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

ReSHAPE: A Framework for Dynamic Resizing and Scheduling of Homogeneous Applications in a Parallel Environment

Applications in science and engineering often require huge computational resources for solving problems within a reasonable time frame. Parallel supercomputers provide the computational infrastructure for solving such problems. A traditional application scheduler running on a parallel cluster only supports static scheduling where the number of processors allocated to an application remains fixed throughout the lifetime of execution of the job. Due to the unpredictability in job arrival times and varying resource requirements, static scheduling can result in idle system resources thereby decreasing the overall system throughput. In this paper we present a prototype framework called ReSHAPE, which supports dynamic resizing of parallel MPI applications executed on distributed memory platforms. The framework includes a scheduler that supports resizing of applications, an API to enable applications to interact with the scheduler, and a library that makes resizing viable. Applications executed using the ReSHAPE scheduler framework can expand to take advantage of additional free processors or can shrink to accommodate a high priority application, without getting suspended. In our research, we have mainly focused on structured applications that have two-dimensional data arrays distributed across a two-dimensional processor grid. The resize library includes algorithms for processor selection and processor mapping. Experimental results show that the ReSHAPE framework can improve individual job turn-around time and overall system throughput.Comment: 15 pages, 10 figures, 5 tables Submitted to International Conference on Parallel Processing (ICPP'07

Dynamic load balancing of parallel road traffic simulation

The objective of this research was to investigate, develop and evaluate dynamic load-balancing strategies for parallel execution of microscopic road traffic simulations. Urban road traffic simulation presents irregular, and dynamically varying distributed computational load for a parallel processor system. The dynamic nature of road traffic simulation systems lead to uneven load distribution during simulation, even for a system that starts off with even load distributions. Load balancing is a potential way of achieving improved performance by reallocating work from highly loaded processors to lightly loaded processors leading to a reduction in the overall computational time. In dynamic load balancing, workloads are adjusted continually or periodically throughout the computation. In this thesis load balancing strategies were evaluated and some load balancing policies developed. A load index and a profitability determination algorithms were developed. These were used to enhance two load balancing algorithms. One of the algorithms exhibits local communications and distributed load evaluation between the neighbour partitions (diffusion algorithm) and the other algorithm exhibits both local and global communications while the decision making is centralized (MaS algorithm). The enhanced algorithms were implemented and synthesized with a research parallel traffic simulation. The performance of the research parallel traffic simulator, optimized with the two modified dynamic load balancing strategies were studied

Analysis of Various Decentralized Load Balancing Techniques with Node Duplication

Experience in parallel computing is an increasingly necessary skill for today’s upcoming computer scientists as processors are hitting a serial execution performance barrier and turning to parallel execution for continued gains. The uniprocessor system has now reached its maximum speed limit and, there is very less scope to improve the speed of such type of system. To solve this problem multiprocessor system is used, which have more than one processor. Multiprocessor system improves the speed of the system but it again faces some problems like data dependency, control dependency, resource dependency and improper load balancing. So this paper presents a detailed analysis of various decentralized load balancing techniques with node duplication to reduce the proper execution time

Task Packing: Efficient task scheduling in unbalanced parallel programs to maximize CPU utilization

Load imbalance in parallel systems can be generated by external factors to the currently running applications like operating system noise or the underlying hardware like a heterogeneous cluster. HPC applications working on irregular data structures can also have difficulties to balance their computations across the parallel tasks. In this article we extend, improve and evaluate more deeply the Task Packing mechanism proposed in a previous work. The main idea of the mechanism is to concentrate the idle cycles of unbalanced applications in such a way that one or more CPUs are freed from execution. To achieve this, CPUs are stressed with just useful work of the parallel application tasks, provided performance is not degraded. The packing is solved by an algorithm based on the Knapsack problem, in a minimum number of CPUs and using oversubscription. We design and implement a more efficient version of such mechanism. To that end, we perform the Task Packing “in place”, taking advantage of idle cycles generated at synchronization points of unbalanced applications. Evaluations are carried out on a heterogeneous platform using FT and miniFE benchmarks. Results showed that our proposal generates low overhead. In addition the amount of freed CPUs are related to a load imbalance metric which can be used as a prediction for it.Peer ReviewedPostprint (author's final draft

Parallel Processes in HPX: Designing an Infrastructure for Adaptive Resource Management

Advancement in cutting edge technologies have enabled better energy efficiency as well as scaling computational power for the latest High Performance Computing(HPC) systems. However, complexity, due to hybrid architectures as well as emerging classes of applications, have shown poor computational scalability using conventional execution models. Thus alternative means of computation, that addresses the bottlenecks in computation, is warranted. More precisely, dynamic adaptive resource management feature, both from systems as well as application\u27s perspective, is essential for better computational scalability and efficiency. This research presents and expands the notion of Parallel Processes as a placeholder for procedure definitions, targeted at one or more synchronous domains, meta data for computation and resource management as well as infrastructure for dynamic policy deployment. In addition to this, the research presents additional guidelines for a framework for resource management in HPX runtime system. Further, this research also lists design principles for scalability of Active Global Address Space (AGAS), a necessary feature for Parallel Processes. Also, to verify the usefulness of Parallel Processes, a preliminary performance evaluation of different task scheduling policies is carried out using two different applications. The applications used are: Unbalanced Tree Search, a reference dynamic graph application, implemented by this research in HPX and MiniGhost, a reference stencil based application using bulk synchronous parallel model. The results show that different scheduling policies provide better performance for different classes of applications; and for the same application class, in certain instances, one policy fared better than the others, while vice versa in other instances, hence supporting the hypothesis of the need of dynamic adaptive resource management infrastructure, for deploying different policies and task granularities, for scalable distributed computing