Verified lifting of stencil computations

This paper demonstrates a novel combination of program synthesis and verification to lift stencil computations from low-level Fortran code to a high-level summary expressed using a predicate language. The technique is sound and mostly automated, and leverages counter-example guided inductive synthesis (CEGIS) to find provably correct translations. Lifting existing code to a high-performance description language has a number of benefits, including maintainability and performance portability. For example, our experiments show that the lifted summaries can enable domain specific compilers to do a better job of parallelization as compared to an off-the-shelf compiler working on the original code, and can even support fully automatic migration to hardware accelerators such as GPUs. We have implemented verified lifting in a system called STNG and have evaluated it using microbenchmarks, mini-apps, and real-world applications. We demonstrate the benefits of verified lifting by first automatically summarizing Fortran source code into a high-level predicate language, and subsequently translating the lifted summaries into Halide, with the translated code achieving median performance speedups of 4.1X and up to 24X for non-trivial stencils as compared to the original implementation.United States. Department of Energy. Office of Science (Award DE-SC0008923)United States. Department of Energy. Office of Science (Award DE-SC0005288

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Environmental impact assessment of a scrap tyre artificial reef

Scrap tyres have been widely used around the world to construct artificial reefs. They are a popular construction material, being readily available at no cost, durable, and with large void spaces. However, published information about the environmental impact of tyres in the marine environment is limited. When used, successful colonization by epibiota and mobile species seems to be taken as empirical proof of their suitability. In 1998, an experimental scrap tyre artificial reef was constructed in Poole Bay to provide data on the environmental impact of the material. Epibiotic colonization is being monitored for comparison with that on concrete control modules deployed at the same time. Samples of the epibiota have been analysed for heavy metals and organic compounds. Results from the first year of deployment are presented

Environmental impact assessment of a scrap tyre artificial reef

Scrap tyres have been widely used around the world to construct artificial reefs. They are a popular construction material, being readily available at no cost, durable, and with large void spaces. However, published information about the environmental impact of tyres in the marine environment is limited. When used, successful colonization by epibiota and mobile species seems to be taken as empirical proof of their suitability. In 1998, an experimental scrap tyre artificial reef was constructed in Poole Bay to provide data on the environmental impact of the material. Epibiotic colonization is being monitored for comparison with that on concrete control modules deployed at the same time. Samples of the epibiota have been analysed for heavy metals and organic compounds. Results from the first year of deployment are presented

Estimating tectonic uplift of the Cape Fear Arch (south-eastern United States) using reconstructions of Holocene relative sea level

We use relative sea-level (RSL) reconstructions and a spatiotemporal statistical model to estimate the rate of uplift of the Cape Fear Arch, a Mesozoic structural high, during the last ~4000 years. We reconstructed RSL using 12 radiocarbon-dated samples of basal salt-marsh sediment preserved at Elizabeth Creek Marsh on the Cape Fear River. The new data show that RSL rose by ~3m during the past ~4.6 ka at an average rate of 0.67±0.12mm a-1. RSL reconstructions from other sites in southern North Carolina (which have rates of 0.91±0.10 to 0.84±0.24mm a-1) probably show (P>0.9) higher rates of regional RSL rise for the same period, while sites from northern South Carolina (which have rates of 0.72±0.17 to 0.80±0.21mm a-1) probably (P>0.67) show the same. We attribute the differences between Elizabeth Creek Marsh and neighboring regions to uplift of the Cape Fear Arch, which we estimate to be 0.24±0.15mm a-1. Uplift of the arch may be responsible for lower rates of 20th century RSL rise recorded by the Wilmington tide gauge relative to rates measured elsewhere along the US mid-Atlantic coast