Jan Prins
University of North Carolina at Chapel Hill, Computer Science, Faculty Member
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Multiphase flow implementations of the lattice Botlzmann method (LBM) are widely applied to the study of porous medium systems. In this work, we construct a new variant of the popular “color” LBM for two-phase flow in which a... more
Multiphase flow implementations of the lattice Botlzmann method (LBM) are widely applied to the study of porous medium systems. In this work, we construct a new variant of the popular “color” LBM for two-phase flow in which a three-dimensional, 19-velocity (D3Q19) lattice is used to compute the momentum transport solution while a three-dimensional, seven velocity (D3Q7) lattice is used to compute the mass transport solution. Based on this formulation, we implement a novel heterogeneous GPU-accelerated algorithm in which the mass transport solution is computed by multiple shared memory CPU cores programmed using OpenMP while a concurrent solution of the momentum transport is performed using a GPU. The heterogeneous solution is demonstrated to provide speedup of 2.6×2.6× as compared to multi-core CPU solution and 1.8×1.8× compared to GPU solution due to concurrent utilization of both CPU and GPU bandwidth. Furthermore, we verify that the proposed formulation provides an accurate physi...
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Protein function prediction is one of the central problems in computational biology. We present a novel automated protein structure-based function prediction method using libraries of local residue packing patterns that are common to most... more
Protein function prediction is one of the central problems in computational biology. We present a novel automated protein structure-based function prediction method using libraries of local residue packing patterns that are common to most proteins in a known functional family. Critical to this approach is the representation of a protein structure as a graph where residue vertices (residue name used as a vertex label) are connected by geometrical proximity edges. The approach employs two steps. First, it uses a fast subgraph mining algorithm to find all occurrences of family-specific labeled subgraphs for all well characterized protein structural and functional families. Second, it queries a new structure for occurrences of a set of motifs characteristic of a known family, using a graph index to speed up Ullman's subgraph isomorphism algorithm. The confidence of function inference from structure depends on the number of family-specific motifs found in the query structure compared...
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The recent addition of task parallelism to the OpenMP shared mem-ory API allows programmers to express concurrency at a high level of abstraction and places the burden of scheduling parallel execu-tion on the OpenMP run time system. This... more
The recent addition of task parallelism to the OpenMP shared mem-ory API allows programmers to express concurrency at a high level of abstraction and places the burden of scheduling parallel execu-tion on the OpenMP run time system. This is a welcome develop-ment for scientific computing as supercomputer nodes grow "fatter" with multicore and manycore processors. But efficient scheduling of tasks on modern multi-socket multicore shared memory systems requires careful consideration of an increasingly complex memory hierarchy, including shared caches and NUMA characteristics. In this paper, we propose a hierarchical scheduling strategy that lever-ages different methods at different levels of the hierarchy. By allow-ing one thread to steal work on behalf of all of the threads within a single chip that share a cache, our scheduler limits the number of costly remote steals. For cores on the same chip, a shared LIFO queue allows exploitation of cache locality between sibling tas...
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The recent addition of task parallelism to the OpenMP shared memory API allows programmers to express concurrency at a high level of abstraction and places the burden of scheduling parallel execution on the OpenMP run-time system.... more
The recent addition of task parallelism to the OpenMP shared memory API allows programmers to express concurrency at a high level of abstraction and places the burden of scheduling parallel execution on the OpenMP run-time system. Efficient scheduling of tasks on modern multi-socket multicore shared memory systems requires careful consideration of an increasingly complex memory hierarchy, including shared caches and non-uniform memory access (NUMA) characteristics. In order to evaluate scheduling strategies, we extended the open source Qthreads threading library to implement different scheduler designs, accepting OpenMP programs through the ROSE compiler. Our comprehensive performance study of diverse OpenMP task-parallel benchmarks compares seven different task-parallel run-time scheduler implementations on an Intel Nehalem multi-socket multicore system: our proposed hierarchical work-stealing scheduler, a per-core work-stealing scheduler, a centralized scheduler, and LIFO and FIFO...
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Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3' ends of RNA molecules to the genome after high-throughput sequencing is challenging,... more
Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3' ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3' ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3' end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3' ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1-2 nt at the 3' end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotid...
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Frequent itemset mining is a popular and important first step in analyzing data sets across a broad range of applications. The traditional,... more
Frequent itemset mining is a popular and important first step in analyzing data sets across a broad range of applications. The traditional, "exact" approach for finding frequent itemsets requires that every item in the itemset occurs in each supporting transaction. However, real data is typically subject to noise, and in the presence of such noise, traditional itemset mining may fail
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This article summarizes the Sigma program for molecular dynamics simulation and describes a generic web browser-based interface (“WASP”) applicable to programs with complex, hierarchical command structures. Use of the interface is... more
This article summarizes the Sigma program for molecular dynamics simulation and describes a generic web browser-based interface (“WASP”) applicable to programs with complex, hierarchical command structures. Use of the interface is illustrated with its application to the Sigma program (“Wigma”).
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We present a novel parallel implementation of N-body grav- itational simulation. Our algorithm uses graphics hardware to accelerate local computation, and is optimized to account for low bandwidth between the CPU and the graphics card, as... more
We present a novel parallel implementation of N-body grav- itational simulation. Our algorithm uses graphics hardware to accelerate local computation, and is optimized to account for low bandwidth between the CPU and the graphics card, as well as low bandwidth across the network. The number of bodies that can be simulated with our implementation is limited only by the memory
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Abstract Effective optimization of FPS Array Processor assembly language (APAL) is difficult. Instructions must be rearranged and consolidated to minimize periods during which the functional units remain idle or perform unnecessary tasks.... more
Abstract Effective optimization of FPS Array Processor assembly language (APAL) is difficult. Instructions must be rearranged and consolidated to minimize periods during which the functional units remain idle or perform unnecessary tasks. Register conflicts and branches ...
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Modern dialects of Fortran enjoy wide use and good support on high- performance computers as performance-oriented programming languages. By pro- viding the ability to express nested data parallelism, modern Fortran dialects en- able... more
Modern dialects of Fortran enjoy wide use and good support on high- performance computers as performance-oriented programming languages. By pro- viding the ability to express nested data parallelism, modern Fortran dialects en- able irregular computations to be incorporated into existing applications with minimal rewriting and without sacrificing performance within the regular por- tions of the application. Since performance of nested
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ABSTRACT Protein local structure comparison aims to recognize structural similarities between parts of proteins. It is an active topic in bioinformatics research, integrating computer science concepts in computational geometry and graph... more
ABSTRACT Protein local structure comparison aims to recognize structural similarities between parts of proteins. It is an active topic in bioinformatics research, integrating computer science concepts in computational geometry and graph theory with empirical observations and physical principles from biochemistry. It has important biological applications, including protein function prediction. In this chapter, we provide an introduction to the protein local structure comparison problem including challenges and applications. Current approaches to the problem are reviewed. Particular consideration is given to the discovery of local structure common to a group of related proteins. We present a new algorithm for this problem that uses a graph-based representation of protein structure and finds recurring subgraphs among a group of protein graphs.
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In recent years technological advances have made the construction of large-scale parallel computers economically at-tractive. These machines have the potential to provide fast solutions to computationally demanding problems that arise in... more
In recent years technological advances have made the construction of large-scale parallel computers economically at-tractive. These machines have the potential to provide fast solutions to computationally demanding problems that arise in computational science, real-time control, computer simulation, large database manipulation and other areas. How-ever, applications that exploit this performance potential have been slow to appear; such applications have proved ex-ceptionally
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this article. Space-filling,ball-stick, or solvent-accessible-surface representations may seem more attractive; however,these presentations can slow down graphical response.When running computation and display on separate platforms, as we... more
this article. Space-filling,ball-stick, or solvent-accessible-surface representations may seem more attractive; however,these presentations can slow down graphical response.When running computation and display on separate platforms, as we used to do (andmay again, depending on available machines), network bandwidth is a potential concern.The upper bound of computing performance on our system is about 15,000 atomic updatesper second, which corresponds to about 180