runtime feedback. A deferred-choice abstraction represents a unified space of alternative structural program variants, allowing static adaptation through model-specific exhaustive calibration with regards to the extrafunctional concerns of runtime, average instantaneous power and total energy usage. Instrumented queues serve as mechanism for structural composition and provide a representation of extrafunctional state that allows realisation of a market-based decentralised coordination heuristic for competitive resource allocation and the Lyapunov drift algorithm for cooperative scheduling

Exploring resource/performance trade-offs for streaming applications on embedded multiprocessors

Embedded system design is challenged by the gap between the ever-increasing customer demands and the limited resource budgets. The tough competition demands ever-shortening time-to-market and product lifecycles. To solve or, at least to alleviate, the aforementioned issues, designers and manufacturers need model-based quantitative analysis techniques for early design-space exploration to study trade-offs of different implementation candidates. Moreover, modern embedded applications, especially the streaming applications addressed in this thesis, face more and more dynamic input contents, and the platforms that they are running on are more flexible and allow runtime configuration. Quantitative analysis techniques for embedded system design have to be able to handle such dynamic adaptable systems. This thesis has the following contributions: - A resource-aware extension to the Synchronous Dataflow (SDF) model of computation. - Trade-off analysis techniques, both in the time-domain and in the iterationdomain (i.e., on an SDF iteration basis), with support for resource sharing. - Bottleneck-driven design-space exploration techniques for resource-aware SDF. - A game-theoretic approach to controller synthesis, guaranteeing performance under dynamic input. As a first contribution, we propose a new model, as an extension of static synchronous dataflow graphs (SDF) that allows the explicit modeling of resources with consistency checking. The model is called resource-aware SDF (RASDF). The extension enables us to investigate resource sharing and to explore different scheduling options (ways to allocate the resources to the different tasks) using state-space exploration techniques. Consistent SDF and RASDF graphs have the property that an execution occurs in so-called iterations. An iteration typically corresponds to the processing of a meaningful piece of data, and it returns the graph to its initial state. On multiprocessor platforms, iterations may be executed in a pipelined fashion, which makes performance analysis challenging. As the second contribution, this thesis develops trade-off analysis techniques for RASDF, both in the time-domain and in the iteration-domain (i.e., on an SDF iteration basis), to dimension resources on platforms. The time-domain analysis allows interleaving of different iterations, but the size of the explored state space grows quickly. The iteration-based technique trades the potential of interleaving of iterations for a compact size of the iteration state space. An efficient bottleneck-driven designspace exploration technique for streaming applications, the third main contribution in this thesis, is derived from analysis of the critical cycle of the state space, to reveal bottleneck resources that are limiting the throughput. All techniques are based on state-based exploration. They enable system designers to tailor their platform to the required applications, based on their own specific performance requirements. Pruning techniques for efficient exploration of the state space have been developed. Pareto dominance in terms of performance and resource usage is used for exact pruning, and approximation techniques are used for heuristic pruning. Finally, the thesis investigates dynamic scheduling techniques to respond to dynamic changes in input streams. The fourth contribution in this thesis is a game-theoretic approach to tackle controller synthesis to select the appropriate schedules in response to dynamic inputs from the environment. The approach transforms the explored iteration state space of a scenario- and resource-aware SDF (SARA SDF) graph to a bipartite game graph, and maps the controller synthesis problem to the problem of finding a winning positional strategy in a classical mean payoff game. A winning strategy of the game can be used to synthesize the controller of schedules for the system that is guaranteed to satisfy the throughput requirement given by the designer

Discrete Event Simulations

Considered by many authors as a technique for modelling stochastic, dynamic and discretely evolving systems, this technique has gained widespread acceptance among the practitioners who want to represent and improve complex systems. Since DES is a technique applied in incredibly different areas, this book reflects many different points of view about DES, thus, all authors describe how it is understood and applied within their context of work, providing an extensive understanding of what DES is. It can be said that the name of the book itself reflects the plurality that these points of view represent. The book embraces a number of topics covering theory, methods and applications to a wide range of sectors and problem areas that have been categorised into five groups. As well as the previously explained variety of points of view concerning DES, there is one additional thing to remark about this book: its richness when talking about actual data or actual data based analysis. When most academic areas are lacking application cases, roughly the half part of the chapters included in this book deal with actual problems or at least are based on actual data. Thus, the editor firmly believes that this book will be interesting for both beginners and practitioners in the area of DES

The fast multipole method at exascale

This thesis presents a top to bottom analysis on designing and implementing fast algorithms for current and future systems. We present new analysis, algorithmic techniques, and implementations of the Fast Multipole Method (FMM) for solving N- body problems. We target the FMM because it is broadly applicable to a variety of scientific particle simulations used to study electromagnetic, fluid, and gravitational phenomena, among others. Importantly, the FMM has asymptotically optimal time complexity with guaranteed approximation accuracy. As such, it is among the most attractive solutions for scalable particle simulation on future extreme scale systems. We specifically address two key challenges. The first challenge is how to engineer fast code for today’s platforms. We present the first in-depth study of multicore op- timizations and tuning for FMM, along with a systematic approach for transforming a conventionally-parallelized FMM into a highly-tuned one. We introduce novel opti- mizations that significantly improve the within-node scalability of the FMM, thereby enabling high-performance in the face of multicore and manycore systems. The second challenge is how to understand scalability on future systems. We present a new algorithmic complexity analysis of the FMM that considers both intra- and inter- node communication costs. Using these models, we present results for choosing the optimal algorithmic tuning parameter. This analysis also yields the surprising prediction that although the FMM is largely compute-bound today, and therefore highly scalable on current systems, the trajectory of processor architecture designs, if there are no significant changes could cause it to become communication-bound as early as the year 2015. This prediction suggests the utility of our analysis approach, which directly relates algorithmic and architectural characteristics, for enabling a new kind of highlevel algorithm-architecture co-design. To demonstrate the scientific significance of FMM, we present two applications namely, direct simulation of blood which is a multi-scale multi-physics problem and large-scale biomolecular electrostatics. MoBo (Moving Boundaries) is the infrastruc- ture for the direct numerical simulation of blood. It comprises of two key algorithmic components of which FMM is one. We were able to simulate blood flow using Stoke- sian dynamics on 200,000 cores of Jaguar, a peta-flop system and achieve a sustained performance of 0.7 Petaflop/s. The second application we propose as future work in this thesis is biomolecular electrostatics where we solve for the electrical potential using the boundary-integral formulation discretized with boundary element methods (BEM). The computational kernel in solving the large linear system is dense matrix vector multiply which we propose can be calculated using our scalable FMM. We propose to begin with the two dielectric problem where the electrostatic field is cal- culated using two continuum dielectric medium, the solvent and the molecule. This is only a first step to solving biologically challenging problems which have more than two dielectric medium, ion-exclusion layers, and solvent filled cavities. Finally, given the difficulty in producing high-performance scalable code, productivity is a key concern. Recently, numerical algorithms are being redesigned to take advantage of the architectural features of emerging multicore processors. These new classes of algorithms express fine-grained asynchronous parallelism and hence reduce the cost of synchronization. We performed the first extensive performance study of a recently proposed parallel programming model, called Concurrent Collections (CnC). In CnC, the programmer expresses her computation in terms of application-specific operations, partially-ordered by semantic scheduling constraints. The CnC model is well-suited to expressing asynchronous-parallel algorithms, so we evaluate CnC using two dense linear algebra algorithms in this style for execution on state-of-the-art mul- ticore systems. Our implementations in CnC was able to match and in some cases even exceed competing vendor-tuned and domain specific library codes. We combine these two distinct research efforts by expressing FMM in CnC, our approach tries to marry performance with productivity that will be critical on future systems. Looking forward, we would like to extend this to distributed memory machines, specifically implement FMM in the new distributed CnC, distCnC to express fine-grained paral- lelism which would require significant effort in alternative models.Ph.D

Dynamic Resource Allocation in Embedded, High-Performance and Cloud Computing

The availability of many-core computing platforms enables a wide variety of technical solutions for systems across the embedded, high-performance and cloud computing domains. However, large scale manycore systems are notoriously hard to optimise. Choices regarding resource allocation alone can account for wide variability in timeliness and energy dissipation (up to several orders of magnitude). Dynamic Resource Allocation in Embedded, High-Performance and Cloud Computing covers dynamic resource allocation heuristics for manycore systems, aiming to provide appropriate guarantees on performance and energy efficiency. It addresses different types of systems, aiming to harmonise the approaches to dynamic allocation across the complete spectrum between systems with little flexibility and strict real-time guarantees all the way to highly dynamic systems with soft performance requirements. Technical topics presented in the book include: Load and Resource Models Admission Control Feedback-based Allocation and Optimisation Search-based Allocation Heuristics Distributed Allocation based on Swarm Intelligence Value-Based Allocation Each of the topics is illustrated with examples based on realistic computational platforms such as Network-on-Chip manycore processors, grids and private cloud environments.Note.-- EUR 6,000 BPC fee funded by the EC FP7 Post-Grant Open Access Pilo

Dynamic Resource Allocation in Embedded, High-Performance and Cloud Computing

The availability of many-core computing platforms enables a wide variety of technical solutions for systems across the embedded, high-performance and cloud computing domains. However, large scale manycore systems are notoriously hard to optimise. Choices regarding resource allocation alone can account for wide variability in timeliness and energy dissipation (up to several orders of magnitude). Dynamic Resource Allocation in Embedded, High-Performance and Cloud Computing covers dynamic resource allocation heuristics for manycore systems, aiming to provide appropriate guarantees on performance and energy efficiency. It addresses different types of systems, aiming to harmonise the approaches to dynamic allocation across the complete spectrum between systems with little flexibility and strict real-time guarantees all the way to highly dynamic systems with soft performance requirements. Technical topics presented in the book include: • Load and Resource Models• Admission Control• Feedback-based Allocation and Optimisation• Search-based Allocation Heuristics• Distributed Allocation based on Swarm Intelligence• Value-Based AllocationEach of the topics is illustrated with examples based on realistic computational platforms such as Network-on-Chip manycore processors, grids and private cloud environments

Bridging a Gap Between Research and Production: Contributions to Scheduling and Simulation

Large scale distributed computing infrastructures (e.g., data centers, grids, or clouds) are used by scientists from various domains to produce outstanding research results, such as the discovery of the Higgs Boson in High Energy Physics. These infrastructures are also studied by Computer Scientists to produce their own set of scientific results. Ideally, a virtuous circle should exist between Domain and Computer Scientists: the former raising challenges that could be addressed by the latter. Unfortunately, in many occasions, a gap exists that prevents such an ideal and fostering collaboration. This habilitation covers research works conducted in the fields of scheduling and simulation that contribute to the filling of this gap. It discusses the necessary conditions to achieve this goal and details concrete initiatives in this endeavor