Multi-Architecture Monte-Carlo (MC) Simulation of Soft Coarse-Grained Polymeric Materials: SOft coarse grained Monte-carlo Acceleration (SOMA)

Multi-component polymer systems are important for the development of new materials because of their ability to phase-separate or self-assemble into nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction with a soft, coarse-grained polymer model is an established technique to investigate these soft-matter systems. Here we present an im- plementation of this method: SOft coarse grained Monte-carlo Accelera- tion (SOMA). It is suitable to simulate large system sizes with up to billions of particles, yet versatile enough to study properties of different kinds of molecular architectures and interactions. We achieve efficiency of the simulations commissioning accelerators like GPUs on both workstations as well as supercomputers. The implementa- tion remains flexible and maintainable because of the implementation of the scientific programming language enhanced by OpenACC pragmas for the accelerators. We present implementation details and features of the program package, investigate the scalability of our implementation SOMA, and discuss two applications, which cover system sizes that are difficult to reach with other, common particle-based simulation methods

Pattern overlap implies runaway growth in hierarchical tile systems

We show that in the hierarchical tile assembly model, if there is a producible assembly that overlaps a nontrivial translation of itself consistently (i.e., the pattern of tile types in the overlap region is identical in both translations), then arbitrarily large assemblies are producible. The significance of this result is that tile systems intended to controllably produce finite structures must avoid pattern repetition in their producible assemblies that would lead to such overlap. This answers an open question of Chen and Doty (SODA 2012), who showed that so-called "partial-order" systems producing a unique finite assembly *and" avoiding such overlaps must require time linear in the assembly diameter. An application of our main result is that any system producing a unique finite assembly is automatically guaranteed to avoid such overlaps, simplifying the hypothesis of Chen and Doty's main theorem

Toward a Formal Semantics for Autonomic Components

Autonomic management can improve the QoS provided by parallel/ distributed applications. Within the CoreGRID Component Model, the autonomic management is tailored to the automatic - monitoring-driven - alteration of the component assembly and, therefore, is defined as the effect of (distributed) management code. This work yields a semantics based on hypergraph rewriting suitable to model the dynamic evolution and non-functional aspects of Service Oriented Architectures and component-based autonomic applications. In this regard, our main goal is to provide a formal description of adaptation operations that are typically only informally specified. We contend that our approach makes easier to raise the level of abstraction of management code in autonomic and adaptive applications.Comment: 11 pages + cover pag

Hierarchical Parallelisation of Functional Renormalisation Group Calculations -- hp-fRG

The functional renormalisation group (fRG) has evolved into a versatile tool in condensed matter theory for studying important aspects of correlated electron systems. Practical applications of the method often involve a high numerical effort, motivating the question in how far High Performance Computing (HPC) can leverage the approach. In this work we report on a multi-level parallelisation of the underlying computational machinery and show that this can speed up the code by several orders of magnitude. This in turn can extend the applicability of the method to otherwise inaccessible cases. We exploit three levels of parallelisation: Distributed computing by means of Message Passing (MPI), shared-memory computing using OpenMP, and vectorisation by means of SIMD units (single-instruction-multiple-data). Results are provided for two distinct High Performance Computing (HPC) platforms, namely the IBM-based BlueGene/Q system JUQUEEN and an Intel Sandy-Bridge-based development cluster. We discuss how certain issues and obstacles were overcome in the course of adapting the code. Most importantly, we conclude that this vast improvement can actually be accomplished by introducing only moderate changes to the code, such that this strategy may serve as a guideline for other researcher to likewise improve the efficiency of their codes

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

A design for an intelligent monitor and controller for space station electrical power using parallel distributed problem solving

The emphasis is on defining a set of communicating processes for intelligent spacecraft secondary power distribution and control. The computer hardware and software implementation platform for this work is that of the ADEPTS project at the Johnson Space Center (JSC). The electrical power system design which was used as the basis for this research is that of Space Station Freedom, although the functionality of the processes defined here generalize to any permanent manned space power control application. First, the Space Station Electrical Power Subsystem (EPS) hardware to be monitored is described, followed by a set of scenarios describing typical monitor and control activity. Then, the parallel distributed problem solving approach to knowledge engineering is introduced. There follows a two-step presentation of the intelligent software design for secondary power control. The first step decomposes the problem of monitoring and control into three primary functions. Each of the primary functions is described in detail. Suggestions for refinements and embelishments in design specifications are given

A Tuned and Scalable Fast Multipole Method as a Preeminent Algorithm for Exascale Systems

Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the order of billions of unknowns. That work led to an extremely parallel FMM, scaling to thousands of GPUs or tens of thousands of CPUs. This paper reports on a a campaign of performance tuning and scalability studies using multi-core CPUs, on the Kraken supercomputer. All kernels in the FMM were parallelized using OpenMP, and a test using 10^7 particles randomly distributed in a cube showed 78% efficiency on 8 threads. Tuning of the particle-to-particle kernel using SIMD instructions resulted in 4x speed-up of the overall algorithm on single-core tests with 10^3 - 10^7 particles. Parallel scalability was studied in both strong and weak scaling. The strong scaling test used 10^8 particles and resulted in 93% parallel efficiency on 2048 processes for the non-SIMD code and 54% for the SIMD-optimized code (which was still 2x faster). The weak scaling test used 10^6 particles per process, and resulted in 72% efficiency on 32,768 processes, with the largest calculation taking about 40 seconds to evaluate more than 32 billion unknowns. This work builds up evidence for our view that FMM is poised to play a leading role in exascale computing, and we end the paper with a discussion of the features that make it a particularly favorable algorithm for the emerging heterogeneous and massively parallel architectural landscape