Software engineering to sustain a high-performance computing scientific application: QMCPACK

We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions runners, and NVIDIA and AMD GPUs in pre-exascale systems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.Comment: Accepted at the first US-RSE Conference, USRSE2023, https://us-rse.org/usrse23/, 8 pages, 3 figures, 4 table

A Large Scale Survey of NGC1333

We observed the clustered star forming complex NGC1333 with the BIMA and FCRAO telescopes in the transitions HCO+(1-0) and N2H+(1-0) over an 11'x11' area with resolution ~10" (0.015pc). The N2H+ emission follows very closely the submillimeter dust continuum emission, while HCO+ emission appears more spatially extended and also traces outflows. We have identified 93 N2H+ cores using the CLUMPFIND algorithm, and we derive N2H+ core masses between 0.05 and 2.5M_sun, with uncertainties of a factor of a few, dominated by the adopted N2H+ abundance. From a comparison with virial masses, we argue that most of these N2H+ cores are likely to be bound, even at the lowest masses, suggesting that the cores do not trace transient structures, and implies the entire mass distribution consists of objects that can potentially form stars. We find that the mass distribution of N2H+ cores resembles the field star IMF, which suggests that the IMF is locked in at the pre-stellar stage of evolution. We find that the N2H+ cores associated with stars identified from Spitzer infrared images have a flat mass distribution. This might be because lower mass cores lose a larger fraction of their mass when forming a star. Even in this clustered environment, we find no evidence for ballistic motions of the cores relative to their lower density surroundings traced by isotopic CO emission, though this conclusion must remain tentative until the surroundings are observed at the same high resolution as the N2H+.Comment: 35 pages, 13 figure

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A New Class of Safe Oligosaccharide Polymer Therapy To Modify the Mucus Barrier of Chronic Respiratory Disease

The host- and bacteria-derived extracellular polysaccharide coating of the lung is a considerable challenge in chronic respiratory disease and is a powerful barrier to effective drug delivery. A low molecular weight 12–15-mer alginate oligosaccharide (OligoG CF-5/20), derived from plant biopolymers, was shown to modulate the polyanionic components of this coating. Molecular modeling and Fourier transform infrared spectroscopy demonstrated binding between OligoG CF-5/20 and respiratory mucins. Ex vivo studies showed binding induced alterations in mucin surface charge and porosity of the three-dimensional mucin networks in cystic fibrosis (CF) sputum. Studies in Humans showed that OligoG CF-5/20 is safe for inhalation in CF patients with effective lung deposition and modifies the viscoelasticity of CF-sputum. OligoG CF-5/20 is the first inhaled polymer therapy, represents a novel mechanism of action and therapeutic approach for the treatment of chronic respiratory disease, and is currently in Phase IIb clinical trials for the treatment of CF

Inclusive jet cross sections and dijet correlations in D∗±D^{*\pm} photoproduction at HERA

Inclusive jet cross sections in photoproduction for events containing a $D^*$ meson have been measured with the ZEUS detector at HERA using an integrated luminosity of $78.6 {\rm pb}^{-1}$. The events were required to have a virtuality of the incoming photon, $Q^2$, of less than 1 GeV$^2$, and a photon-proton centre-of-mass energy in the range $130<W_{\gamma p}<280 {\rm GeV}$. The measurements are compared with next-to-leading-order (NLO) QCD calculations. Good agreement is found with the NLO calculations over most of the measured kinematic region. Requiring a second jet in the event allowed a more detailed comparison with QCD calculations. The measured dijet cross sections are also compared to Monte Carlo (MC) models which incorporate leading-order matrix elements followed by parton showers and hadronisation. The NLO QCD predictions are in general agreement with the data although differences have been isolated to regions where contributions from higher orders are expected to be significant. The MC models give a better description than the NLO predictions of the shape of the measured cross sections.Comment: 43 pages, 12 figures, charm jets ZEU

Dissociation of virtual photons in events with a leading proton at HERA

The ZEUS detector has been used to study dissociation of virtual photons in events with a leading proton, gamma^* p -> X p, in e^+p collisions at HERA. The data cover photon virtualities in two ranges, 0.03<Q^2<0.60 GeV^2 and 2<Q^2<100 GeV^2, with M_X>1.5 GeV, where M_X is the mass of the hadronic final state, X. Events were required to have a leading proton, detected in the ZEUS leading proton spectrometer, carrying at least 90% of the incoming proton energy. The cross section is presented as a function of t, the squared four-momentum transfer at the proton vertex, Phi, the azimuthal angle between the positron scattering plane and the proton scattering plane, and Q^2. The data are presented in terms of the diffractive structure function, F_2^D(3). A next-to-leading-order QCD fit to the higher-Q^2 data set and to previously published diffractive charm production data is presented

Visualisation to enhance biomechanical tuning of ankle-foot orthoses (AFOs) in stroke: study protocol for a randomised controlled trial

There are a number of gaps in the evidence base for the use of ankle-foot orthoses for stroke patients. Three dimensional motion analysis offers an ideal method for objectively obtaining biomechanical gait data from stroke patients, however there are a number of major barriers to its use in routine clinical practice. One significant problem is the way in which the biomechanical data generated by these systems is presented. Through the careful design of bespoke biomechanical visualisation software it may be possible to present such data in novel ways to improve clinical decision making, track progress and increase patient understanding in the context of ankle-foot orthosis tuning

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie