I. Parallelism 1. Introduction 2. Parallel Computer Architectures 3. Parallel Programming Considerations II. Applications 4. General Application Issues 5. Parallel Computing in CFD 6. Parallel Computing in Environment and Energy 7. Parallel Computational Chemistry 8. Application Overviews III. Software technologies 9. Software Technologies 10. Message Passing and Threads 11. Parallel I/O 12. Languages and Compilers 13. Parallel Object-Oriented Libraries 14. Problem-Solving Environments 15. Tools for Performance Tuning and Debugging 16. The 2-D Poisson Problem IV. Enabling Technologies and Algorithms 17. Reusable Software and Algorithms 18. Graph Partitioning for Scientific Simulations 19. Mesh Generation 20. Templates and Numerical Linear Algebra 21. Software for the Scalable Solutions of PDEs 22. Parallel Continuous Optimization 23. Path Following in Scientific Computing 24. Automatic Differentiation V. Conclusion 25. Wrap-up and Features

Sourcebook of parallel computing

The architecture of the earth system modeling framework

The Earth System Modeling Framework (ESMF) project is developing a standard software platform for Earth system models. The standard, which defines a component architecture and a support infrastructure, is being developed under open-software practices. Target applications range from operational numerical weather prediction to climate-system change and predictability studies.

The architecture of the Earth System Modeling Framework

This paper describes capabilities, evolution, performance, and applications of the Global Arrays (GA) toolkit. GA was created to provide application programmers with an inteface that allows them to distribute data while maintaining the type of global index space and programming syntax similar to that available when programming on a single processor. The goal of GA is to free the programmer from the low level management of communication and allow them to deal with their problems at the level at which they were originally formulated. At the same time, compatibility of GA with MPI enables the programmer to take advatage of the existing MPI software/libraries when available and appropriate. The variety of applications that have been implemented using Global Arrays attests to the attractiveness of using higher level abstractions to write parallel code.

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Advances, Applications and Performance of the Global Arrays Shared Memory Programming Toolkit

A recent trend in mainstream desktop systems is the use of general-purpose graphics processor units (GPGPUs) to obtain order-of-magnitude performance improvements. CUDA has emerged as a popular programming model for GPGPUs for use by C/C++ programmers. Given the widespread use of modern object-oriented languages with managed runtimes like Java and C#, it is natural to explore how CUDA-like capabilities can be made accessible to those programmers as well. In this paper, we present a programming interface called JCUDA that can be used by Java programmers to invoke CUDA kernels. Using this interface, programmers can write Java codes that directly call CUDA kernels, and delegate the responsibility of generating the Java-CUDA bridge codes and host-device data transfer calls to the compiler. Our preliminary performance results show that this interface can deliver significant performance improvements to Java programmers. For future work, we plan to use the JCUDA interface as a target language for supporting higher level parallel programming languages like X10 and Habanero-Java.

/pdf/jcuda-a-programmer-friendly-interface-for-accelerating-java-4xwleu38k7.pdf

JCUDA: A Programmer-Friendly Interface for Accelerating Java Programs with CUDA

Self-tuning objects for developing programs to be executed on parallel computers. A trace file reflecting the sequence of expressions in a user program that include the self-tuning objects is generated during simulation. The trace file is divided into trace file blocks such that data and computational dependencies between trace blocks is minimized. The trace file blocks are converted into source code expression blocks, which are each parameterized to reflect a number of conventional compiler optimization techniques. Various optimization parameter values are applied to the expression blocks to generate minimal timing, compiled versions. The minimal timing compilations of the expression blocks are linked into the user program and executed in response to detection of self-tuning object expressions in the user code. The minimal timing compilations are then mapped to processors within the target parallel computer system for execution.

Self-tuning object libraries

The present disclosure provides alternative nucleosides, nucleotides, and nucleic acids, and methods of using them. In some aspects, the disclosure provides mRNA wherein the uracil content has been modified and which may be particularly effective for use in therapeutic compositions, because they may benefit from both high expression levels and limited induction of the innate immune response. In some aspects, the disclosure provides methods for the production of pharmaceutical compositions including mRNA without reverse phase chromatography.

Alternative nucleic acid molecules containing reduced uracil content and uses thereof

A system and method for calculating a deadlock-free set of paths in a network which generates an ordered set of deadlock-free sub-topologies, referred to as “layers.”The ordered set of layers is used to determine a deadlock-free set of paths through the network. The resulting paths allow data to be efficiently routed through the network without causing traffic to be disproportionately routed through any subset of links. Each of the deadlock-free layers may be any type of deadlock-free sub-topology. The generated ordering may be any arbitrary ordering of the layers. A shortest-path route calculation is performed with the following constraint: starting at any given layer, for each node, proceed to calculate a shortest path to every other node in the graph where at any node being utilized to assess a given minimum path, the path may move to any higher-ordered layer, but may never return to a lower ordered layer. In this way, within each layer, a path moves through a tree and thus avoids deadlock. Between layers, a path may move only in a single direction, thus also avoiding deadlock.

System and method for deadlock-free routing on arbitrary network topologies

One embodiment of the present invention provides a system that facilitates instant failover during packet routing by employing a flooding protocol to send packets between a source and a destination. Upon receiving a packet containing data at an intermediate node located between the source and the destination, the system determines whether the packet has been seen before at the intermediate node. If not, the system forwards the packet to neighboring nodes of the intermediate node. In one embodiment of the present invention, forwarding the packet to neighboring needs involves forwarding the packet to all neighboring nodes except the node from which the packet was received. In one embodiment of the present invention, determining whether the packet has been seen before involves examining a sequence number, SR, contained within the packet to determine whether the sequence number has been seen before.

Method and apparatus for facilitating instant failover during packet routing

The Parallel Object-Oriented Methods and Applications (POOMA) Framework is described. The POOMA FrameworK is an integrated collection of C++ classes designed to increase simulation lifetime and agility, ease data-parallel interfaces, and improve portability across rapidly evolving high-performance computing architectures. (AIP)

John Reynders

Papers

Self-tuning object libraries

Alternative nucleic acid molecules containing reduced uracil content and uses thereof

System and method for deadlock-free routing on arbitrary network topologies

Method and apparatus for facilitating instant failover during packet routing

The POOMA framework