Extending OmpSs for OpenCL kernel co-execution in heterogeneous systems

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Heterogeneous systems have a very high potential performance but present difficulties in their programming. OmpSs is a well known framework for task based parallel applications, which is an interesting tool to simplify the programming of these systems. However, it does not support the co-execution of a single OpenCL kernel instance on several compute devices. To overcome this limitation, this paper presents an extension of the OmpSs framework that solves two main objectives: the automatic division of datasets among several devices and the management of their memory address spaces. To adapt to different kinds of applications, the data division can be performed by the novel HGuided load balancing algorithm or by the well known Static and Dynamic. All this is accomplished with negligible impact on the programming. Experimental results reveal that there is always one load balancing algorithm that improves the performance and energy consumption of the system.This work has been supported by the University of Cantabria with grant CVE-2014-18166, the Generalitat de Catalunya under grant 2014-SGR-1051, the Spanish Ministry of Economy, Industry and Competitiveness under contracts TIN2016- 76635-C2-2-R (AEI/FEDER, UE) and TIN2015-65316-P. The Spanish Government through the Programa Severo Ochoa (SEV-2015-0493). The European Research Council under grant agreement No 321253 European Community’s Seventh Framework Programme [FP7/2007-2013] and Horizon 2020 under the Mont-Blanc Projects, grant agreement n 288777, 610402 and 671697 and the European HiPEAC Network.Peer ReviewedPostprint (published version

Architectural support for task dependence management with flexible software scheduling

The growing complexity of multi-core architectures has motivated a wide range of software mechanisms to improve the orchestration of parallel executions. Task parallelism has become a very attractive approach thanks to its programmability, portability and potential for optimizations. However, with the expected increase in core counts, finer-grained tasking will be required to exploit the available parallelism, which will increase the overheads introduced by the runtime system. This work presents Task Dependence Manager (TDM), a hardware/software co-designed mechanism to mitigate runtime system overheads. TDM introduces a hardware unit, denoted Dependence Management Unit (DMU), and minimal ISA extensions that allow the runtime system to offload costly dependence tracking operations to the DMU and to still perform task scheduling in software. With lower hardware cost, TDM outperforms hardware-based solutions and enhances the flexibility, adaptability and composability of the system. Results show that TDM improves performance by 12.3% and reduces EDP by 20.4% on average with respect to a software runtime system. Compared to a runtime system fully implemented in hardware, TDM achieves an average speedup of 4.2% with 7.3x less area requirements and significant EDP reductions. In addition, five different software schedulers are evaluated with TDM, illustrating its flexibility and performance gains.This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the European HiPEAC Network of Excellence, by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P, TIN2016-76635-C2-2-R and TIN2016-81840-REDT), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 671697 and No. 671610. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047.Peer ReviewedPostprint (author's final draft

Regional differences in the profile of disabled community-dwelling older adults: a European population-based cross-sectional study

The main objective of this work was to estimate the prevalence of disability in European community-dwelling older adults, as well as to investigate differences in the profile of disabled older adults between European regions (Northern, Central, Eastern and Southern). A cross-sectional study based on wave 6 (2015) of the Survey of Health, Ageing and Retirement in Europe (SHARE) was conducted. Community-dwelling participants aged 65-84 were selected (n = 33,369). Disability was defined as presenting at least one functional limitation in basic activities of daily living (BADL). Sociodemographic, health services, lifestyle and health-related variables were analyzed. Statistical analysis was carried out through the Chi-square and ANOVA tests for bivariate analysis, and Poisson regression for multivariate analysis. Overall prevalence of disability was 13.8%: 9.4% in the Northern region, 13.1% in the Southern region, 13.6% in the Central region, and 16.6% in the Eastern region. Portugal, Poland, Estonia and Belgium showed the highest prevalence of BADL limitations, while Sweden, Denmark, Greece and Switzerland showed the lowest prevalence. Besides, disabled older adults from East Europe presented the most disadvantaged health profile, followed by the Southern region. On the other hand, disabled older adults living in the Northern region showed the most advantaged characteristics of most variables, except for smoking and polypharmacy

To distribute or not to distribute: The question of load balancing for performance or energy

Heterogeneous systems are nowadays a common choice in the path to Exascale. Through the use of accelerators they offer outstanding energy efficiency. The programming of these devices employs the host-device model, which is suboptimal as CPU remains idle during kernel executions, but still consumes energy. Making the CPU contribute computin effort might improve the performance and energy consumption of the system. This paper analyses the advantages of this approach and sets the limits of when its beneficial. The claims are supported by a set of models that determine how to share a single data-parallel task between the CPU and the accelerator for optimum performance, energy consumption or efficiency. Interestingly, the models show that optimising performance does not always mean optimum energy or efficiency as well. The paper experimentally validates the models, which represent an invaluable tool for programmers when faced with the dilemma of whether to distribute their workload in these systems.This work has been supported by the University of Cantabria (CVE-2014-18166), the Spanish Science and Technology Commission (TIN2016-76635-C2-2-R), the European Research Council (G.A. No 321253) and the European HiPEAC Network of Excellence. The Mont-Blanc project has received funding from the European Unions Horizon 2020 research and innovation programme under grant agreement No 671697.Peer ReviewedPostprint (author's final draft

The Secret Life of Oilbirds: New Insights into the Movement Ecology of a Unique Avian Frugivore

Background: Steatornis caripensis (the oilbird) is a very unusual bird. It supposedly never sees daylight, roosting in huge aggregations in caves during the day and bringing back fruit to the cave at night. As a consequence a large number of the seeds from the fruit they feed upon germinate in the cave and spoil. Methodology/Principal Findings: Here we use newly developed GPS/acceleration loggers with remote UHF readout to show that several assumptions about the behaviour of Steatornis caripensis need to be revised. On average, they spend only every 3 rd day in a cave, individuals spent most days sitting quietly in trees in the rainforest where they regurgitate seeds. Conclusions/Significance: This provides new data on the extent of seed dispersal and the movement ecology of Steatornis caripensis. It suggests that Steatornis caripensis is perhaps the most important long-distance seed disperser in Neotropical forests. We also show that colony-living comes with high activity costs to individuals

Comparative proteomics of exosomes secreted by tumoral jurkat t cells and normal human t cell blasts unravels a potential tumorigenic role for valosin-containing protein

We have previously characterized that FasL and Apo2L/TRAIL are stored in their bioactive form inside human T cell blasts in intraluminal vesicles present in multivesicular bodies. These vesicles are rapidly released to the supernatant in the form of exosomes upon re-activation of T cells. In this study we have compared for the first time proteomics of exosomes produced by normal human T cell blasts with those produced by tumoral Jurkat cells, with the objective of identify proteins associated with tumoral exosomes that could have a previously unrecognized role in malignancy. We have identified 359 and 418 proteins in exosomes from T cell blasts and Jurkat cells, respectively. Interestingly, only 145 (around a 40%) are common. The major proteins in both cases are actin and tubulin isoforms and the common interaction nodes correspond to these cytoskeleton and related proteins, as well as to ribosomal and mRNA granule proteins. We detected 14 membrane proteins that were especially enriched in exosomes from Jurkat cells as compared with T cell blasts. The most abundant of these proteins was valosin-containing protein (VCP), a membrane ATPase involved in ER homeostasis and ubiquitination. In this work, we also show that leukemic cells are more sensitive to cell death induced by the VCP inhibitor DBeQ than normal T cells. Furthermore, VCP inhibition prevents functional exosome secretion only in Jurkat cells, but not in T cell blasts. These results suggest VCP targeting as a new selective pathway to exploit in cancer treatment to prevent tumoral exosome secretion

Chronic renal disease in Spain: Prevalence and related factors in persons with diabetes mellitus older than 64 years

Introducción La diabetes mellitus tipo 2 y la enfermedad renal crónica (ERC) son afecciones de elevada prevalencia en personas = 65 años y constituyen un importante problema de salud pública. Objetivos Conocer la prevalencia de la ERC, sus categorías y su relación con diversos factores demográficos y clínicos, en pacientes ancianos con diabetes mellitus tipo 2 en España. Métodos Estudio epidemiológico, observacional, transversal, multicéntrico, ámbito nacional. Se incluyeron pacientes con diabetes mellitus tipo 2 conocida, edad = 65 años atendidos en Atención Primaria. Se recogieron variables demográficas, antropométricas y analíticas de los últimos 12 meses, incluyendo el cociente albúmina-creatinina y el filtrado glomerular estimado para evaluar la función renal. Resultados La prevalencia de ERC fue del 37, 2% (IC95%, 34, 1-40, 3%), de insuficiencia renal del 29, 7% (IC95%, 26, 8-32, 6%) y de elevación de la albuminuria del 20, 6% (IC95%, 17, 3-23, 9%), moderadamente elevada 17, 8% (IC95%, 14, 7-20, 9%), severamente elevada 2, 8% (IC95%, 1, 4-4, 2%). La prevalencia de las categorías de ERC fueron: G1 1, 3% (IC95%, 0, 6-2%), G2 6, 2% (IC95%, 4, 6-7, 8%), G3a 17, 2% (IC95%, 14, 8-19, 6%), G3b 9, 8% (IC95%, 7, 9-11, 7%), G4 2% (IC95%, 1, 1-2, 9%) y G5 0, 7% (IC95%, 0, 2-1, 2%). En el análisis multivariante, después de ajustar por el resto de variables, la ERC se asoció a mayor edad OR 5, 13, (IC95%, 3, 15-8, 35), alta comorbilidad OR 3, 36 (IC95%, 2, 2-5, 12) y la presencia de tratamiento antihipertensivo OR 2, 43 (IC95%, 1, 48-4, 02). Conclusiones La ERC es frecuente en la población diabética = 65 años y se asocia con mayor edad, alta comorbilidad e hipertensión tratada. No se ha encontrado asociación con el género y años de evolución de la diabetes. Introduction: Type 2 diabetes mellitus and chronic kidney disease (CKD) are conditions which have a high prevalence in individuals =65 years of age and represent a major public health problem. Objectives: To determine the prevalence of CKD, its categories and its relationship with various demographic and clinical factors in elderly patients with type 2 diabetes mellitus in Spain. Methods: Observational, cross-sectional, multicenter, Spanish epidemiological study. Patients with known type 2 diabetes mellitus, age =65 years of age treated in Primary Care were included. We collected demographic, anthropometric and analytical variables from the previous 12 months, including the albumin-to-creatinine ratio and estimated glomerular filtration rate to evaluate renal function. Results: The prevalence of CKD was 37.2% (95% CI, 34.1–40.3%), renal failure was 29.7% (95% CI, 26.8–32.6%) and increased albuminuria was 20.6% (95% CI, 17.3–23.9%), moderately increased albuminuria was 17.8% (95% CI, 14.7–20.9%) and severely increased albuminuria was 2.8% (95% CI, 1.4–4.2%). In turn, the prevalence of CKD categories were: G1 1.3% (95% CI, 0.6–2%), G2 6.2% (95% CI, 4.6–7.8%), G3a 17.2% (95% CI, 14.8–19.6%), G3b 9.8% (95% CI, 7.9–11.7%), G4 2% (95% CI, 1.1–2.9%) and G5 0.7% (95% CI, 0.2–1.2%). In the multivariate analysis, after adjusting for the remaining variables, CKD was associated with elderly age (OR 5.13, 95% CI, 3.15–8.35), high comorbidity (OR 3.36, 95% CI, 2.2–5.12) and presence of antihypertensive treatment (OR 2.43, 95% CI, 1.48–4.02). Conclusions: CKD is frequent in the diabetic population =65 years of age and is associated with elderly age, high comorbidity and with treated hypertension. No relationship has been found with gender and time in years since onset of diabetes

SAMHD1 Phosphorylation Coordinates the Anti-HIV-1 Response by Diverse Interferons and Tyrosine Kinase Inhibition.

Macrophages are susceptible to human immunodeficiency virus type 1 (HIV-1) infection despite abundant expression of antiviral proteins. Perhaps the most important antiviral protein is the restriction factor sterile alpha motif domain and histidine/aspartic acid domain-containing protein 1 (SAMHD1). We investigated the role of SAMHD1 and its phospho-dependent regulation in the context of HIV-1 infection in primary human monocyte-derived macrophages and the ability of various interferons (IFNs) and pharmacologic agents to modulate SAMHD1. Here we show that stimulation by type I, type II, and to a lesser degree, type III interferons share activation of SAMHD1 via dephosphorylation at threonine-592 as a consequence of signaling. Cyclin-dependent kinase 1 (CDK1), a known effector kinase for SAMHD1, was downregulated at the protein level by all IFN types tested. Pharmacologic inhibition or small interfering RNA (siRNA)-mediated knockdown of CDK1 phenocopied the effects of IFN on SAMHD1. A panel of FDA-approved tyrosine kinase inhibitors potently induced activation of SAMHD1 and subsequent HIV-1 inhibition. The viral restriction imposed via IFNs or dasatinib could be overcome through depletion of SAMHD1, indicating that their effects are exerted primarily through this pathway. Our results demonstrate that SAMHD1 activation, but not transcriptional upregulation or protein induction, is the predominant mechanism of HIV-1 restriction induced by type I, type II, and type III IFN signaling in macrophages. Furthermore, SAMHD1 activation presents a pharmacologically actionable target through which HIV-1 infection can be subverted

Tripled critical current in racetrack coils made of Bi-2212 Rutherford cables with overpressure processing and leakage control

We fabricated three racetrack coils (RC1, RC2, and RC3) from Bi-2212 Rutherford cables (17-strand, thickness × width = 1.44 mm × 7.8 mm, strand diameter = 0.8 mm) and applied overpressure processing heat treatment (OPHT). The quench currents of RC1 and RC2 reached 5268 A and 5781 A, respectively, despite them still, surprisingly, exhibiting some Bi-2212 leakage to the surface. After removing most of the leakages using a simple-to-implement insulation scheme, the quench current of RC3 improved to 6485 A, which is about three times the average quench current of a dozen racetrack coils that had been fabricated and reacted using the conventional 1 bar heat treatment. The results confirm the effectiveness of the OPHT technology and the new leakage control scheme for coils made from Bi-2212 Rutherford cables. Coils exhibited an increased quench current with increasing the current ramp rate from 5 to 200 A s ; they were quite stable against point and transient disturbances, and were capable of adsorbing persistent Joule heating at ∼80 mW for >15 s before quenching. These behaviors are different from Nb-Ti and Nb Sn accelerator magnets. Overall, our results provide a critical evaluation and verification of Bi-2212 wire and magnet technologies (wire, insulation, heat treatment, coil fabrication, and coil operation), reveal crucial new stability features of Bi-2212 magnets, and demonstrate technological options for it to become a practical high-field magnet technology. -1