Hardware acceleration of reaction-diffusion systems:a guide to optimisation of pattern formation algorithms using OpenACC

Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability

Using Graph Properties to Speed-up GPU-based Graph Traversal: A Model-driven Approach

While it is well-known and acknowledged that the performance of graph algorithms is heavily dependent on the input data, there has been surprisingly little research to quantify and predict the impact the graph structure has on performance. Parallel graph algorithms, running on many-core systems such as GPUs, are no exception: most research has focused on how to efficiently implement and tune different graph operations on a specific GPU. However, the performance impact of the input graph has only been taken into account indirectly as a result of the graphs used to benchmark the system. In this work, we present a case study investigating how to use the properties of the input graph to improve the performance of the breadth-first search (BFS) graph traversal. To do so, we first study the performance variation of 15 different BFS implementations across 248 graphs. Using this performance data, we show that significant speed-up can be achieved by combining the best implementation for each level of the traversal. To make use of this data-dependent optimization, we must correctly predict the relative performance of algorithms per graph level, and enable dynamic switching to the optimal algorithm for each level at runtime. We use the collected performance data to train a binary decision tree, to enable high-accuracy predictions and fast switching. We demonstrate empirically that our decision tree is both fast enough to allow dynamic switching between implementations, without noticeable overhead, and accurate enough in its prediction to enable significant BFS speedup. We conclude that our model-driven approach (1) enables BFS to outperform state of the art GPU algorithms, and (2) can be adapted for other BFS variants, other algorithms, or more specific datasets

Towards Energy Efficiency in Heterogeneous Processors: Findings on Virtual Screening Methods

The integration of the latest breakthroughs in computational modeling and high performance computing (HPC) has leveraged advances in the fields of healthcare and drug discovery, among others. By integrating all these developments together, scientists are creating new exciting personal therapeutic strategies for living longer that were unimaginable not that long ago. However, we are witnessing the biggest revolution in HPC in the last decade. Several graphics processing unit architectures have established their niche in the HPC arena but at the expense of an excessive power and heat. A solution for this important problem is based on heterogeneity. In this paper, we analyze power consumption on heterogeneous systems, benchmarking a bioinformatics kernel within the framework of virtual screening methods. Cores and frequencies are tuned to further improve the performance or energy efficiency on those architectures. Our experimental results show that targeted low‐cost systems are the lowest power consumption platforms, although the most energy efficient platform and the best suited for performance improvement is the Kepler GK110 graphics processing unit from Nvidia by using compute unified device architecture. Finally, the open computing language version of virtual screening shows a remarkable performance penalty compared with its compute unified device architecture counterpart.Ingeniería, Industria y Construcció

A Framework for Megascale Agent Based Model Simulations on Graphics Processing Units

Agent-based modeling is a technique for modeling dynamic systems from the bottom up. Individual elements of the system are represented computationally as agents. The system-level behaviors emerge from the micro-level interactions of the agents. Contemporary state-of-the-art agent-based modeling toolkits are essentially discrete-event simulators designed to execute serially on the Central Processing Unit (CPU). They simulate Agent-Based Models (ABMs) by executing agent actions one at a time. In addition to imposing an un-natural execution order, these toolkits have limited scalability. In this article, we investigate data-parallel computer architectures such as Graphics Processing Units (GPUs) to simulate large scale ABMs. We have developed a series of efficient, data parallel algorithms for handling environment updates, various agent interactions, agent death and replication, and gathering statistics. We present three fundamental innovations that provide unprecedented scalability. The first is a novel stochastic memory allocator which enables parallel agent replication in O(1) average time. The second is a technique for resolving precedence constraints for agent actions in parallel. The third is a method that uses specialized graphics hardware, to gather and process statistical measures. These techniques have been implemented on a modern day GPU resulting in a substantial performance increase. We believe that our system is the first ever completely GPU based agent simulation framework. Although GPUs are the focus of our current implementations, our techniques can easily be adapted to other data-parallel architectures. We have benchmarked our framework against contemporary toolkits using two popular ABMs, namely, SugarScape and StupidModel.GPGPU, Agent Based Modeling, Data Parallel Algorithms, Stochastic Simulations

Mixing multi-core CPUs and GPUs for scientific simulation software

Recent technological and economic developments have led to widespread availability of multi-core CPUs and specialist accelerator processors such as graphical processing units (GPUs). The accelerated computational performance possible from these devices can be very high for some applications paradigms. Software languages and systems such as NVIDIA's CUDA and Khronos consortium's open compute language (OpenCL) support a number of individual parallel application programming paradigms. To scale up the performance of some complex systems simulations, a hybrid of multi-core CPUs for coarse-grained parallelism and very many core GPUs for data parallelism is necessary. We describe our use of hybrid applica- tions using threading approaches and multi-core CPUs to control independent GPU devices. We present speed-up data and discuss multi-threading software issues for the applications level programmer and o er some suggested areas for language development and integration between coarse-grained and ne-grained multi-thread systems. We discuss results from three common simulation algorithmic areas including: partial di erential equations; graph cluster metric calculations and random number generation. We report on programming experiences and selected performance for these algorithms on: single and multiple GPUs; multi-core CPUs; a CellBE; and using OpenCL. We discuss programmer usability issues and the outlook and trends in multi-core programming for scienti c applications developers

Heterogeneity, High Performance Computing, Self-Organization and the Cloud

application; blueprints; self-management; self-organisation; resource management; supply chain; big data; PaaS; Saas; HPCaa

A Study of Hardware Performance Counters Selection for Cross Architectural GPU Power Modeling

In the exascale race where huge corporations are spending billions of dollars on designing highly efficient heterogeneous supercomputers, the real need to reduce power envelopes forces current technologies to face crucial challenges as well as it demands the scientific community to evaluate and optimize the performance-power ratio. While energy consumption continues to climb up, the viability of these massive systems becomes a growing concern. In this context, the relevance of specific power-related research works turns into a priority. So we here develop an exhaustive step-by-step process for selecting a comprehensive set of hardware performance counters to serve as an input in an eventual GPU cross-architectural power consumption model. Our experiments show a high power-performance correlation between shared GPU events. Also, we present a set of events that delivers exclusive performance information in order to predict accurately GPU power fluctuations.XX Workshop Procesamiento Distribuido y Paralelo.Red de Universidades con Carreras en Informátic