Portable high-performance programs

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1999.Includes bibliographical references (p. 159-169).by Matteo Frigo.Ph.D

Software and hardware methods for memory access latency reduction on ILP processors

While microprocessors have doubled their speed every 18 months, performance improvement of memory systems has continued to lag behind. to address the speed gap between CPU and memory, a standard multi-level caching organization has been built for fast data accesses before the data have to be accessed in DRAM core. The existence of these caches in a computer system, such as L1, L2, L3, and DRAM row buffers, does not mean that data locality will be automatically exploited. The effective use of the memory hierarchy mainly depends on how data are allocated and how memory accesses are scheduled. In this dissertation, we propose several novel software and hardware techniques to effectively exploit the data locality and to significantly reduce memory access latency.;We first presented a case study at the application level that reconstructs memory-intensive programs by utilizing program-specific knowledge. The problem of bit-reversals, a set of data reordering operations extensively used in scientific computing program such as FFT, and an application with a special data access pattern that can cause severe cache conflicts, is identified in this study. We have proposed several software methods, including padding and blocking, to restructure the program to reduce those conflicts. Our methods outperform existing ones on both uniprocessor and multiprocessor systems.;The access latency to DRAM core has become increasingly long relative to CPU speed, causing memory accesses to be an execution bottleneck. In order to reduce the frequency of DRAM core accesses to effectively shorten the overall memory access latency, we have conducted three studies at this level of memory hierarchy. First, motivated by our evaluation of DRAM row buffer\u27s performance roles and our findings of the reasons of its access conflicts, we propose a simple and effective memory interleaving scheme to reduce or even eliminate row buffer conflicts. Second, we propose a fine-grain priority scheduling scheme to reorder the sequence of data accesses on multi-channel memory systems, effectively exploiting the available bus bandwidth and access concurrency. In the final part of the dissertation, we first evaluate the design of cached DRAM and its organization alternatives associated with ILP processors. We then propose a new memory hierarchy integration that uses cached DRAM to construct a very large off-chip cache. We show that this structure outperforms a standard memory system with an off-level L3 cache for memory-intensive applications.;Memory access latency has become a major performance bottleneck for memory-intensive applications. as long as DRAM technology remains its most cost-effective position for making main memory, the memory performance problem will continue to exist. The studies conducted in this dissertation attempt to address this important issue. Our proposed software and hardware schemes are effective and applicable, which can be directly used in real-world memory system designs and implementations. Our studies also provide guidance for application programmers to understand memory performance implications, and for system architects to optimize memory hierarchies

Ab initio study of the work functions of elemental metal crystals

This thesis is concerned with the theoretical study of the physical characteristics of metallic surfaces. Ab initio quantum calculations are performed to determine the electronic properties of clean elemental metal surfaces, fully accounting for the material's atomic structure. We aim to understand the atomicscale mechanisms responsible for the dependence of the work function on the surface geometry, including the crystallographic orientation of the surface, the atomic relaxation and reconstruction, as well as the effect of surface edges. We present an accurate method to derive work functions from self-consistent thin-film calculations. By applying a technique based on a macroscopic average, we filter the atomic oscillations in the electronic density to measure precisely the electrostatic potential step at the crystal surface. Combining this quantity with the Fermi energy of a bulk crystal is shown to reduce size effects on the work functions and to yield very precise values. The microscopic origin of the work function anisotropy is studied in sodium, aluminium, copper and gold. For these metals, we find that the trends of increasing work functions for the principal surface orientations reproduce the experimental data and that the trend in aluminium is different from most other metals. The origin of the work function anisotropy is discussed in relation with the orbital character of the electronic states at the Fermi energy. Our study of metal surfaces is extended to the facets of a finite crystal. First-principles studies of the electronic structure of nanowires enable us to obtain the electrostatic potential outside a variety of infinitely-long facet edges. In particular, we determine the microscopic mechanism that allows two different work functions to coexist on either side of a facet edge

CLASSICAL LIQUIDS: EXACT RESULTS, INTEGRAL EQUATIONS THEORY, AND MONTE CARLO SIMULATIONS

2002/2003XVI Ciclo1970Versione digitalizzata della tesi di dottorato cartacea

Molecular Techniques Reveal Wide Phyletic Diversity of Heterotrophic Microbes Associated with Discodermia spp. (Porifera: Demospongiae)

Sponges are well known to harbor large numbers of heterotrophic microbes within their mesohyl. Studies to determine the diversity of these associated microbes have been attempted for only a few shallow water species. We cultured various microorganisms from several species of Discodermia collected from deep water using the \u27Johnson-Sea-Link\u27 manned submersibles, and characterised them by standard microbiological identification methods. Characterisation of a small proportion (ca. 10%) of the total and potential eubacterial isolate collection with molecular systematics techniques revealed a wide diversity of microbes. Phylogenetic analyses of 32 small subunit (SSU) 16S-like rRNA gene sequences from different micorbes indicated high levels of taxonomic diversity assoiated with this genus of sponge. For example, bacteria from at least five cubacterial subdivisions - gamma, alpha, beta, Cytophaga and Gram positive - were isolated from the mesohyl of Discodermia. Several strains were unidentifiable from current sequence databases. No overlap was found between sequences of 24 isolates and 8 sequences obtained by PCR and cloning directly from sponge samples. The abundance and diversity of microbes associated with sponges such as Discodermia suggest that they may play important roles in marine microbial ecology, dispersal and evolution

Lack of Chemical Defense in Two Species of Stalked Crinoids: Support for the Predation Hypothesis for Mesozoic Bathymetric Restriction

Methanol/dichloromethane extracts of (1) the arms and pinnules, and (2) the stalk and cirri of the deep water stalked crinoids Endoxocrinus parrae (Gervais) and Neocrinus decorus (Carpenter) were imbedded at ecologically relevant volumetric concentrations in alginate food pellets containing 2% krill as a feeding stimulant and presented in situ to an assemblage of shallow-water reef fish. Experimental pellets were highly palatable to reef fish; no significant differences in pellet consumption occurred between experimental pellets containing extracts from either species of stalked crinoid or control pellets. Small pieces of cirri, stalks, calyx, arms and pinnules of both species were also tested in in situ feeding assays. While immediate consumption by fish was not apparent, Blue Headed Wrasse (Thalassoma bifasciatum (Block)) and Dusky Damselfish (Stegastes fuscus (Cuvier)) bit at pieces of each body component. Similar fish biting behaviors were also observed when two living Endoxocrinus parrae were deployed on the shallow reef. Observations indicate that neither species of stalked crinoid is chemically defended from predation by a natural assemblage of reef fish. This supports the predation hypothesis that restriction of stalked crinoids in deep-water habitats may have resulted from the Mesozoic radiation of durophagous fishes in shallow seas, resulting in a reduction of stalked crinoids from shallow water

Physics Division annual report, April 1, 1995--March 31, 1996

The past year has seen several major advances in the Division`s research programs. In heavy-ion physics these include experiments with radioactive beams of interest to nuclear astrophysics, a first exploration of the structure of nuclei situated beyond the proton drip line, the discovery of new proton emitters--the heaviest known, the first unambiguous detection of discrete linking transitions between superdeformed and normal deformed states, and the impact of the APEX results which were the first to report, conclusively, no sign of the previously reported sharp electron positron sum lines. The medium energy nuclear physics program of the Division has led the first round of experiments at the CEBAF accelerator at the Thomas Jefferson National Accelerator Facility and the study of color transparency in rho meson propagation at the HERMES experiment at DESY, and it has established nuclear polarization in a laser driven polarized hydrogen target. In atomic physics, the non-dipolar contribution to photoionization has been quantitatively established for the first time, the atomic physics beamline at the Argonne 7 GeV Advanced Photon Source was constructed and, by now, first experiments have been successfully performed. The theory program has pushed exact many-body calculations with fully realistic interactions (the Argonne v{sub 18} potential) to the seven-nucleon system, and interesting results have been obtained for the structure of deformed nuclei through meanfield calculations and for the structure of baryons with QCD calculations based on the Dyson-Schwinger approach. Brief summaries are given of the individual research programs