Heterogeneous CPU/GPU co-execution of CFD simulations on the POWER9 architecture: Application to airplane aerodynamics

High fidelity Computational Fluid Dynamics simulations are generally associated with large computing requirements, which are progressively acute with each new generation of supercomputers. However, significant research efforts are required to unlock the computing power of leading-edge systems, currently referred to as pre-Exascale systems, based on increasingly complex architectures. In this paper, we present the approach implemented in the computational mechanics code Alya. We describe in detail the parallelization strategy implemented to fully exploit the different levels of parallelism, together with a novel co-execution method for the efficient utilization of heterogeneous CPU/GPU architectures. The latter is based on a multi-code co-execution approach with a dynamic load balancing mechanism. The assessment of the performance of all the proposed strategies has been carried out for airplane simulations on the POWER9 architecture accelerated with NVIDIA Volta V100 GPUs

On the benefits of tasking with OpenMP

Tasking promises a model to program parallel applications that provides intuitive semantics. In the case of tasks with dependences, it also promises better load balancing by removing global synchronizations (barriers), and potential for improved locality. Still, the adoption of tasking in production HPC codes has been slow. Despite OpenMP supporting tasks, most codes rely on worksharing-loop constructs alongside MPI primitives. This paper provides insights on the benefits of tasking over the worksharing-loop model by reporting on the experience of taskifying an adaptive mesh refinement proxy application: miniAMR. The performance evaluation shows the taskified implementation being 15–30% faster than the loop-parallel one for certain thread counts across four systems, three architectures and four compilers thanks to better load balancing and system utilization. Dynamic scheduling of loops narrows the gap but still falls short of tasking due to serial sections between loops. Locality improvements are incidental due to the lack of locality-aware scheduling. Overall, the introduction of asynchrony with tasking lives up to its promises, provided that programmers parallelize beyond individual loops and across application phases.Peer ReviewedPostprint (author's final draft

Spatial Division Multiplexed Microwave Signal processing by selective grating inscription in homogeneous multicore fibers

[EN] The use of Spatial Division Multiplexing for Microwave Photonics signal processing is proposed and experimentally demonstrated, for the first time to our knowledge, based on the selective inscription of Bragg gratings in homogeneous multicore fibers. The fabricated devices behave as sampled true time delay elements for radiofrequency signals offering a wide range of operation possibilities within the same optical fiber. The key to processing flexibility comes from the implementation of novel multicavity configurations by inscribing a variety of different fiber Bragg gratings along the different cores of a 7-core fiber. This entails the development of the first fabrication method to inscribe high-quality gratings characterized by arbitrary frequency spectra and located in arbitrary longitudinal positions along the individual cores of a multicore fiber. Our work opens the way towards the development of unique compact fiber-based solutions that enable the implementation of a wide variety of 2D (spatial and wavelength diversity) signal processing functionalities that will be key in future fiber-wireless communications scenarios. We envisage that Microwave Photonics systems and networks will benefit from this technology in terms of compactness, operation versatility and performance stability.We thank Prof. Jose Capmany for the thoughtful discussions and recommendations that greatly contribute to this work. This research was supported by the Spanish MINECO Projects TEC2014-60378-C2-1-R and TEC2015-62520-ERC, the Valencian Research Excellency Award Program GVA PROMETEO 2013/012, the Spanish MECD FPU Scholarship (FPU13/04675) for J. Hervas, and the Spanish MINECO Ramon y Cajal Program (RYC-2014-16247) for I. Gasulla.Gasulla Mestre, I.; Barrera Vilar, D.; Hervás-Peralta, J.; Sales Maicas, S. (2017). Spatial Division Multiplexed Microwave Signal processing by selective grating inscription in homogeneous multicore fibers. Scientific Reports. 7(41727):1-10. https://doi.org/10.1038/srep41727S110741727Samsung Electronics Co, “5G Vision”, available at http://www.samsung.com/global/business-images/insights/2015/Samsung-5G-Vision-0.pdf (2015).Technology Focus on Microwave Photonics. Nat. Photonics 5, 723 (2011).J. Capmany, J. Mora, I. Gasulla, J. Sancho, J. Lloret & S. Sales . Microwave photonic signal processing. IEEE J. Lightw. Technol. 31, 571–586 (2013).Y. Long & J. Wang . Ultra-high peak rejection notch microwave photonic filter using a single silicon microring resonator. Opt. Express 23, 17739–17750 (2015).Y. Long & J. Wang . All-optical tuning of a nonlinear silicon microring assisted microwave photonic filter: theory and experiment. Opt. Express 23, 17758–17771 (2015).Y. Long, L. Zhou & J. Wang . Photonic-assisted microwave signal multiplication and modulation using a silicon Mach–Zehnder modulator. Sci. Reports 6, 20215 (2016).J. Sancho, J. Bourderionnet, J. Lloret, S. Combrié, I. Gasulla, S. Xavier, S. Sales, P. Colman, G. Lehoucq, D. Dolfi, J. Capmany & A. De Rossi . Integrable microwave filter based on a photonic crystal delay line. Nat. Commun. 3, 1075 (2012).F. Ohman, K. Yvind & J. Mørk . Slow Light in a Semiconductor Waveguide for True-Time Delay Applications in Microwave Photonics. IEEE Photon. Technol. Lett. 19, 1145–1157 (2007).P. A. Morton & J. B. Khurgin. Microwave photonic delay line with separate tuning of the optical carrier. IEEE Photon. Technol. Lett. 21, 1686–1688 (2009).D. Marpaung, C. Roeloffzen, R. Heideman, A. Leinse, S. Sales & J. Capmany . Integrated microwave photonics. Lasers Photon. Rev. 7, 506–538 (2013).I. Gasulla & J. Capmany . Microwave photonics applications of multicore fibers. Photonics J. 4, 877–888 (2012).S. Garcia & I. Gasulla . Design of Heterogeneous Multicore fibers as sampled True Time Delay Lines. Opt. Lett. 40, 621–624 (2015).F. Zeng & J. Yao . All-optical microwave filters using uniform fiber Bragg gratings with identical reflectivities. IEEE J. Lightw. Technol. 23, 1410 (2005).C. Wang & J. Yao . Fiber Bragg gratings for microwave photonics subsystems. Opt. Express 21, 22868–22884 (2013).I. Gasulla, D. Barrera & S. Sales . Microwave photonic devices based on multicore fibers. 16th International Conference on Transparent Optical Networks (ICTON), Graz, Austria, 2014.I. Gasulla, D. Barrera, J. Hervás, S. García & S. Sales . Multi-cavity Microwave Photonics devices built upon multicore fibres. 18th International Conference on Transparent Optical Networks (ICTON), Trento (Italy), pp. 1–4, 2016.K. O. Hill & G. Meltz . Fiber Bragg grating technology fundamentals and overview. IEEE J. Lightw. Technol. 15, 1263–1276 (1997).T. Erdogan . Fiber grating spectra. IEEE J. Lightw. Technol. 15, 1277–1294 (1997).D. Barrera, I. Gasulla & S. Sales . Multipoint two-dimensional curvature optical fiber sensor based on a non-twisted homogeneous four-core fiber. IEEE J. Lightw. Technol. 33, 2445–2450 (2015).T. Birks, B. Mangan, A. Diez, J. Cruz, S. Leon-Saval, J. Bland-Hawthorn & D. Murphy . Multicore optical fibres for astrophotonics. In CLEO/Europe and EQEC 2011 Conference Digest, OSA Technical Digest (CD)d (Optical Society of America, 2011), paper JSIII2_1.C. Wang, Z. Yan, Q. Sun, Z. Sun, C. Mou, J. Zhang, A. Badmos & L. Zhang . Fibre Bragg gratings fabrication in four core fibres. Proc. SPIE 9886, Micro-Structured and Specialty Optical Fibres IV, 98860H (2016).M. J. Cole, W. H. Loh, R. I. Laming, M. N. Zervas & S. Barcelos . Moving fibre/phase mask-scanning beam technique for enhanced flexibility in producing fibre gratings with uniform phase mask. Electron. Lett. 31, 1488–1490 (1995).M. Gallagher & U. Österberg . Time resolved 3.10 eV luminescence in germanium-doped silica glass. Appl. Phys. Lett. 63, 2987–2988 (1993).T. Komukai & M. Nakazawa . Fabrication of high-quality long fiber Bragg grating by monitoring 3.1 eV radiation (400 nm) from GeO defects. IEEE Photon. Tech. Lett. 8, 1495–1497 (1996).R. R. Thomson, H. T. Bookey, N. D. Psaila, A. Fender, S. Campbell, W. N. MacPherson, J. S. Barton, D. T. Reid & A. K. Kar . Ultrafast-laser inscription of a three dimensional fan-out device for multicore fiber coupling applications. Opt. Express 15, 11691–11697 (2007)

Genome-wide transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection

Background: Up to 80% of patients surviving acute respiratory distress syndrome (ARDS) secondary to SARS-CoV- 2 infection present persistent anomalies in pulmonary function after hospital discharge. There is a limited un-derstanding of the mechanistic pathways linked to post-acute pulmonary sequelae. Aim: To identify the molecular underpinnings associated with severe lung diffusion involvement in survivors of SARS-CoV-2-induced ARDS. Methods: Survivors attended to a complete pulmonary evaluation 3 months after hospital discharge. RNA sequencing (RNA-seq) was performed using Illumina technology in whole-blood samples from 50 patients with moderate to severe diffusion impairment (DLCO<60%) and age- and sex-matched individuals with mild-normal lung function (DLCO≥60%). A transcriptomic signature for optimal classification was constructed using random forest. Transcriptomic data were analyzed for biological pathway enrichment, cellular deconvolution, cell/tissue-specific gene expression and candidate drugs. Results: RNA-seq identified 1357 differentially expressed transcripts. A model composed of 14 mRNAs allowed the optimal discrimination of survivors with severe diffusion impairment (AUC=0.979). Hallmarks of lung sequelae involved cell death signaling, cytoskeleton reorganization, cell growth and differentiation and the immune response. Resting natural killer (NK) cells were the most important immune cell subtype for the pre-diction of severe diffusion impairment. Components of the signature correlated with neutrophil, lymphocyte and monocyte counts. A variable expression profile of the transcripts was observed in lung cell subtypes and bodily tissues. One upregulated gene, TUBB4A, constitutes a target for FDA-approved drugs. Conclusions: This work defines the transcriptional programme associated with post-acute pulmonary sequelae and provides novel insights for targeted interventions and biomarker development.MCGH is the recipient of a predoctoral fellowship from the University of Lleida. MM is the recipient of a predoctoral fellowship (PFIS: FI21/00187) from Instituto de Salud Carlos III. AC is supported by Instituto de Salud Carlos III (Sara Borrell 2021: CD21/00087). DdGC has received financial support from Instituto de Salud Carlos III (Miguel Servet 2020: CP20/00041), co-funded by the European Social Fund (ESF) “Investing in your future”. IML is supported by a Miguel Servet contract (CPII20/00029) from the Instituto de Salud Carlos III, co-funded by the European Social Fund (ESF) “Investing in your future”. CIBERES is an initiative of the Instituto de Salud Carlos III. This work is supported by the Instituto de Salud Carlos III (COV20/00110), co-funded by the European Regional Development Fund (ERDF) “A way to make Europe”. Supported by: Programa de donaciones "estar preparados"; UNESPA (Madrid, Spain) and Fundación Francisco Soria Melguizo (Madrid, Spain). Funded by: La Fundació La Marató de TV3, project with code 202108–30/ 31. COVIDPONENT is funded by the Institut Català de la Salut and Gestió de Serveis Sanitaris. This research was funded in part by a grant (PI19/01805) from the Instituto de Salud Carlos III, co-funded by the European Regional Development Fund (ERDF) “A way to build Europe” and by the Fundación Rioja Salu

Prognostic implications of comorbidity patterns in critically ill COVID-19 patients: A multicenter, observational study

Background The clinical heterogeneity of COVID-19 suggests the existence of different phenotypes with prognostic implications. We aimed to analyze comorbidity patterns in critically ill COVID-19 patients and assess their impact on in-hospital outcomes, response to treatment and sequelae. Methods Multicenter prospective/retrospective observational study in intensive care units of 55 Spanish hospitals. 5866 PCR-confirmed COVID-19 patients had comorbidities recorded at hospital admission; clinical and biological parameters, in-hospital procedures and complications throughout the stay; and, clinical complications, persistent symptoms and sequelae at 3 and 6 months. Findings Latent class analysis identified 3 phenotypes using training and test subcohorts: low-morbidity (n=3385; 58%), younger and with few comorbidities; high-morbidity (n=2074; 35%), with high comorbid burden; and renal-morbidity (n=407; 7%), with chronic kidney disease (CKD), high comorbidity burden and the worst oxygenation profile. Renal-morbidity and high-morbidity had more in-hospital complications and higher mortality risk than low-morbidity (adjusted HR (95% CI): 1.57 (1.34-1.84) and 1.16 (1.05-1.28), respectively). Corticosteroids, but not tocilizumab, were associated with lower mortality risk (HR (95% CI) 0.76 (0.63-0.93)), especially in renal-morbidity and high-morbidity. Renal-morbidity and high-morbidity showed the worst lung function throughout the follow-up, with renal-morbidity having the highest risk of infectious complications (6%), emergency visits (29%) or hospital readmissions (14%) at 6 months (p<0.01). Interpretation Comorbidity-based phenotypes were identified and associated with different expression of in-hospital complications, mortality, treatment response, and sequelae, with CKD playing a major role. This could help clinicians in day-to-day decision making including the management of post-discharge COVID-19 sequelae. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd

Effects of intubation timing in patients with COVID-19 throughout the four waves of the pandemic : a matched analysis

The primary aim of our study was to investigate the association between intubation timing and hospital mortality in critically ill patients with COVID-19-associated respiratory failure. We also analysed both the impact of such timing throughout the first four pandemic waves and the influence of prior non-invasive respiratory support on outcomes. This is a secondary analysis of a multicentre, observational and prospective cohort study that included all consecutive patients undergoing invasive mechanical ventilation due to COVID-19 from across 58 Spanish intensive care units (ICU) participating in the CIBERESUCICOVID project. The study period was between 29 February 2020 and 31 August 2021. Early intubation was defined as that occurring within the first 24 h of intensive care unit (ICU) admission. Propensity score (PS) matching was used to achieve balance across baseline variables between the early intubation cohort and those patients who were intubated after the first 24 h of ICU admission. Differences in outcomes between early and delayed intubation were also assessed. We performed sensitivity analyses to consider a different timepoint (48 h from ICU admission) for early and delayed intubation. Of the 2725 patients who received invasive mechanical ventilation, a total of 614 matched patients were included in the analysis (307 for each group). In the unmatched population, there were no differences in mortality between the early and delayed groups. After PS matching, patients with delayed intubation presented higher hospital mortality (27.3% versus 37.1%, p =0.01), ICU mortality (25.7% versus 36.1%, p=0.007) and 90-day mortality (30.9% versus 40.2%, p=0.02) when compared to the early intubation group. Very similar findings were observed when we used a 48-hour timepoint for early or delayed intubation. The use of early intubation decreased after the first wave of the pandemic (72%, 49%, 46% and 45% in the first, second, third and fourth wave, respectively; first versus second, third and fourth waves p<0.001). In both the main and sensitivity analyses, hospital mortality was lower in patients receiving high-flow nasal cannula (n=294) who were intubated earlier. The subgroup of patients undergoing NIV (n=214) before intubation showed higher mortality when delayed intubation was set as that occurring after 48 h from ICU admission, but not when after 24 h. In patients with COVID-19 requiring invasive mechanical ventilation, delayed intubation was associated with a higher risk of hospital mortality. The use of early intubation significantly decreased throughout the course of the pandemic. Benefits of such an approach occurred more notably in patients who had received high-flow nasal cannul

HSCW intelligent management

This work is motivated by the difficulty of representing Environmental domains in a functional way. We present a formalization approach covering both environmental and computational needs. It allows us to produce an operational software for intelligent decision support on a Horizontal Subsurface Constructed Wetlands (HSCW) while capturing the most significant elements of the domain.Peer ReviewedPostprint (published version