/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

NAMD2: Greater Scalability for Parallel Molecular Dynamics

Kokkos: Enabling manycore performance portability through polymorphic memory access patterns

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net.

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Ray Meta: scalable de novo metagenome assembly and profiling

NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par allel multipole tree algorithm for full electrostatic force evaluation in ON time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illus trates the performance of NAMD.

NAMD: a Parallel, Object-Oriented Molecular Dynamics Program

We describe Charm++, an object oriented portable parallel programming language based on C++. Its design philosophy, implementation, sample applications and their performance on various parallel machines are described. Charm++ is an explicitly parallel language consisting of C++ with a few extensions. It provides a clear separation between sequential and parallel objects. The execution model of Charm++ is message driven, thus helping one write programs that are latency-tolerant. The language supports multiple inheritance, dynamic binding, overloading, strong typing, and reuse for parallel objects, all of which are more difficult problems in a parallel context. Charm++ provides specific modes for sharing information between parallel objects. It is based on the Charm parallel programming system, and its runtime system implementation reuses most of the runtime system for Charm.

CHARM++: a portable concurrent object oriented system based on C++

Many different parallel languages and paradigms have been developed, each with its own advantages. To benefit from all of them, it should be possible to link together modules written in different parallel languages in a single application. Since the paradigms sometimes differ in fundamental ways, this is difficult to accomplish. This paper describes a framework, Converse, that supports such multi-lingual interoperability. The framework is meant to be inclusive, and has been verified to support the SPMD programming style, message-driven programming, parallel object-oriented programming, and thread-based paradigms. The framework aims at extracting the essential aspects of the runtime support into a set of core components, so that language-specific code does not have to pay overhead for features that it does not need.

Converse: an interoperable framework for parallel programming

We present a fast comparison based parallel sorting algorithm that can handle arbitrary key types. Data movement is the major portion of sorting time for most algorithms in the literature. Our algorithm is parameterized so that is can be tuned to control data movement time, especially for large data sets. Parallel histograms are used to partition the key set exactly. The algorithm is architecture independent, and has been implemented in the CHARM portable parallel programming system, allowing it to be efficiently run on virtually any MIMD computer. Performance results for sorting different data sets are presented.

A Comparison Based Parallel Sorting Algorithm

We describe the design and implementation of a parallel adaptive fast multipole algorithm (AFMA) for N-body problems. Our AFMA algorithm can organize particles in cells of arbitrary shape. This simpliies its paralleliza-tion, so that good locality and load balance are both easily achieved. We describe a tighter well-separatedness criterion , and improved techniques for constructing the AFMA tree. We describe how to avoid redundant computation of pair-wise interactions while maintaining load balance, using a fast edge-partitioning algorithm. The AFMA algorithm is designed in an object oriented, message-driven manner, allowing latency tolerance by overlapping computation and communication easily. It also incorporates several optimizations for message prioritization and communication reduction. Preliminary performance results of our implementation using the Charm++ parallel programming system are presented.

A Parallel Adaptive Fast Multipole Algorithm for n -Body Problems.

Attaining good performance for parallel programs frequently requires substantial expertise and effort, which can be reduced by automated optimization. In this paper we concentrate on run-time optimizations and techniques to automate them without programmer intervention, using post-mortem analysis of parallel program execution. We classify the characteristics of parallel programs with respect to object placement (mapping), scheduling and communication, then describe techniques to discover these characteristics by post-mortem analysis, present heuristics to choose appropriate optimizations based on these characteristics, and describe techniques to generate concise hints to runtime optimization libraries. Our ideas have been developed in the framework of the Paradise post-mortem analysis tool for the parallel object-oriented language Charm++. We also present results for optimizing simple parallel programs running on the Thinking Machines CM-5.

Sanjeev Krishnan

Papers

CHARM++: a portable concurrent object oriented system based on C++

Converse: an interoperable framework for parallel programming

A Comparison Based Parallel Sorting Algorithm

A Parallel Adaptive Fast Multipole Algorithm for n -Body Problems.

Automating parallel runtime optimizations using post-mortem analysis