bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Triplet Repeat Expansion and Mismatch Repair
Authors: Iyer Ravi R. , Pluciennik Anna , Napierala Marek , Wells Robert D.
Published: January 2015

DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway.
Mechanisms of ATM Activation
Authors: Paull Tanya T.
Published: January 2015

The ataxia-telangiectasia mutated (ATM) protein kinase is a master regulator of the DNA damage response, and it coordinates checkpoint activation, DNA repair, and metabolic changes in eukaryotic cells in response to DNA double-strand breaks and oxidative stress. Loss of ATM activity in humans results in the pleiotropic neurodegeneration disorder ataxia-telangiectasia. ATM exists in an inactive state in resting cells but can be activated by the Mre11–Rad50–Nbs1 (MRN) complex and other factors at sites of DNA breaks. In addition, oxidation of ATM activates the kinase independently of the MRN complex. This review discusses these mechanisms of activation, as well as the posttranslational modifications that affect this process and the cellular factors that affect the efficiency and specificity of ATM activation and substrate phosphorylation. I highlight functional similarities between the activation mechanisms of ATM, phosphatidylinositol 3-kinases (PI3Ks), and the other PI3K-like kinases, as well as recent structural insights into their regulation.
Obsessive-Compulsive and Related Disorders: A Critical Review of the New Diagnostic Class
Authors: Abramowitz Jonathan S. , Jacoby Ryan J.
Published: January 2015

The fifth edition of the Diagnostic and Statistical Manual of Mental Disorders includes a new class of obsessive-compulsive and related disorders (OCRDs) that includes obsessive-compulsive disorder (OCD) and a handful of other putatively related conditions. Although this new category promises to raise awareness of underrecognized and understudied problems, its empirical validity and practical utility are questionable. This article reviews the phenomenology of OCD and then presents a critical analysis of the arguments underlying the new OCRD class. This analysis leads to a rejection of the OCRD classification on both scientific and logical grounds. The article closes with a discussion of the treatment implications of the OCRDs approach.
Thinking About Rumination: The Scholarly Contributions and Intellectual Legacy of Susan Nolen-Hoeksema
Authors: Lyubomirsky Sonja , Layous Kristin , Chancellor Joseph , Nelson S. Katherine
Published: January 2015

Our article reviews and celebrates Susan Nolen-Hoeksema's remarkable contributions to psychological and clinical science, focusing on her vast body of theoretical and empirical work and her influence on colleagues and students. Susan spent her career trying to understand how and why a style of regulating emotions called rumination increases vulnerability to depression and exacerbates and perpetuates negative moods. More broadly, we describe research by Susan and her colleagues on the predictors of depression in childhood and adolescence; gender differences in depression and rumination in adolescence and adulthood; roots, correlates, and adverse consequences of ruminative response styles; and rumination as a transdiagnostic risk factor for not only depression but also a host of psychological disorders, including anxiety, substance abuse, and eating disorders. Susan's intellectual legacy is evident in her impressive publication and citation record, the clinical applications of her work, and the flourishing careers of the students she mentored.
Emotion Regulation and Psychopathology
Authors: Sheppes Gal , Suri Gaurav , Gross James J.
Published: January 2015

Emotional problems figure prominently in many clinical conditions. Recent efforts to explain and treat these conditions have emphasized the role of emotion dysregulation. However, emotional problems are not always the result of emotion dysregulation, and even when emotional problems do arise from emotion dysregulation, it is necessary to specify precisely what type of emotion dysregulation might be operative. In this review, we present an extended process model of emotion regulation, and we use this model to describe key points at which emotion-regulation difficulties can lead to various forms of psychopathology. These difficulties are associated with (a) identification of the need to regulate emotions, (b) selection among available regulatory options, (c) implementation of a selected regulatory tactic, and (d) monitoring of implemented emotion regulation across time. Implications and future directions for basic research, assessment, and intervention are discussed.
Amplitude/Higgs Modes in Condensed Matter Physics
Authors: Pekker David , Varma C.M.
Published: January 2015

The order parameter and its variations in space and time in many different states in condensed matter physics at low temperatures are described by the complex function Ψ(r, t). These states include superfluids, superconductors, and a subclass of antiferromagnets and charge density waves. The collective fluctuations in the ordered state may then be categorized as oscillations of phase and amplitude of Ψ(r, t). The phase oscillations are the Goldstone modes of the broken continuous symmetry. The amplitude modes, even at long wavelengths, are well defined and are decoupled from the phase oscillations only near particle-hole symmetry, where the equations of motion have an effective Lorentz symmetry, as in particle physics and if there are no significant avenues for decay into other excitations. They bear close correspondence with the so-called Higgs modes in particle physics, whose prediction and discovery are very important for the standard model of particle physics. In this review, we discuss the theory and the possible observation of the amplitude or Higgs modes in condensed matter physics—in superconductors, cold atoms in periodic lattices, and uniaxial antiferromagnets. We discuss the necessity for at least approximate particle-hole symmetry as well as the special conditions required to couple to such modes because, being scalars, they do not couple linearly to the usual condensed matter probes.
Macroevolutionary History of the Planktic Foraminifera
Authors: Fraass Andrew J. , Kelly D. Clay , Peters Shanan E.
Published: January 2015

Planktic foraminifera are an abundant component of deep-sea sediment and are critical to geohistorical research, primarily because as a biological and geochemical system they are sensitive to coupled bio-hydro-lithosphere interactions. They are also well sampled and studied throughout their evolutionary history. Here, we combine a synoptic global compilation of planktic foraminifera with a stochastic null model of taxonomic turnover to identify statistically significant increases in macroevolutionary rates. There are three taxonomic diversifications and two distinct extinctions in the history of the group. The well-known Cretaceous–Paleogene extinction is of unprecedented magnitude and abruptness and is linked to rapid environmental perturbations associated with bolide impact. The Eocene–Oligocene boundary extinction occurs due to a combination of factors related to a major reorganization of the global climate system. Changes in ocean stratification, seawater chemistry, and global climate recur as primary determinants of both macroevolutionary turnover in planktic foraminifera and spatiotemporal patterns of deep-sea sedimentation over the past 130 Myr.
Innate Immune Pattern Recognition: A Cell Biological Perspective
Authors: Brubaker Sky W. , Bonham Kevin S. , Zanoni Ivan , Kagan Jonathan C.
Published: January 2015

Receptors of the innate immune system detect conserved determinants of microbial and viral origin. Activation of these receptors initiates signaling events that culminate in an effective immune response. Recently, the view that innate immune signaling events rely on and operate within a complex cellular infrastructure has become an important framework for understanding the regulation of innate immunity. Compartmentalization within this infrastructure provides the cell with the ability to assign spatial information to microbial detection and regulate immune responses. Several cell biological processes play a role in the regulation of innate signaling responses; at the same time, innate signaling can engage cellular processes as a form of defense or to promote immunological memory. In this review, we highlight these aspects of cell biology in pattern-recognition receptor signaling by focusing on signals that originate from the cell surface, from endosomal compartments, and from within the cytosol.
Remembrance of Immunology Past: Conversations with Herman Eisen
Authors: Eisen Herman N. , Schlesinger Sondra
Published: January 2015

Herman Eisen and Sondra Schlesinger spent several days together in September 2007 in Woods Hole, Massachusetts, talking about immunology, focusing on his remembrances of the field over the more than 60 years of his involvement. This article is an abridged version of those discussions (the full version is available on the Annual Reviews website). It is both an oral history and a written memory of some important but selected areas of immunology.
Technology and Assessment in Selection
Authors: Tippins Nancy T.
Published: January 2015

As technology evolves and is incorporated into testing and assessment applications, psychologists have opportunities to improve testing processes making scores on measurement tools more accurate, the administration process more efficient, and often the assessment process more realistic. At the same time, they also must contend with fundamental changes in the assumptions made about good testing practices and confront new problems that are created by technological enhancements. Issues such as distractions and their implications for test performance, changes to the applicant pool and their effect on adverse impact, and cheating and its impact on test scores must be explored. This article provides examples of how technology is being used in tests and assessments, discusses the advantages and disadvantages of relying on technology, and offers an agenda for future research.
Leadership Development: An Outcome-Oriented Review Based on Time and Levels of Analyses
Authors: Day David V. , Dragoni Lisa
Published: January 2015

Contemporary organizations face critical challenges associated with possessing and leveraging leadership capabilities. Researchers studying leadership development have responded to this practical imperative, although research on the topic is still in the early stages of scientific development. In assessing the state of the science in leadership development, we review an array of theoretical and research approaches with the goal of stimulating thoughtful intellectual discourse regarding fundamental questions, such as, what is leadership, and what is development. We highlight the breadth of this phenomenon by reviewing theory and research that has considered the development of leadership in individuals, dyads, and teams/organizations. Additionally, we describe a set of proximal and distal signs that indicate leadership may be developing, and we promote experiences, interventions, and interactions as factors that enhance the leadership development process.
Pay, Intrinsic Motivation, Extrinsic Motivation, Performance, and Creativity in the Workplace: Revisiting Long-Held Beliefs
Authors: Gerhart Barry , Fang Meiyu
Published: January 2015

The role of compensation or extrinsic rewards, including pay for performance (PFP), has received relatively little attention in the organizational behavior/psychology literature on work motivation. What attention it has received has often taken the form of raising cautions about the potential harmful effects of PFP on (intrinsic) work motivation, as well as on creativity. We critically assess the theory and evidence that have provided the basis for such arguments and conclude that support for such claims (in workplace settings) is lacking. We seek to provide a more accurate view of how extrinsic rewards such as PFP operate in the workplace and how they influence workplace motivation, creativity, and performance. We document how social determination theory and creativity theory have recently undergone major changes that better recognize the potential positive influence of extrinsic rewards such as PFP. Finally, we identify areas in need of further research.
Supporting the Aging Workforce: A Review and Recommendations for Workplace Intervention Research
Authors: Truxillo Donald M. , Cadiz David M. , Hammer Leslie B.
Published: January 2015

The workforce in most industrialized countries is aging and becoming more age-diverse, and this trend is expected to continue throughout the twenty-first century. Although there has been an increased interest in research on age differences at work, few studies have examined actual interventions designed to support workers at different points across the life span. In this article, we review the literature related to aging at work, including physical, cognitive, personality, and motivational changes; life-span development theories; age stereotyping; age diversity; and work–life balance. Based on this review, we propose a number of avenues for intervention research to address age differences at work. We conclude by identifying critical challenges specific to studying age at work that should be addressed to advance research on interventions.
Justice, Fairness, and Employee Reactions
Authors: Colquitt Jason A. , Zipay Kate P.
Published: January 2015

Of all the issues that employees consider in organizational life, justice and fairness are among the most salient. Justice reflects the perceived adherence to rules that represent appropriateness in decision contexts (e.g., equity, consistency, respect, truthfulness). Fairness reflects a more global perception of appropriateness that lies downstream of justice. Our review integrates justice theories (fairness heuristic theory, the relational model, the group engagement model, fairness theory, deonance theory, uncertainty management theory) and broader theories (social exchange theory, affective events theory) to examine three questions: (a) Why do employees think about justice issues in the first place? (b) how do employees form fairness perceptions? and (c) how do employees react to those perceptions? We close by describing how justice and fairness can be managed in organizations, especially given new technological trends in how people work.
Policy Dilemmas in Latino Health Care and Implementation of the Affordable Care Act
Authors: Ortega Alexander N. , Rodriguez Hector P. , Vargas Bustamante Arturo
Published: January 2015

The changing Latino demographic in the United States presents a number of challenges to health care policy makers, clinicians, organizations, and other stakeholders. Studies have demonstrated that Latinos tend to have worse patterns of access to, and utilization of, health care than other ethnic and racial groups. The implementation of the Affordable Care Act (ACA) of 2010 may ameliorate some of these disparities. However, even with the ACA, it is expected that Latinos will continue to have problems accessing and using high-quality health care, especially in states that are not expanding Medicaid eligibility as provided by the ACA. We identify four current policy dilemmas relevant to Latinos' health and ACA implementation: (a) the need to extend coverage to the undocumented; (b) the growth of Latino populations in states with limited insurance expansion; (c) demands on public and private systems of care; and (d) the need to increase the number of Latino physicians while increasing the direct patient-care responsibilities of nonphysician Latino health care workers.
Commentary: Evidence to Guide Gun Violence Prevention in America
Authors: Webster Daniel W.
Published: January 2015

Gun violence is a major threat to the public's health and safety in the United States. The articles in this volume's symposium on gun violence reveal the scope of the problem and new trends in mortality rates from gunfire. Leading scholars synthesize research evidence that demonstrates the ability of numerous policies and programs—each consistent with lessons learned from successful efforts to combat public health problems—to prevent gun violence. Each approach presents challenges to successful implementation. Future research should inform efforts to assess which approaches are most effective and how to implement evidence-based interventions most effectively.
Cross-Sector Partnerships and Public Health: Challenges and Opportunities for Addressing Obesity and Noncommunicable Diseases Through Engagement with the Private Sector
Authors: Johnston Lee M. , Finegood Diane T.
Published: January 2015

Over the past few decades, cross-sector partnerships with the private sector have become an increasingly accepted practice in public health, particularly in efforts to address infectious diseases in low- and middle-income countries. Now these partnerships are becoming a popular tool in efforts to reduce and prevent obesity and the epidemic of noncommunicable diseases. Partnering with businesses presents a means to acquire resources, as well as opportunities to influence the private sector toward more healthful practices. Yet even though collaboration is a core principle of public health practice, public–private or nonprofit–private partnerships present risks and challenges that warrant specific consideration. In this article, we review the role of public health partnerships with the private sector, with a focus on efforts to address obesity and noncommunicable diseases in high-income settings. We identify key challenges—including goal alignment and conflict of interest—and consider how changes to partnership practice might address these.
Stress and Type 2 Diabetes: A Review of How Stress Contributes to the Development of Type 2 Diabetes
Authors: Kelly Shona J. , Ismail Mubarak
Published: January 2015

Current policy and research around type 2 diabetes (T2D) interventions largely invoke a behavioral model. We suggest that activation of the physiologic stress response (PSR) from chronic exposure to stressors, low socioeconomic status (SES), severe mental health problems, or aggressive behavior increases the risk of T2D. This article is a comprehensive review of the literature on the link between T2D and psychosocial factors focusing on prospective studies of the risk for developing diabetes. The review found an increased risk for T2D in people: exposed to stressful working conditions or traumatic events; with depression; with personality traits or mental health problems that put them in conflict with others; of low SES, either currently or in childhood; and in racial/ethnic minority populations, independent of current SES. This review suggests that T2D prevention research would be more effective if (a) the PSR to psychosocial factors (especially social disparities) was recognized and (b) intervention programs evaluated reduction in social disparities as part of a comprehensive approach.
The Prescription Opioid and Heroin Crisis: A Public Health Approach to an Epidemic of Addiction
Authors: Kolodny Andrew , Courtwright David T. , Hwang Catherine S. , Kreiner Peter , Eadie John L. , Clark Thomas W. , Alexander G. Caleb
Published: January 2015

Public health authorities have described, with growing alarm, an unprecedented increase in morbidity and mortality associated with use of opioid pain relievers (OPRs). Efforts to address the opioid crisis have focused mainly on reducing nonmedical OPR use. Too often overlooked, however, is the need for preventing and treating opioid addiction, which occurs in both medical and nonmedical OPR users. Overprescribing of OPRs has led to a sharp increase in the prevalence of opioid addiction, which in turn has been associated with a rise in overdose deaths and heroin use. A multifaceted public health approach that utilizes primary, secondary, and tertiary opioid addiction prevention strategies is required to effectively reduce opioid-related morbidity and mortality. We describe the scope of this public health crisis, its historical context, contributing factors, and lines of evidence indicating the role of addiction in exacerbating morbidity and mortality, and we provide a framework for interventions to address the epidemic of opioid addiction.
Misleading Performance Reporting in the Supercomputing Field
Authors: Bailey David H.
Published: January 2015

In a previous humorous note, I outlined 12 ways in which performance figures for scientific supercomputers can be distorted. In this paper, the problem of potentially misleading performance reporting is discussed in detail. Included are some examples that have appeared in recent published scientific papers. This paper also includes some proposed guidelines for reporting performance, the adoption of which would raise the level of professionalism and reduce the level of confusion in the field of supercomputing.
Algorithm Development for Distributed Memory Multicomputers Using CONLAB
Authors: Jacobson Peter , Kågström Bo , Rännar Mikael
Published: January 2015

CONLAB (CONcurrent LABoratory) is an environment for developing algorithms for parallel computer architectures and for simulating different parallel architectures. A user can experimentally verify and obtain a picture of the real performance of a parallel algorithm executing on a simulated target architecture. CONLAB gives a high‐level support for expressing computations and communications in a distributed memory multicomputer (DMM) environment. A development methodology for DMM algorithms that is based on different levels of abstraction of the problem, the target architecture, and the CONLAB language itself is presented and illustrated with two examples. Simulotion results for and real experiments on the Intel iPSC/2 hypercube are presented. Because CONLAB is developed to run on uniprocessor UNIX workstations, it is an educational tool that offers interactive (simulated) parallel computing to a wide audience.
A Linked‐Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor
Authors: Yang L.H. , Brooks E.D. , Belak J.
Published: January 2015

A molecular dynamics algorithm for performing large‐scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked‐cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.
Productive Parallel Programming: The PCN Approach
Authors: Foster Ian , Olson Robert , Tuecke Steven
Published: January 2015

We describe the PCN programming system, focusing on those features designed to improve the productivity of scientists and engineers using parallel supercomputers. These features include a simple notation for the concise specification of concurrent algorithms, the ability to incorporate existing Fortran and C code into parallel applications, facilities for reusing parallel program components, a portable toolkit that allows applications to be developed on a workstation or small parallel computer and run unchanged on supercomputers, and integrated debugging and performance analysis tools. We survey representative scientific applications and identify problem classes for which PCN has proved particularly useful.
An Initial Evaluation of the NAG f90 Compiler
Authors: Metcalf Michael
Published: January 2015

A few weeks before the formal publication of the ISO Fortran 90 Standard, NAG announced the world′s first f90 compiler. We have evaluated the compiler by using it to assess the impact of Fortran 90 on the CERN Program Library.
The Parallel C Preprocessor
Authors: Brooks Eugene D. , Gorda Brent C. , Warren Karen H.
Published: January 2015

We describe a parallel extension of the C programming language designed for multiprocessors that provide a facility for sharing memory between processors. The programming model was initially developed on conventional shared memory machines with small processor counts such as the Sequent Balance and Alliant FX/8, but has more recently been used on a scalable massively parallel machine, the BBN TC2000. The programming model is split-join rather than fork-join. Concurrency is exploited to use a fixed number of processors more efficiently rather than to exploit more processors as in the fork‐join model. Team splitting, a mechanism to split the team of processors executing a code into subteams to handle parallel subtasks, is used to provide an efficient mechanism to exploit nested concurrency. We have found the split‐join programming model to have an inherent implementation advantage, compared to the fork‐join model, when the number of processors in a machine becomes large.
A C++ Class for Rule‐Base Objects
Authors: Grenney William J.
Published: January 2015

A C++ class, called Tripod, was created as a tool to assist with the development of rule‐base decision support systems. The Tripod class contains data structures for the rule‐base and member functions for operating on the data. The rule‐base is defined by three ASCII files. These files are translated by a preprocessor into a single file that is located when a rule‐base object is instantiated. The Tripod class was tested as part of a proto‐type decision support system (DSS) for winter highway maintenance in the Intermountain West. The DSS is composed of two principal modules: the main program, called the wrapper, and a Tripod rule‐base object. The wrapper is a procedural module that interfaces with remote sensors and an external meterological database. The rule‐base contains the logic for advising an inexperienced user and for assisting with the decision making process.
Efficient Parallel Programming with Linda
Authors: Deshpande Ashish , Schultz Martin
Published: January 2015

Linda is a coordination language inverted by David Gelernter at Yale University, which when combined with a computation language (like C) yields a high‐level parallel programming language for MIMD machines. Linda is based on a virtual shared associative memory containing objects called tuples. Skeptics have long claimed that Linda programs could not be efficient on distributed memory architectures. In this paper, we address this claim by discussing C‐Linda′s performance in solving a particular scientific computing problem, the shallow water equations, and make comparisons with alternatives available on various shared and distributed memory parallel machines.
Speeding up N‐body Calculations on Machines without Hardware Square Root
Authors: Karp Alan H.
Published: January 2015

The most time consuming part of an N‐body simulation is computing the components of the accelerations of the particles. On most machines the slowest part of computing the acceleration is in evaluating r-3/2, which is especially true on machines that do the square root in software. This note shows how to cut the time for this part of the calculation by a factor of 3 or more using standard Fortran.
Parallel Array Classes and Lightweight Sharing Mechanisms
Authors: Otto Steve W.
Published: January 2015

We discuss a set of parallel array classes, MetaMP, for distributed‐memory architectures. The classes are implemented in C++ and interface to the PVM or Intel NX message‐passing systems. An array class implements a partitioned array as a set of objects distributed across the nodes – a "collective" object. Object methods hide the low‐level message‐passing and implement meaningful array operations. These include transparent guard strips (or sharing regions) that support finite‐difference stencils, reductions and multibroadcasts for support of pivoting and row operations, and interpolation/contraction operations for support of multigrid algorithms. The concept of guard strips is generalized to an object implementation of lightweight sharing mechanisms for finite element method (FEM) and particle‐in‐cell (PIC) algorithms. The sharing is accomplished through the mechanism of weak memory coherence and can be efficiently implemented. The price of the efficient implementation is memory usage and the need to explicitly specify the coherence operations. An intriguing feature of this programming model is that it maps well to both distributed‐memory and shared‐memory architectures.
A Parallel Implementation of Particle Tracking with Space Charge Effects on an Intel iPSC/860
Authors: Chang L. , Bourianoff G. , Cole B. , Machida S.
Published: January 2015

Particle‐tracking simulation is one of the scientific applications that is well suited to parallel computations. At the Superconducting Super Collider, it has been theoretically and empirically demonstrated that particle tracking on a designed lattice can achieve very high parallel efficiency on a MIMD Intel iPSC/860 machine. The key to such success is the realization that the particles can be tracked independently without considering their interaction. The perfectly parallel nature of particle tracking is broken if the interaction effects between particles are included. The space charge introduces an electromagnetic force that will affect the motion of tracked particles in three‐dimensional (3‐D) space. For accurate modeling of the beam dynamics with space charge effects, one needs to solve 3‐D Maxwell field equations, usually by a particle‐in‐cell (PIC) algorithm. This will require each particle to communicate with its neighbor grids to compute the momentum changes at each time step. It is expected that the 3‐D PIC method will degrade parallel efficiency of particle‐tracking implementation on any parallel computer. In this paper, we describe an efficient scheme for implementing particle tracking with space charge effects on an INTEL iPSC/860 machine. Experimental results show that a parallel efficiency of 75% can be obtained.
Instruction Scheduling Across Control Flow
Authors: Golumbic Martin Charles , Rainish Vladimir
Published: January 2015

Instruction scheduling algorithms are used in compilers to reduce run‐time delays for the compiled code by the reordering or transformation of program statements, usually at the intermediate language or assembly code level. Considerable research has been carried out on scheduling code within the scope of basic blocks, i.e., straight line sections of code, and very effective basic block schedulers are now included in most modern compilers and especially for pipeline processors. In previous work Golumbic and Rainis: IBM J. Res. Dev., Vol. 34, pp.93–97, 1990, we presented code replication techniques for scheduling beyond the scope of basic blocks that provide reasonable improvements of running time of the compiled code, but which still leaves room for further improvement. In this article we present a new method for scheduling beyond basic blocks called SHACOOF. This new technique takes advantage of a conventional, high quality basic block scheduler by first suppressing selected subsequences of instructions and then scheduling the modified sequence of instructions using the basic block scheduler. A candidate subsequence for suppression can be found by identifying a region of a program control flow graph, called an S‐region, which has a unique entry and a unique exit and meets predetermined criteria. This enables scheduling of a sequence of instructions beyond basic block boundaries, with only minimal changes to an existing compiler, by identifying beneficial opportunities to cover delays that would otherwise have been beyond its scope.
Sensitivity Analysis of a Dynamical System Using C++
Authors: Calhoun Donna , Overstreet Roy
Published: January 2015

This article introduces basic principles of first order sensitivity analysis and presents an algorithm that can be used to compute the sensitivity of a dynamical system to a selected parameter. This analysis is performed by extending with sensitivity equations the set of differential equations describing the dynamical system. These additional equations require the evaluation of partial derivatives, and so a technique known as the table algorithm, which can be used to exactly and automatically compute these derivatives, is described. A C++ class which can be used to implement the table algorithm is presented along with a driver routine for evaluating the output of a model and its sensitivity to a single parameter. The use of this driver routine is illustrated with a specific application from environmental hazards modeling.
The P4 Parallel Programming System, the Linda Environment, and Some Experiences with Parallel Computation
Authors: Larrabee Allan R.
Published: January 2015

The first digital computers consisted of a single processor acting on a single stream of data. In this so‐called "von Neumann" architecture, computation speed is limited mainly by the time required to transfer data between the processor and memory. This limiting factor has been referred to as the "von Neumann bottleneck". The concern that the miniaturization of silicon‐based integrated circuits will soon reach theoretical limits of size and gate times has led to increased interest in parallel architectures and also spurred research into alternatives to silicon‐based implementations of processors. Meanwhile, sequential processors continue to be produced that have increased clock rates and an increase in memory locally available to a processor, and an increase in the rate at which data can be transferred to and from memories, networks, and remote storage. The efficiency of compilers and operating systems is also improving over time. Although such characteristics limit maximum performance, a large improvement in the speed of scientific computations can often be achieved by utilizing more efficient algorithms, particularly those that support parallel computation. This work discusses experiences with two tools for large grain (or "macro task") parallelism.
Development of Generic Field Classes for Finite Element and Finite Difference Problems
Authors: Verner Diane A. , Heileman Gregory L. , Budge Kent G. , Robinson Allen C.
Published: January 2015

This article considers the development of a reusable object‐oriented array library, as well as the use of this library in the construction of finite difference and finite element codes. The classes in this array library are also generic enough to be used to construct other classes specific to finite difference and finite element methods. We demonstrate the usefulness of this library by inserting it into two existing object‐oriented scientific codes developed at Sandia National Laboratories. One of these codes is based on finite difference methods, whereas the other is based on finite element methods. Previously, these codes were separately maintained across a variety of sequential and parallel computing platforms. The use of object‐oriented programming allows both codes to make use of common base classes. This offers a number of advantages related to optimization and portability. Optimization efforts, particularly important in large scientific codes, can be focused on a single library. Furthermore, by encapsulating machine dependencies within this library, the optimization of both codes on different architec‐tures will only involve modification to a single library.
AIPS++ N‐Dimensional Array Classes
Authors: Willis A. G. , Healey M. P. , Glendenning B. E.
Published: January 2015

This article describes a set of C++ classes developed for the AIPS++ project. These classes handle arrays having an arbitrary number of dimensions. We give an overview of the methods available in these classes and show some simple examples of their use. Finally we describe the use of these classes to develop a radio astronomy application and discuss some of the performance issues that must be considered when these classes are used.
Number‐Crunching Software and the Input Problem: Guidelines and a Case Study
Authors: Gerber Stefan , Burkhart Helmar
Published: January 2015

Most of the number‐crunching software running on supercomputers lack a concept for an error‐free input processing. The programs often terminate after several hours due to user input errors. We present an analysis of this input problem. First, we separate the input parsing system from the number‐crunching code. Second, we define a general grammar suitable for an automatic generation of a parsing system using the LEX/YACC tools. This concept leads to an input system that is easy to use and the generated input data for the number‐crunching software is as error free as possible. We discuss the implementation of such an input system for an ab initio quantum chemical package.
High Performance Fortran: A Practical Analysis
Authors: Knies Allan , O′keefe Matthew , Macdonald Tom
Published: January 2015

The recently released high performance Fortran forum (HPFF) proposal has stirred much interest in the high performance computing industry. HPFF′s most important design goal is to create a language that has source code portability and that achieves high performance on single instruction multiple data (SIMD), distributed‐memory multiple instruction multiple data (MIMD), and shared‐memory MIMD architectures. The HPFF proposal brings to the forefront many questions about design of portable and efficient languages for parallel machines. In this article, we discuss issues that need to be addressed before an efficient production quality compiler will be available for any such language. We examine some specific issues that are related to HPF′s model of computation and analyze several implementation issues. We also provide some results from another data parallel compiler to help gain insight on some of the implementation issues that are relevant to HPF. Finally, we provide a summary of options currently available for application developers in industry.
Compiler Technology for Parallel Scientific Computation
Authors: Özturan Can , Sinharoy Balaram , Szymanski Boleslaw K.
Published: January 2015

There is a need for compiler technology that, given the source program, will generate efficient parallel codes for different architectures with minimal user involvement. Parallel computation is becoming indispensable in solving large‐scale problems in science and engineering. Yet, the use of parallel computation is limited by the high costs of developing the needed software. To overcome this difficulty we advocate a comprehensive approach to the development of scalable architecture‐independent software for scientific computation based on our experience with equational programming language (EPL). Our approach is based on a program decomposition, parallel code synthesis, and run‐time support for parallel scientific computation. The program decomposition is guided by the source program annotations provided by the user. The synthesis of parallel code is based on configurations that describe the overall computation as a set of interacting components. Run‐time support is provided by the compiler‐generated code that redistributes computation and data during object program execution. The generated parallel code is optimized using techniques of data alignment, operator placement, wavefront determination, and memory optimization. In this article we discuss annotations, configurations, parallel code generation, and run‐time support suitable for parallel programs written in the functional parallel programming language EPL and in Fortran.
Support for Implementing Scheduling Algorithms Using MESSIAHS
Authors: Chapin Steve J. , Spafford Eugene H.
Published: January 2015

The MESSIAHS project is investigating mechanisms that support task placement in heterogeneous, distributed, autonomous systems. MESSIAHS provides a substrate on which scheduling algorithms can be implemented. These mechanisms were designed to support diverse task placement and load balancing algorithms. As part of this work, we have constructed an interface layer to the underlying mechanisms. This includes the MESSIAHS interface language (MIL) and a library of function calls for constructing distributed schedulers. This article gives an overview of MESSIAHS, describes two sample interface layers in detail, and gives example implementations of well‐known algorithms from the literature built using these layers.
An Empirical Study of Precise Interprocedural Array Analysis
Authors: Hind Michael , Burke Michael , Carini Paul , Midkiff Sam
Published: January 2015

In this article we examine the role played by the interprocedural analysis of array accesses in the automatic parallelization of Fortran programs. We use the PTRAN system to provide measurements of several benchmarks to compare different methods of representing interprocedurally accessed arrays. We examine issues concerning the effectiveness of automatic parallelization using these methods and the efficiency of a precise summarization method.
PUMA: An Operating System for Massively Parallel Systems
Authors: Wheat Stephen R. , Maccabe Arthur B. , Riesen Rolf , Van Dresser David W. , Stallcup T. Mack
Published: January 2015

This article presents an overview of PUMA (Performance‐oriented, User‐managed Messaging Architecture), a message‐passing kernel for massively parallel systems. Message passing in PUMA is based on portals – an opening in the address space of an application process. Once an application process has established a portal, other processes can write values into the portal using a simple send operation. Because messages are written directly into the address space of the receiving process, there is no need to buffer messages in the PUMA kernel and later copy them into the applications address space. PUMA consists of two components: the quintessential kernel (Q‐Kernel) and the process control thread (PCT). Although the PCT provides management decisions, the Q‐Kernel controls access and implements the policies specified by the PCT.
The Performance of an Object‐Oriented, Parallel Operating System
Authors: Kohr, David R. , Zhang Xingbin , Rahman Mustafizur , Reed Daniel A.
Published: January 2015

The nascent and rapidly evolving state of parallel systems often leaves parallel application developers at the mercy of inefficient, inflexible operating system software. Given the relatively primitive state of parallel systems software, maximizing the performance of parallel applications not only requires judicious tuning of the application software, but occasionally, the replacement of specific system software modules with others that can more readily respond to the imposed pattern of resource demands. To assess the feasibility of application and performance tuning via malleable system software and to understand the performance penalties for detailed operating system performance data capture, we describe a set of performance instrumentation techniques for parallel, object‐oriented operating systems and a set of performance experiments with Choices, an experimental, object‐oriented operating system designed for use with parallel sys‐ tems. These performance experiments show that (a) the performance overhead for operating system data capture is modest, (b) the penalty for malleable, object‐oriented operating systems is negligible, but (c) techniques are needed to strictly enforce adherence of implementation to design if operating system modules are to be replaced.
Graph Contraction for Mapping Data on Parallel Computers: A Quality–Cost Tradeoff
Authors: Ponnusamy R. , Mansour N. , Choudhary A. , Fox G. C.
Published: January 2015

Mapping data to parallel computers aims at minimizing the execution time of the associated application. However, it can take an unacceptable amount of time in comparison with the execution time of the application if the size of the problem is large. In this article, first we motivate the case for graph contraction as a means for reducing the problem size. We restrict our discussion to applications where the problem domain can be described using a graph (e.g., computational fluid dynamics applications). Then we present a mapping‐oriented parallel graph contraction (PGC) heuristic algorithm that yields a smaller representation of the problem to which mapping is then applied. The mapping solution for the original problem is obtained by a straightforward interpolation. We then present experimental results on using contracted graphs as inputs to two physical optimization methods; namely, genetic algorithm and simulated annealing. The experimental results show that the PGC algorithm still leads to a reasonably good quality mapping solutions to the original problem, while producing a substantial reduction in mapping time. Finally, we discuss the cost‐quality tradeoffs in performing graph contraction.
Adaptive Dynamic Process Scheduling on Distributed Memory Parallel Computers
Authors: Shu Wei
Published: January 2015

One of the challenges in programming distributed memory parallel machines is deciding how to allocate work to processors. This problem is particularly important for computations with unpredictable dynamic behaviors or irregular structures. We present a scheme for dynamic scheduling of medium‐grained processes that is useful in this context. The adaptive contracting within neighborhood (ACWN) is a dynamic, distributed, load‐dependent, and scalable scheme. It deals with dynamic and unpredictable creation of processes and adapts to different systems. The scheme is described and contrasted with two other schemes that have been proposed in this context, namely the randomized allocation and the gradient model. The performance of the three schemes on an Intel iPSC/2 hypercube is presented and analyzed. The experimental results show that even though the ACWN algorithm incurs somewhat larger overhead than the randomized allocation, it achieves better performance in most cases due to its adaptiveness. Its feature of quickly spreading the work helps it outperform the gradient model in performance and scalability.
Parallel Algorithms for Molecular Dynamics Simulation of Irradiation Effects in Crystals
Authors: Glikman Eli , Ioffe Ludmila , Kelson Itzhak , Pinter Shlomit S.
Published: January 2015

We present new parallel algorithms for solving the problem of many body interactions in molecular dynamics (MD). Such algorithms are essential in the simulation of irradiation effects in crystals, where the high energy of the impinging particles dictates computing with large numbers of atoms and for many time cycles. We realized the algorithms using two parallelization methods and compared their performance. Experimental results obtained on a Meiko machine demonstrate that the new algorithms exploit parallelism effectively and can be used to simulate large crystals.