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

A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems

Heterogeneous systems are becoming more common on High Performance Computing (HPC) systems. Even using tools like CUDA and OpenCL it is a non-trivial task to obtain optimal performance on the GPU. Approaches to simplifying this task include Merge (a library based framework for heterogeneous multi-core systems), Zippy (a framework for parallel execution of codes on multiple GPUs), BSGP (a new programming language for general purpose computation on the GPU) and CUDA-lite (an enhancement to CUDA that transforms code based on annotations). In addition, efforts are underway to improve compiler tools for automatic parallelization and optimization of affine loop nests for GPUs and for automatic translation of OpenMP parallelized codes to CUDA. In this paper we present an alternative approach: a new computational framework for the development of massively data parallel scientific codes applications suitable for use on such petascale/exascale hybrid systems built upon the highly scalable Cactus framework. As the first non-trivial demonstration of its usefulness, we successfully developed a new 3D CFD code that achieves improved performance.Comment: Parallel Computing 2011 (ParCo2011), 30 August -- 2 September 2011, Ghent, Belgiu

A Micro Power Hardware Fabric for Embedded Computing

Field Programmable Gate Arrays (FPGAs) mitigate many of the problemsencountered with the development of ASICs by offering flexibility, faster time-to-market, and amortized NRE costs, among other benefits. While FPGAs are increasingly being used for complex computational applications such as signal and image processing, networking, and cryptology, they are far from ideal for these tasks due to relatively high power consumption and silicon usage overheads compared to direct ASIC implementation. A reconfigurable device that exhibits ASIC-like power characteristics and FPGA-like costs and tool support is desirable to fill this void. In this research, a parameterized, reconfigurable fabric model named as domain specific fabric (DSF) is developed that exhibits ASIC-like power characteristics for Digital Signal Processing (DSP) style applications. Using this model, the impact of varying different design parameters on power and performance has been studied. Different optimization techniques like local search and simulated annealing are used to determine the appropriate interconnect for a specific set of applications. A design space exploration tool has been developed to automate and generate a tailored architectural instance of the fabric.The fabric has been synthesized on 160 nm cell-based ASIC fabrication process from OKI and 130 nm from IBM. A detailed power-performance analysis has been completed using signal and image processing benchmarks from the MediaBench benchmark suite and elsewhere with comparisons to other hardware and software implementations. The optimized fabric implemented using the 130 nm process yields energy within 3X of a direct ASIC implementation, 330X better than a Virtex-II Pro FPGA and 2016X better than an Intel XScale processor

Analysis of Statistical QoS in Half Duplex and Full Duplex Dense Heterogeneous Cellular Networks

Statistical QoS provisioning as an important performance metric in analyzing next generation mobile cellular network, aka 5G, is investigated. In this context, by quantifying the performance in terms of the effective capacity, we introduce a lower bound for the system performance that facilitates an efficient analysis. Based on the proposed lower bound, which is mainly built on a per resource block analysis, we build a basic mathematical framework to analyze effective capacity in an ultra dense heterogeneous cellular network. We use our proposed scalable approach to give insights about the possible enhancements of the statistical QoS experienced by the end users if heterogeneous cellular networks migrate from a conventional half duplex to an imperfect full duplex mode of operation. Numerical results and analysis are provided, where the network is modeled as a Matern point process. The results demonstrate the accuracy and computational efficiency of the proposed scheme, especially in large scale wireless systems. Moreover, the minimum level of self interference cancellation for the full duplex system to start outperforming its half duplex counterpart is investigated.Comment: arXiv admin note: substantial text overlap with arXiv:1604.0058

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions