MPI Advance : Open-Source Message Passing Optimizations

The large variety of production implementations of the message passing interface (MPI) each provide unique and varying underlying algorithms. Each emerging supercomputer supports one or a small number of system MPI installations, tuned for the given architecture. Performance varies with MPI version, but application programmers are typically unable to achieve optimal performance with local MPI installations and therefore rely on whichever implementation is provided as a system install. This paper presents MPI Advance, a collection of libraries that sit on top of MPI, optimizing the underlying performance of any existing MPI library. The libraries provide optimizations for collectives, neighborhood collectives, partitioned communication, and GPU-aware communication.Comment: Available on conference website : https://eurompi23.github.io/assets/papers/EuroMPI23_paper_33.pd

Collective-Optimized FFTs

This paper measures the impact of the various alltoallv methods. Results are analyzed within Beatnik, a Z-model solver that is bottlenecked by HeFFTe and representative of applications that rely on FFTs

Overview of ExaMPI

ExaMPI is a new, experimental implementation of the Message Passing Interface (MPI) Standard. Our goal is to enable researchers to experiment rapidly and easily with new concepts, algorithms, and internal protocols for MPI

A Few Points on Point-to-Point Correlation Functions

The short-time regime of QCD two-point correlation functions is examined through a QCD-Sum-Rule-inspired continuum model. QCD Sum Rule techniques are tested and alternate nucleon interpolating fields are discussed. The techniques presented here may be of practical use in determining heavy-light meson decay constants.Comment: Lattice '93 presentation. UU-File is a single postscript file of a 4 page manuscript including figures. Ohio State U. PP #93-112

Implementation-Oblivious Transparent Checkpoint-Restart for MPI

This work presents experience with traditional use cases of checkpointing on a novel platform. A single codebase (MANA) transparently checkpoints production workloads for major available MPI implementations: "develop once, run everywhere". The new platform enables application developers to compile their application against any of the available standards-compliant MPI implementations, and test each MPI implementation according to performance or other features.Comment: 17 pages, 4 figure

Comparison of |Q|=1 and |Q|=2 gauge-field configurations on the lattice four-torus

It is known that exactly self-dual gauge-field configurations with topological charge |Q|=1 cannot exist on the untwisted continuum 4-torus. We explore the manifestation of this remarkable fact on the lattice 4-torus for SU(3) using advanced techniques for controlling lattice discretization errors, extending earlier work of De Forcrand et. al. for SU(2). We identify three distinct signals for the instability of |Q|=1 configurations, and show that these manifest themselves early in the cooling process, long before the would-be instanton has shrunk to a size comparable to the lattice discretization threshold. These signals do not appear for our |Q|=2 configurations. This indicates that these signals reflect the truly global nature of the instability, rather than local discretization effects. Monte-Carlo generated SU(3) gauge field configurations are cooled to the self-dual limit using an O(a^4)-improved gauge action chosen to have small but positive O(a^6) errors. This choice prevents lattice discretization errors from destroying instantons provided their size exceeds the dislocation threshold of the cooling algorithm. Lattice discretization errors are evaluated by comparing the O(a^4)-improved gauge-field action with an O(a^4)-improved action constructed from the square of an O(a^4)-improved lattice field-strength tensor, thus having different O(a^6) discretization errors. The number of action-density peaks, the instanton size and the topological charge of configurations is monitored. We observe a fluctuation in the total topological charge of |Q|=1 configurations, and demonstrate that the onset of this unusual behavior corresponds with the disappearance of multiple-peaks in the action density. At the same time discretization errors are minimal.Comment: 12 pages, 9 figures, submitted to Phys. Rev.

Cardiorespiratory Phase-Coupling Is Reduced in Patients with Obstructive Sleep Apnea

Cardiac and respiratory rhythms reveal transient phases of phase-locking which were proposed to be an important aspect of cardiorespiratory interaction. The aim of this study was to quantify cardio-respiratory phase-locking in obstructive sleep apnea (OSA). We investigated overnight polysomnography data of 248 subjects with suspected OSA. Cardiorespiratory phase-coupling was computed from the R-R intervals of body surface ECG and respiratory rate, calculated from abdominal and thoracic sensors, using Hilbert transform. A significant reduction in phase-coupling was observed in patients with severe OSA compared to patients with no or mild OSA. Cardiorespiratory phase-coupling was also associated with sleep stages and was significantly reduced during rapid-eye-movement (REM) sleep compared to slow-wave (SW) sleep. There was, however, no effect of age and BMI on phase coupling. Our study suggests that the assessment of cardiorespiratory phase coupling may be used as an ECG based screening tool for determining the severity of OSA

Psychometric properties of the Tinnitus Functional Index (TFI): assessment in a UK research volunteer population

Objectives Questionnaires are essential for measuring tinnitus severity and intervention-related change but there is no standard instrument used routinely in research settings. Most tinnitus questionnaires are optimised for measuring severity but not change. However, the Tinnitus Functional Index (TFI) claims to be optimised for both. It has not however been fully validated for research purposes. Here we evaluate the relevant psychometric properties of the TFI, specifically the questionnaire factor structure, reproducibility, validity and responsiveness guided by quality criteria for the measurement properties of health-related questionnaires. Methods The study involved a retrospective analysis of data collected for 294 members of the general public who participated in a randomised controlled trial of a novel tinnitus device (ClinicalTrials.gov Identifier: NCT01541969). Participants completed up to eight commonly used assessment questionnaires including the TFI, Tinnitus Handicap Inventory (THI), Tinnitus Handicap Questionnaire (THQ), a Visual Analogue Scale of loudness (VAS-Loudness), Percentage Annoyance question, the Beck's Depression Inventory (BDI), Beck's Anxiety Inventory (BAI), and the World Health Organisation Quality of Life-Bref (WHOQOL-BREF). A series of analyses assessed the study objectives. Forty four participants completed the TFI at a second visit (within 7–21 days and before receiving any intervention) providing data for reproducibility assessments. Results The 8-factor structure was not fully confirmed for this general (non-clinical) population. Whilst it was acceptable standalone subscale, the ‘auditory’ factor showed poor loading with the higher order factor ‘functional impact of tinnitus’. Reproducibility assessments for the overall TFI indicate high internal consistency (α = 0.80) and extremely high reliability (ICC: 0.91), whilst agreement was borderline acceptable (93%). Construct validity was demonstrated by high correlations between scores on the TFI and THI (r = 0.82) and THQ (r = 0.82), moderate correlations with VAS-L (r = 0.46), PR-A (r = 0.58), BDI (r = 0.57), BAI (r = 0.39) and WHOQOL (r = −0.48). Floor effects were observed for more than 50% of the items. A smallest detectable change score of 22.4 is proposed for the TFI global score. Conclusion Even though the proposed 8-factor structure was not fully confirmed for this population, the TFI appears to cover multiple symptom domains, and to measure the construct of tinnitus with an excellent reliability in distinguishing between patients. While the TFI may discriminate those whose tinnitus is not a problem, floor effects in many items means it is less appropriate as a measure of change in this subgroup. Further investigation is needed to determine whether these effects are relevant in other populations

Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan

Cells are organized into distinct compartments to perform specific tasks with spatial precision. In neurons, presynaptic specializations are biochemically complex subcellular structures dedicated to neurotransmitter secretion. Activity-dependent changes in the abundance of presynaptic proteins are thought to endow synapses with different functional states; however, relatively little is known about the rules that govern changes in the composition of presynaptic terminals. We describe a genetic strategy to systematically analyze protein localization at Caenorhabditis elegans presynaptic specializations. Nine presynaptic proteins were GFP-tagged, allowing visualization of multiple presynaptic structures. Changes in the distribution and abundance of these proteins were quantified in 25 mutants that alter different aspects of neurotransmission. Global analysis of these data identified novel relationships between particular presynaptic components and provides a new method to compare gene functions by identifying shared protein localization phenotypes. Using this strategy, we identified several genes that regulate secretion of insulin-like growth factors (IGFs) and influence lifespan in a manner dependent on insulin/IGF signaling