High-level programming of stencil computations on multi-GPU systems using the SkelCL library

The implementation of stencil computations on modern, massively parallel systems with GPUs and other accelerators currently relies on manually-tuned coding using low-level approaches like OpenCL and CUDA. This makes development of stencil applications a complex, time-consuming, and error-prone task. We describe how stencil computations can be programmed in our SkelCL approach that combines high-level programming abstractions with competitive performance on multi-GPU systems. SkelCL extends the OpenCL standard by three high-level features: 1) pre-implemented parallel patterns (a.k.a. skeletons); 2) container data types for vectors and matrices; 3) automatic data (re)distribution mechanism. We introduce two new SkelCL skeletons which specifically target stencil computations – MapOverlap and Stencil – and we describe their use for particular application examples, discuss their efficient parallel implementation, and report experimental results on systems with multiple GPUs. Our evaluation of three real-world applications shows that stencil code written with SkelCL is considerably shorter and offers competitive performance to hand-tuned OpenCL code

Introducing Parallelism to the Ranges TS

The current interface provided by the C++17 parallel algorithms poses some limitations with respect to parallel data access and heterogeneous systems, such as personal computers and server nodes with GPUs, smartphones, and embedded System on a Chip chipsets. In this paper, we present a summary of why we believe the Ranges TS solves these problems, and also improves both programmability and performance on heterogeneous platforms. The complete paper has been submitted to WG21 for consideration, and here we present a summary of the changes proposed alongside new performance results. To the best of our knowledge, this is the first paper presented to WG21 that unifies the Ranges TS with the parallel algorithms introduced in C++17. Although there are various points of intersection, we will focus on the composability of functions, and the benefit that this brings to accelerator devices via kernel fusion

Lifetime Analysis of Energy Storage Systems for Sustainable Transportation

On the path to a low-carbon future, advancements in energy storage seem to be achieved on a nearly daily basis. However, for the use-case of sustainable transportation, only a handful of technologies can be considered, as these technologies must be reliable, economical, and suitable for transportation applications. This paper describes the characteristics and aging process of two well-established and commercially available technologies, namely Lithium-Ion batteries and supercaps, and one less known system, flywheel energy storage, in the context of public transit buses. Beyond the obvious use-case of onboard energy storage, stationary buffer storage inside the required fast-charging stations for the electric vehicles is also discussed. Calculations and considerations are based on actual zero-emission buses operating in Graz, Austria. The main influencing parameters and effects related to energy storage aging are analyzed in detail.Based on the discussed aging behavior, advantages, disadvantages, and a techno-economic analysis for both use-cases is presented. A final suitability assessment of each energy storage technology concludes the use-case analysis. Document type: Articl

Towards Composable GPU Programming: Programming GPUs with Eager Actions and Lazy Views

In this paper, we advocate a composable approach to programming systems with Graphics Processing Units (GPU): programs are developed as compositions of generic, reusable patterns. Current GPU programming approaches either rely on low-level, monolithic code without patterns (CUDA and OpenCL), which achieves high performance at the cost of cumbersome and error-prone programming, or they improve the programmability by using pattern-based abstractions (e.g., Thrust) but pay a performance penalty due to inefficient implementations of pattern composition. We develop an API for GPUs based programming on C++ with STL-style patterns and its compiler-based implementation. Our API gives the application developers the native C++ means (views and actions) to specify precisely which pattern compositions should be automatically fused during code generation into a single efficient GPU kernel, thereby ensuring a high target performance. We implement our approach by extending the range-v3 library which is currently being developed for the forthcoming C++ standards. The composable programming in our approach is done exclusively in the standard C++14, with STL algorithms used as patterns which we re-implemented in parallel for GPU. Our compiler implementation is based on the LLVM and Clang frameworks, and we use advanced multi-stage programming techniques for aggressive runtime optimizations. We experimentally evaluate our approach using a set of benchmark applications and a real-world case study from the area of image processing. Our codes achieve performance competitive with CUDA monolithic implementations, and we outperform pattern-based codes written using Nvidia’s Thrust

The endogenous thrombin potential in patients with left ventricular assist device or heart transplant

BackgroundThe Heartmate 3 (HM 3) is a left ventricular assist device featuring less shear stress, milder acquired von Willebrand syndrome, and fewer bleeding incidences than its predecessor the Heartmate II (HM II). The novel surface coating of the HM 3 suggests less contact activation of plasmatic coagulation. We hypothesized that patients with HM 3 exhibit fewer aberrations in their thrombin potential than patients with HM II. We compared these results with the thrombin potential of patients with heart transplantation (HTX).MethodsThrombin generation in plasma samples of patients with HM II (n = 16), HM 3 (n = 20), and HTX (n = 13) was analyzed 3 days after implantation/transplantation and after long-term support (3–24 months) with HM II (n = 16) or HM 3 (n = 12) using calibrated automated thrombography. Heparin in postoperative samples was antagonized with polybrene.ResultsThree days postoperatively HM II patients exhibited a lower endogenous thrombin potential (ETP) than HM 3 and HTX patients (HM II: 947 ± 291 nM*min; HM 3: 1231 ± 176 nM*min; HTX: 1376 ± 162 nM*min, p < 0.001) and a lower velocity index of thrombin generation (HM II: 18.74 ± 10.90 nM/min; HM 3: 32.41 ± 9.51 nM/min; HTX: 37.65 ± 9.41 nM/min, p < 0.01). Subtle differences in the thrombin generation profiles remained in HM II and HM 3 patients under long-term support (Velocity Index: HM II: 38.70 ± 28.46 nM/min; HM 3: 73.32 ± 32.83 nM/min, p < 0.05). Prothrombin fragments 1 + 2 were higher in HM II than in HM 3 patients (HM II: 377.7 ± 208.4 pM; HM 3: 202.1 ± 87.7 pM, p < 0.05) and correlated inversely with the ETP (r = −0.584, p < 0.05).ConclusionWe observed a more aberrant thrombin generation in HM II than in HM 3 despite comparable anticoagulation and routine parameters. A trend toward lower values was still observable in HM 3 compared to HTX patients. Calibrated automated thrombography may be a good tool to monitor the coagulation state of these patients and guide anticoagulation in the future

Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study

BackgroundThe PERFORM study aimed to understand causes of febrile childhood illness by comparing molecular pathogen detection with current clinical practice.MethodsFebrile children and controls were recruited on presentation to hospital in 9 European countries 2016-2020. Each child was assigned a standardized diagnostic category based on retrospective review of local clinical and microbiological data. Subsequently, centralised molecular tests (CMTs) for 19 respiratory and 27 blood pathogens were performed.FindingsOf 4611 febrile children, 643 (14%) were classified as definite bacterial infection (DB), 491 (11%) as definite viral infection (DV), and 3477 (75%) had uncertain aetiology. 1061 controls without infection were recruited. CMTs detected blood bacteria more frequently in DB than DV cases for N. meningitidis (OR: 3.37, 95% CI: 1.92-5.99), S. pneumoniae (OR: 3.89, 95% CI: 2.07-7.59), Group A streptococcus (OR 2.73, 95% CI 1.13-6.09) and E. coli (OR 2.7, 95% CI 1.02-6.71). Respiratory viruses were more common in febrile children than controls, but only influenza A (OR 0.24, 95% CI 0.11-0.46), influenza B (OR 0.12, 95% CI 0.02-0.37) and RSV (OR 0.16, 95% CI: 0.06-0.36) were less common in DB than DV cases. Of 16 blood viruses, enterovirus (OR 0.43, 95% CI 0.23-0.72) and EBV (OR 0.71, 95% CI 0.56-0.90) were detected less often in DB than DV cases. Combined local diagnostics and CMTs respectively detected blood viruses and respiratory viruses in 360 (56%) and 161 (25%) of DB cases, and virus detection ruled-out bacterial infection poorly, with predictive values of 0.64 and 0.68 respectively.InterpretationMost febrile children cannot be conclusively defined as having bacterial or viral infection when molecular tests supplement conventional approaches. Viruses are detected in most patients with bacterial infections, and the clinical value of individual pathogen detection in determining treatment is low. New approaches are needed to help determine which febrile children require antibiotics.FundingEU Horizon 2020 grant 668303

Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens

Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children