Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Revisiting Actor Programming in C++

The actor model of computation has gained significant popularity over the last decade. Its high level of abstraction makes it appealing for concurrent applications in parallel and distributed systems. However, designing a real-world actor framework that subsumes full scalability, strong reliability, and high resource efficiency requires many conceptual and algorithmic additives to the original model. In this paper, we report on designing and building CAF, the "C++ Actor Framework". CAF targets at providing a concurrent and distributed native environment for scaling up to very large, high-performance applications, and equally well down to small constrained systems. We present the key specifications and design concepts---in particular a message-transparent architecture, type-safe message interfaces, and pattern matching facilities---that make native actors a viable approach for many robust, elastic, and highly distributed developments. We demonstrate the feasibility of CAF in three scenarios: first for elastic, upscaling environments, second for including heterogeneous hardware like GPGPUs, and third for distributed runtime systems. Extensive performance evaluations indicate ideal runtime behaviour for up to 64 cores at very low memory footprint, or in the presence of GPUs. In these tests, CAF continuously outperforms the competing actor environments Erlang, Charm++, SalsaLite, Scala, ActorFoundry, and even the OpenMPI.Comment: 33 page

Scheduling and Tuning Kernels for High-performance on Heterogeneous Processor Systems

Accelerated parallel computing techniques using devices such as GPUs and Xeon Phis (along with CPUs) have proposed promising solutions of extending the cutting edge of high-performance computer systems. A significant performance improvement can be achieved when suitable workloads are handled by the accelerator. Traditional CPUs can handle those workloads not well suited for accelerators. Combination of multiple types of processors in a single computer system is referred to as a heterogeneous system. This dissertation addresses tuning and scheduling issues in heterogeneous systems. The first section presents work on tuning scientific workloads on three different types of processors: multi-core CPU, Xeon Phi massively parallel processor, and NVIDIA GPU; common tuning methods and platform-specific tuning techniques are presented. Then, analysis is done to demonstrate the performance characteristics of the heterogeneous system on different input data. This section of the dissertation is part of the GeauxDock project, which prototyped a few state-of-art bioinformatics algorithms, and delivered a fast molecular docking program. The second section of this work studies the performance model of the GeauxDock computing kernel. Specifically, the work presents an extraction of features from the input data set and the target systems, and then uses various regression models to calculate the perspective computation time. This helps understand why a certain processor is faster for certain sets of tasks. It also provides the essential information for scheduling on heterogeneous systems. In addition, this dissertation investigates a high-level task scheduling framework for heterogeneous processor systems in which, the pros and cons of using different heterogeneous processors can complement each other. Thus a higher performance can be achieve on heterogeneous computing systems. A new scheduling algorithm with four innovations is presented: Ranked Opportunistic Balancing (ROB), Multi-subject Ranking (MR), Multi-subject Relative Ranking (MRR), and Automatic Small Tasks Rearranging (ASTR). The new algorithm consistently outperforms previously proposed algorithms with better scheduling results, lower computational complexity, and more consistent results over a range of performance prediction errors. Finally, this work extends the heterogeneous task scheduling algorithm to handle power capping feature. It demonstrates that a power-aware scheduler significantly improves the power efficiencies and saves the energy consumption. This suggests that, in addition to performance benefits, heterogeneous systems may have certain advantages on overall power efficiency

High-Performance and Time-Predictable Embedded Computing

Nowadays, the prevalence of computing systems in our lives is so ubiquitous that we live in a cyber-physical world dominated by computer systems, from pacemakers to cars and airplanes. These systems demand for more computational performance to process large amounts of data from multiple data sources with guaranteed processing times. Actuating outside of the required timing bounds may cause the failure of the system, being vital for systems like planes, cars, business monitoring, e-trading, etc. High-Performance and Time-Predictable Embedded Computing presents recent advances in software architecture and tools to support such complex systems, enabling the design of embedded computing devices which are able to deliver high-performance whilst guaranteeing the application required timing bounds. Technical topics discussed in the book include: Parallel embedded platforms Programming models Mapping and scheduling of parallel computations Timing and schedulability analysis Runtimes and operating systems The work reflected in this book was done in the scope of the European project P SOCRATES, funded under the FP7 framework program of the European Commission. High-performance and time-predictable embedded computing is ideal for personnel in computer/communication/embedded industries as well as academic staff and master/research students in computer science, embedded systems, cyber-physical systems and internet-of-things.info:eu-repo/semantics/publishedVersio

QoS-aware mechanisms for improving cost-efficiency of datacenters

Warehouse Scale Computers (WSCs) promise high cost-efficiency by amortizing power, cooling, and management overheads. WSCs today host a large variety of jobs with two broad performance requirements categories: latency-critical (LC) and best-effort (BE). Ideally, to fully utilize all hardware resources, WSC operators can simply fill all the nodes with computing jobs. Unfortunately, because colocated jobs contend for shared resources, systems with high loads often experience performance degradation, which negatively impacts the Quality of Service (QoS) for LC jobs. In fact, service providers usually over-provision resources to avoid any interference with LC jobs, leading to significant resource inefficiencies. In this dissertation, I explore opportunities across different system-abstraction layers to improve the cost-efficiency of dataceters by increasing resource utilization of WSCs with little or no impact on the performance of LC jobs. The dissertation has three main components. First, I explore opportunities to improve the throughput of multicore systems by reducing the performance variation of LC jobs. The main insight is that by reshaping the latency distribution curve, performance headroom of LC jobs can be effectively converted to improved BE throughput. I develop, implement, and evaluate a runtime system that achieves this goal with existing hardware. I leverage the cache partitioning, per-core frequency scaling, and thread masking of server processors. Evaluation results show the proposed solution enables 30% higher system throughput compared to solutions proposed in prior works while maintaining at least as good QoS for LC jobs. Second, I study resource contention in near-future heterogeneous memory architectures (HMA). This study is motivated by recent developments in non-volatile memory (NVM) technologies, which enable higher storage density at the cost of same performance. To understand the performance and QoS impact of HMAs, I design and implement a performance emulator in the Linux kernel that runs unmodified workloads with high accuracy, low overhead, and complete transparency. I further propose and evaluate multiple data and resource management QoS mechanisms, such as locality-aware page admission, occupancy management, and write buffer jailing. Third, I focus on accelerated machine learning (ML) systems. By profiling the performance of production workloads and accelerators, I show that accelerated ML tasks are highly sensitive to main memory interference due to fine-grained interaction between CPU and accelerator tasks. As a result, memory resource contention can significantly decreases the performance and efficiency gains of accelerators. I propose a runtime system that leverages existing hardware capabilities and show 17% higher system efficiency compared to previous approaches. This study further exposes opportunities for future processor architecturesElectrical and Computer Engineerin