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Open Access Publications from the University of California

Scholarly Works (15 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2014)
Traditional particle simulation methods are used to calculate pair wise potentials, but some problems require 3-body potentials that calculate over triplets of particles. A direct calculation of 3-body interactions involves O(n3) interactions, but has significant redundant computations that occur in a nested loop formulation. In this paper we explore algorithms for 3-body computations that simultaneously optimize three criteria: computation minimization through symmetries, communication optimality, and load balancing. We present a new 3-body algorithm that is both communication and computation optimal. Its optional replication factor, c, saves c3 in latency (number of messages) and c2 in bandwidth (volume), with bounded load imbalance. We also consider the k-body case and discuss an algorithm that is optimal if there is a cut off distance of less than 1/3 of the domain. The 3-body algorithm demonstrates 99% efficiency on tens of thousands of cores, showing strong scaling properties with order of magnitude speedups over the nïve algorithm.
    • Article
    LBL Publications (2001)

    17th Edition of TOP500 List of World s Fastest Supercomputers Released MANNHEIM, GERMANY; KNOXVILLE, TENN.; & BERKELEY, CALIF. In what has become a much-anticipated event in the world of high-performance computing, the 17th edition of the TOP500 list of the world s fastest supercomputers was released today (June 21). The latest edition of the twice-yearly ranking finds IBM as the leader in the field, with 40 percent in terms of installed systems and 43 percent in terms of total performance of all the installed systems. In second place in terms of installed systems is Sun Microsystems with 16 percent, while Cray Inc. retained second place in terms of performance (13 percent). SGI Inc. was third both with respect to systems with 63 (12.6 percent) and performance (10.2 percent).

      Cover page: 17th Edition of TOP500 List of World's Fastest Supercomputers Reseased
      • Article
      Lawrence Berkeley National Laboratory (2008)
        Cover page: The use of bulk states to accelerate the band edge state calculation of a semiconductor quantum dot
        • Article
        LBL Publications (2000)
          Cover page: TOP500 Supercomputer sites 11/2000
          • Article
          LBL Publications (2005)
          In this paper we analyze major recent trends and changes in the High Performance Computing (HPC) market place. The introduction of vector computers started the area of Supercomputing . The initial success of vector computers in the seventies was driven by raw performance. Massive Parallel Systems (MPP) became successful in the early nineties due to their better price/performance ratios, which was enabled by the attack of the killer-micros . The success of microprocessor based SMP concepts even for the very high-end systems, was the basis for the emerging cluster concepts in the early 2000s. Within the first half of this decade clusters of PC s and workstations have become the prevalent architecture for many HPC application areas on all ranges of performance. However, the Earth Simulator vector system demonstrated that many scientific applications could benefit greatly from other computer architectures. At the same time there is renewed broad interest in the scientific HPC community for new hardware architectures and new programming paradigms. The IBM BlueGene/L system is one early example of a shifting design focus for large-scale system. The DARPA HPCS program has the declared goal of building a Petaflops computer system by the end of the decade using novel computer architectures.
            Cover page: Recent Trends in the Marketplace of High Performance Computing
            • Peer Reviewed
            UC Berkeley Previously Published Works (2010)
              Cover page: Mixed-Precision GPU-Multigrid Solvers with Strong Smoothers
              • Article
              LBL Publications (2001)

              18th Edition of TOP500 List of World s Fastest Supercomputers Released MANNHEIM, GERMANY; KNOXVILLE, TENN.; & BERKELEY, CALIF. In what has become a much-anticipated event in the world of high-performance computing, the 18th edition of the TOP500 list of the world s fastest supercomputers was released today (November 9, 2001). The latest edition of the twice-yearly ranking finds IBM as the leader in the field, with 32 percent in terms of installed systems and 37 percent in terms of total performance of all the installed systems. In a surprise move Hewlett-Packard captured the second place with 30 percent of the systems. Most of these systems are smaller in size and as a consequence HP s share of installed performance is smaller with 15 percent. This is still enough for second place in this category. SGI, Cray and Sun follow in the number of TOP500 systems with 41 (8 percent), 39 (8 percent), and 31 (6 percent) respectively. In the category of installed performance Cray Inc. keeps the third position with 11 percent ahead of SGI (8 percent) and Compaq (8 percent).

                Cover page: TOP500 Sublist for November 2001
                • Article
                LBL Publications (2000)
                  Cover page: Top 500 Supercomputer Sites 11/2000Creative Commons 'BY' version 4.0 license
                  • Article
                  LBL Publications (2005)
                    Cover page: Introduction to the HPC Challenge Benchmark Suite
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2014)
                    De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous fragments called reads. We study optimized parallelization of the most time-consuming phases of Meraculous, a state of-the-art production assembler. First, we present a new parallel algorithm for k-mer analysis, characterized by intensive communication and I/O requirements, and reduce the memory requirements by 6.93×. Second, we efficiently parallelize de Bruijn graph construction and traversal, which necessitates a distributed hash table and is a key component of most de novo assemblers. We provide a novel algorithm that leverages one-sided communication capabilities of the Unified Parallel C (UPC) to facilitate the requisite fine-grained parallelism and avoidance of data hazards, while analytically proving its scalability properties. Overall results show unprecedented performance and efficient scaling on up to 15,360 cores of a Cray XC30, on human genome as well as the challenging wheat genome, with performance improvement from days to seconds.
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