Performance Evaluation of MPI, UPC and OpenMP on Multicore Architectures

This is a post-peer-review, pre-copyedit version of an article published in Lecture Notes in Computer Science. The final authenticated version is available online at: https://doi.org/10.1007/978-3-642-03770-2_24[Abstract] The current trend to multicore architectures underscores the need of parallelism. While new languages and alternatives for supporting more efficiently these systems are proposed, MPI faces this new challenge. Therefore, up-to-date performance evaluations of current options for programming multicore systems are needed. This paper evaluates MPI performance against Unified Parallel C (UPC) and OpenMP on multicore architectures. From the analysis of the results, it can be concluded that MPI is generally the best choice on multicore systems with both shared and hybrid shared/distributed memory, as it takes the highest advantage of data locality, the key factor for performance in these systems. Regarding UPC, although it exploits efficiently the data layout in memory, it suffers from remote shared memory accesses, whereas OpenMP usually lacks efficient data locality support and is restricted to shared memory systems, which limits its scalability.Gobierno de España; TIN2007-67537-C03-0

Proteomics: a poweful tool to deepen the molecular mechanisms of ischemic stroke

Comunicaciones a congreso

Performance Evaluation of Unified Parallel C Collective Communications

This is a post-peer-review, pre-copyedit version. The final authenticated version is available online at: http://dx.doi.org/10.1109/HPCC.2009.88[Abstract] Unified Parallel C (UPC) is an extension of ANSI C designed for parallel programming. UPC collective primitives, which are part of the UPC standard, increase programming productivity while reducing the communication overhead. This paper presents an up-to-date performance evaluation of two publicly available UPC collective implementations on three scenarios: shared, distributed, and hybrid shared/distributed memory architectures. The characterization of the throughput of collective primitives is useful for increasing performance through the runtime selection of the appropriate primitive implementation, which depends on the message size and the memory architecture, as well as to detect inefficient implementations. In fact, based on the analysis of the UPC collectives performance, we proposed some optimizations for the current UPC collective libraries. We have also compared the performance of the UPC collective primitives and their MPI counterparts, showing that there is room for improvement. Finally, this paper concludes with an analysis of the influence of the performance of the UPC collectives on a representative communication-intensive application, showing that their optimization is highly important for UPC scalability.Ministerio de Ciencia e Innovación; TIN2007-67537-C03-02Xunta de Galicia; 3/2006 DOGA 13/12/200

Submesoscale physicochemical dynamics directly shape bacterioplankton community structure in space and time

Submesoscale eddies and fronts are important components of oceanic mixing and energy fluxes. These phenomena occur in the surface ocean for a period of several days, on scales between a few hundred meters and few tens of kilometers. Remote sensing and modeling suggest that eddies and fronts may influence marine ecosystem dynamics, but their limited temporal and spatial scales make them challenging for observation and in situ sampling. Here, the study of a submesoscale filament in summerly Arctic waters (depth 0–400 m) revealed enhanced mixing of Polar and Atlantic water masses, resulting in a ca. 4 km wide and ca. 50 km long filament with distinct physical and biogeochemical characteristics. Compared to the surrounding waters, the filament was characterized by a distinct phytoplankton bloom, associated with depleted inorganic nutrients, elevated chlorophyll a concentrations, as well as twofold higher phyto- and bacterioplankton cell abundances. High-throughput 16S rRNA gene sequencing of bacterioplankton communities revealed enrichment of typical phytoplankton bloom-associated taxonomic groups (e.g., Flavobacteriales) inside the filament. Furthermore, linked to the strong water subduction, the vertical export of organic matter to 400 m depth inside the filament was twofold higher compared to the surrounding waters. Altogether, our results show that physical submesoscale mixing can shape distinct biogeochemical conditions and microbial communities within a few kilometers of the ocean. Hence, the role of submesoscale features in polar waters for surface ocean biodiversity and biogeochemical processes need further investigation, especially with regard to the fate of sea ice in the warming Arctic Ocean

Solubility and stability studies of benzoyl peroxide in non-polar, non-comedogenic solvents for use in topical pharmaceutical formulation developments

Non-irritant, non-comedogenic and non-polar emollients were pre-selected for determinations of relative dielectric permittivity and solubility of benzoyl peroxide (BP). Those solvents capable of solubilizing BP in concentrations commonly utilised in topical formulations (between 1 and 10 %) were taken into account for stability studies. The developed pre-formulations were also studied for acute irritation both clinically and instrumentally. Even though the solubility of BP in the solvents studied had relatively low values; in some cases, such as with caprylic/capric triglyceride (CapCap) and dicaprylyl carbonate (DicCar) it has been possible to obtain acceptable concentrations of BP from a therapeutic viewpoint (19.9 and 19.5 mg/mL, respectively). Two BP pre-formulations (PBCapCap and PBDicCar) with enhanced stability and with the capability to decrease adverse application site reaction by maintaining moisture in the stratum corneum were developed with potential application in topical formulations of BP with solvents of low relative dielectric permittivity (CapCap and DicCar, respectively).Colegio de Farmacéuticos de la Provincia de Buenos Aire

Isolamento e seleção de bactérias ácido-láticas com potencial probiótico para pirarucu.

A demanda crescente do mercado mundial por proteínas de alta qualidade tem estimulado o crescimento da aquicultura. Esse crescimento ocorre pelo aumento das áreas de produção e a intensificação no sistema de criação e expõe os peixes à diversas variações ambientais provocando desequilíbrio na tríade hospedeiro-patógeno-ambiente que pode favorecer a invasão de patógenos (vírus, bactéria e parasitas) e o desenvolvimento de enfermidades resultando em perdas na produção (TORANZO et al., 2004)bitstream/item/118392/1/Isolamento-e-selecao-Cot-148.pd

Metallic ions as therapeutic agents in tissue engineering scaffolds: an overview of their biological applications and strategies for new developments

This article provides an overview on the application of metallic ions in the fields of regenerative medicine and tissue engineering, focusing on their therapeutic applications and the need to design strategies for controlling the release of loaded ions from biomaterial scaffolds. A detailed summary of relevant metallic ions with potential use in tissue engineering approaches is presented. Remaining challenges in the field and directions for future research efforts with focus on the key variables needed to be taken into account when considering the controlled release of metallic ions in tissue engineering therapeutics are also highlighted

Relationship between damage and mortality in juvenile-onset systemic lupus erythematosus: Cluster analyses in a large cohort from the Spanish Society of Rheumatology Lupus Registry (RELESSER)

Objectives: To identify patterns (clusters) of damage manifestation within a large cohort of juvenile SLE (jSLE) patients and evaluate their possible association with mortality. Methods: This is a multicentre, descriptive, cross-sectional study of a cohort of 345 jSLE patients from the Spanish Society of Rheumatology Lupus Registry. Organ damage was ascertained using the Systemic Lupus International Collaborating Clinics Damage Index. Using cluster analysis, groups of patients with similar patterns of damage manifestation were identified and compared. Results: Mean age (years) ± S.D. at diagnosis was 14.2 ± 2.89; 88.7% were female and 93.4% were Caucasian. Mean SLICC/ACR DI ± S.D. was 1.27 ± 1.63. A total of 12 (3.5%) patients died. Three damage clusters were identified: Cluster 1 (72.7% of patients) presented a lower number of individuals with damage (22.3% vs. 100% in Clusters 2 and 3, P < 0.001); Cluster 2 (14.5% of patients) was characterized by renal damage in 60% of patients, significantly more than Clusters 1 and 3 (P < 0.001), in addition to increased more ocular, cardiovascular and gonadal damage; Cluster 3 (12.7%) was the only group with musculoskeletal damage (100%), significantly higher than in Clusters 1 and 2 (P < 0.001). The overall mortality rate in Cluster 2 was 2.2 times higher than that in Cluster 3 and 5 times higher than that in Cluster 1 (P < 0.017 for both comparisons). Conclusions: In a large cohort of jSLE patients, renal and musculoskeletal damage manifestations were the two dominant forms of damage by which patients were sorted into clinically meaningful clusters. We found two clusters of jSLE with important clinical damage that were associated with higher rates of mortality, especially for the cluster of patients with predominant renal damage. Physicians should be particularly vigilant to the early prevention of damage in this subset of jSLE patients with kidney involvement