71,899 research outputs found

    Navigating the Maize: Cyclic and conditional computational graphs for molecular simulation

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    Many computational chemistry and molecular simulation workflows can be expressed as graphs. This abstraction is useful to modularize and potentially reuse existing components, as well as provide parallelization and ease reproducibility. Existing tools represent the computation as a directed acyclic graph (DAG), thus allowing efficient execution by parallelization of concurrent branches. These systems can, however, generally not express cyclic and conditional workflows. We therefore developed Maize, a workflow manager for cyclic and conditional graphs based on the principles of flow-based programming. By running each node of the graph concurrently in separate processes and allowing communication at any time through dedicated inter-node channels, arbitrary graph structures can be executed. We demonstrate the effectiveness of the tool on a dynamic active learning task in computational drug design, involving the use of a small molecule generative model and an associated scoring system

    Dynamic Graphs on the GPU

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    We present a fast dynamic graph data structure for the GPU. Our dynamic graph structure uses one hash table per vertex to store adjacency lists and achieves 3.4–14.8x faster insertion rates over the state of the art across a diverse set of large datasets, as well as deletion speedups up to 7.8x. The data structure supports queries and dynamic updates through both edge and vertex insertion and deletion. In addition, we define a comprehensive evaluation strategy based on operations, workloads, and applications that we believe better characterize and evaluate dynamic graph data structures

    Formal Derivation of Concurrent Garbage Collectors

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    Concurrent garbage collectors are notoriously difficult to implement correctly. Previous approaches to the issue of producing correct collectors have mainly been based on posit-and-prove verification or on the application of domain-specific templates and transformations. We show how to derive the upper reaches of a family of concurrent garbage collectors by refinement from a formal specification, emphasizing the application of domain-independent design theories and transformations. A key contribution is an extension to the classical lattice-theoretic fixpoint theorems to account for the dynamics of concurrent mutation and collection.Comment: 38 pages, 21 figures. The short version of this paper appeared in the Proceedings of MPC 201

    A study of event traffic during the shared manipulation of objects within a collaborative virtual environment

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    Event management must balance consistency and responsiveness above the requirements of shared object interaction within a Collaborative Virtual Environment (CVE) system. An understanding of the event traffic during collaborative tasks helps in the design of all aspects of a CVE system. The application, user activity, the display interface, and the network resources, all play a part in determining the characteristics of event management. Linked cubic displays lend themselves well to supporting natural social human communication between remote users. To allow users to communicate naturally and subconsciously, continuous and detailed tracking is necessary. This, however, is hard to balance with the real-time consistency constraints of general shared object interaction. This paper aims to explain these issues through a detailed examination of event traffic produced by a typical CVE, using both immersive and desktop displays, while supporting a variety of collaborative activities. We analyze event traffic during a highly collaborative task requiring various forms of shared object manipulation, including the concurrent manipulation of a shared object. Event sources are categorized and the influence of the form of object sharing as well as the display device interface are detailed. With the presented findings the paper wishes to aid the design of future systems
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