GPU Accelerated Particle Visualization with Splotch

Splotch is a rendering algorithm for exploration and visual discovery in particle-based datasets coming from astronomical observations or numerical simulations. The strengths of the approach are production of high quality imagery and support for very large-scale datasets through an effective mix of the OpenMP and MPI parallel programming paradigms. This article reports our experiences in re-designing Splotch for exploiting emerging HPC architectures nowadays increasingly populated with GPUs. A performance model is introduced for data transfers, computations and memory access, to guide our re-factoring of Splotch. A number of parallelization issues are discussed, in particular relating to race conditions and workload balancing, towards achieving optimal performances. Our implementation was accomplished by using the CUDA programming paradigm. Our strategy is founded on novel schemes achieving optimized data organisation and classification of particles. We deploy a reference simulation to present performance results on acceleration gains and scalability. We finally outline our vision for future work developments including possibilities for further optimisations and exploitation of emerging technologies.Comment: 25 pages, 9 figures. Astronomy and Computing (2014

Evaluating Versal AI Engines for option price discovery in market risk analysis

Whilst Field-Programmable Gate Arrays (FPGAs) have been popular in accelerating high-frequency financial workload for many years, their application in quantitative finance, the utilisation of mathematical models to analyse financial markets and securities, is less mature. Nevertheless, recent work has demonstrated the benefits that FPGAs can deliver to quantitative workloads, and in this paper, we study whether the Versal ACAP and its AI Engines (AIEs) can also deliver improved performance. We focus specifically on the industry standard Strategic Technology Analysis Center's (STAC) derivatives risk analysis benchmark STAC-A2. Porting a purely FPGA-based accelerator STAC-A2 inspired market risk (SIMR) benchmark to the Versal ACAP device by combining Programmable Logic (PL) and AIEs, we explore the development approach and techniques, before comparing performance across PL and AIEs. Ultimately, we found that our AIE approach is slower than a highly optimised existing PL-only version due to limits on both the AIE and PL that we explore and describe

Bostonia

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

The US Navy coupled ocean-wave prediction system

A new coupled ocean-wave model has been developed and tested as a new component of the Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS(circle)). The modeling system is comprised of the Simulating WAves Nearshore (SWAN) wave model and the Navy Coastal Ocean Model (NCOM). The models are two-way coupled using the Earth System Modeling Framework (ESMF). The ocean model has been modified to incorporate the effect of the Stokes drift current, wave radiation stresses due to horizontal gradients of the momentum flux of surface waves, enhancement of bottom drag in shallow water, and enhanced vertical mixing due to Langmuir turbulence. The wave model ingests surface currents (wave-current interaction) and water levels. The system is designed to support the Navy's ocean forecast requirements for regional and coastal domains. Validation studies for the Florida Straits and Virginia coastal area are presented. The system will run at the Naval Oceanographic Office and at the Fleet Numerical Meteorology and Oceanography Center

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

RtD Comics: A Medium for Representing Research Through Design

This paper argues that comics are a powerful and valuable medium for representing research through design. We review different formats for representing design including the academic paper, the photo-essay and the annotated portfolio. We argue that the comic book form can be better suited to representing various aspects of the design process including interaction, form and aesthetics. We illustrate our argument with examples taken from a comic book about the design of Paper Street View, an interactive system, which allows users to navigate Google Street View with a paper map and brass marker. We argue that comics are well suited to capturing the dynamic process of making, the dialogue and different viewpoints that contribute to interdisciplinary work as well as the interactive and aesthetic elements of a final design