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

Insights from the Inventory of Smart Grid Projects in Europe: 2012 Update

By the end of 2010 the Joint Research Centre, the European Commission’s in-house science service, launched the first comprehensive inventory of smart grid projects in Europe1. The final catalogue was published in July 2011 and included 219 smart grid and smart metering projects from the EU-28 member states, Switzerland and Norway. The participation of the project coordinators and the reception of the report by the smart grid community were extremely positive. Due to its success, the European Commission decided that the project inventory would be carried out on a regular basis so as to constantly update the picture of smart grid developments in Europe and keep track of lessons learnt and of challenges and opportunities. For this, a new on-line questionnaire was launched in March 2012 and information on projects collected up to September 2012. At the same time an extensive search of project information on the internet and through cooperation links with other European research organizations was conducted. The resulting final database is the most up to date and comprehensive inventory of smart grids and smart metering projects in Europe, including a total of 281 smart grid projects and 90 smart metering pilot projects and rollouts from the same 30 countries that were included in the 2011 inventory database. Projects surveyed were classified into three categories: R&D, demonstration or pre-deployment) and deployment, and for the first time a distinction between smart grid and smart metering projects was made. The following is an insight into the 2012 report.JRC.F.3-Energy securit

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

Integration of all FSSIM components within SEAMLESS-IF and a stand alone Graphical User Interface for FSSIM

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use,

Architecting Data Centers for High Efficiency and Low Latency

Modern data centers, housing remarkably powerful computational capacity, are built in massive scales and consume a huge amount of energy. The energy consumption of data centers has mushroomed from virtually nothing to about three percent of the global electricity supply in the last decade, and will continuously grow. Unfortunately, a significant fraction of this energy consumption is wasted due to the inefficiency of current data center architectures, and one of the key reasons behind this inefficiency is the stringent response latency requirements of the user-facing services hosted in these data centers such as web search and social networks. To deliver such low response latency, data center operators often have to overprovision resources to handle high peaks in user load and unexpected load spikes, resulting in low efficiency. This dissertation investigates data center architecture designs that reconcile high system efficiency and low response latency. To increase the efficiency, we propose techniques that understand both microarchitectural-level resource sharing and system-level resource usage dynamics to enable highly efficient co-locations of latency-critical services and low-priority batch workloads. We investigate the resource sharing on real-system simultaneous multithreading (SMT) processors to enable SMT co-locations by precisely predicting the performance interference. We then leverage historical resource usage patterns to further optimize the task scheduling algorithm and data placement policy to improve the efficiency of workload co-locations. Moreover, we introduce methodologies to better manage the response latency by automatically attributing the source of tail latency to low-level architectural and system configurations in both offline load testing environment and online production environment. We design and develop a response latency evaluation framework at microsecond-level precision for data center applications, with which we construct statistical inference procedures to attribute the source of tail latency. Finally, we present an approach that proactively enacts carefully designed causal inference micro-experiments to diagnose the root causes of response latency anomalies, and automatically correct them to reduce the response latency.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/144144/1/yunqi_1.pd

Master of Science

thesisTo address the need of understanding and optimizing the performance of complex applications and achieving sustained application performance across different architectures, we need performance models and tools that could quantify the theoretical performance and the resultant gap between theoretical and observed performance. This thesis proposes a benchmark-driven Roofline Model Toolkit to provide theoretical and achievable performance, and their resultant gap for multicore, manycore, and accelerated architectures. Roofline micro benchmarks are specialized to quantify the behavior of different architectural features. Compared to previous work on performance characterization, these micro benchmarks focus on capturing the performance of each level of the memory hierarchy, along with thread-level parallelism(TLP), instruction-level parallelism(ILP), and explicit Single Instruction, Multiple Data(SIMD) parallelism, measured in the context of the compilers and runtime environment on the target architecture. We also developed benchmarks to explore detailed memory subsystems behaviors and evaluate parallelization overhead. Beyond on-chip performance, we measure sustained Peripheral Component Interconnect Express(PCIe) throughput with four Graphics Processing Unit(GPU) memory managed mechanisms. By combining results from the architecture characterization with the Roofline Model based solely on architectural specification, this work offers insights for performance prediction of current and future architectures and their software systems. To that end, we instrument three applications and plot their resultant performance on the corresponding Roofline Model when run on a Blue Gene/Q architecture