Reducing memory requirements for large size LBM simulations on GPUs

The scientific community in its never-ending road of larger and more efficient computational resources is in need of more efficient implementations that can adapt efficiently on the current parallel platforms. Graphics processing units are an appropriate platform that cover some of these demands. This architecture presents a high performance with a reduced cost and an efficient power consumption. However, the memory capacity in these devices is reduced and so expensive memory transfers are necessary to deal with big problems. Today, the lattice-Boltzmann method (LBM) has positioned as an efficient approach for Computational Fluid Dynamics simulations. Despite this method is particularly amenable to be efficiently parallelized, it is in need of a considerable memory capacity, which is the consequence of a dramatic fall in performance when dealing with large simulations. In this work, we propose some initiatives to minimize such demand of memory, which allows us to execute bigger simulations on the same platform without additional memory transfers, keeping a high performance. In particular, we present 2 new implementations, LBM-Ghost and LBM-Swap, which are deeply analyzed, presenting the pros and cons of each of them.This project was funded by the Spanish Ministry of Economy and Competitiveness (MINECO): BCAM Severo Ochoa accreditation SEV-2013-0323, MTM2013-40824, Computación de Altas Prestaciones VII TIN2015-65316-P, by the Basque Excellence Research Center (BERC 2014-2017) pro- gram by the Basque Government, and by the Departament d' Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programació i Entorns d' Execució Paral·lels (2014-SGR-1051). We also thank the support of the computing facilities of Extremadura Research Centre for Advanced Technologies (CETA-CIEMAT) and NVIDIA GPU Research Center program for the provided resources, as well as the support of NVIDIA through the BSC/UPC NVIDIA GPU Center of Excellence.Peer ReviewedPostprint (author's final draft

The role of estradiol metabolism in urogenital schistosomiasis-induced bladder cancer

Urogenital schistosomiasis is a neglected tropical disease that can lead to bladder cancer. How urogenital schistosomiasis induces carcinogenesis remains unclear, although there is evidence that the human blood fluke Schistosoma haematobium, the infectious agent of urogenital schistosomiasis, releases estradiol-like metabolites. These kind of compounds have been implicated in other cancers. Aiming for enhanced understanding of the pathogenesis of the urogenital schistosomiasisinduced bladder cancer, here we review, interpret, and discuss findings of estradiol-like metabolites detected in both the parasite and in the human urine during urogenital schistosomiasis. Moreover, we predict pathways and enzymes that are involved in the production of these metabolites emphasizing their potential effects on the dysregulation of the tumor suppressor gene p53 expression during urogenital schistosomiasis. Enhanced understanding of these potential carcinogens may not only shed light on urogenital schistosomiasis-induced neoplasia of the bladder, but would also facilitate development of interventions and biomarkers for this and other infection-associated cancers at large

Accelerating fluid-solid simulations (Lattice-Boltzmann & Immersed-Boundary) on heterogeneous architectures

We propose a numerical approach based on the Lattice-Boltzmann (LBM) and Immersed Boundary (IB) methods to tackle the problem of the interaction of solids with an incompressible fluid flow, and its implementation on heterogeneous platforms based on data-parallel accelerators such as NVIDIA GPUs and the Intel Xeon Phi. We explain in detail the parallelization of these methods and describe a number of optimizations, mainly focusing on improving memory management and reducing the cost of host-accelerator communication. As previous research has consistently shown, pure LBM simulations are able to achieve good performance results on heterogeneous systems thanks to the high parallel efficiency of this method. Unfortunately, when coupling LBM and IB methods, the overheads of IB degrade the overall performance. As an alternative, we have explored different hybrid implementations that effectively hide such overheads and allow us to exploit both the multi-core and the hardware accelerator in a cooperative way, with excellent performance results

Leveraging the performance of LBM-HPC for large sizes on GPUs using ghost cells

Today, we are living a growing demand of larger and more efficient computational resources from the scientific community. On the other hand, the appearance of GPUs for general purpose computing supposed an important advance for covering such demand. These devices offer an impressive computational capacity at low cost and an efficient power consumption. However, the memory available in these devices is (sometimes) not enough, and so it is necessary computationally expensive memory transfers from (to) CPU to (from) GPU, causing a dramatic fall in performance. Recently, the Lattice-Boltzmann Method has positioned as an efficient methodology for fluid simulations. Although this method presents some interesting features particularly amenable to be efficiently exploited on parallel computers, it requires a considerable memory capacity, which can suppose an important drawback, in particular, on GPUs. In the present paper, it is proposed a new GPU-based implementation, which minimizes such requirements with respect to other state-of-the-art implementations. It allows us to execute almost 2$x$ bigger problems without additional memory transfers, achieving faster executions when dealing with large problems

Size-resolved aerosol composition at an urban and a rural site in the Po Valley in summertime: implications for secondary aerosol formation

The aerosol size-segregated chemical composition was analyzed at an urban (Bologna) and a rural (San Pietro Capofiume) site in the Po Valley, Italy, during June and July 2012, by ion-chromatography (major water-soluble ions and organic acids) and evolved gas analysis (total and water-soluble carbon), to investigate sources and mechanisms of secondary aerosol formation during the summer. A significant enhancement of secondary organic and inorganic aerosol mass was observed under anticyclonic conditions with recirculation of planetary boundary layer air but with substantial differences between the urban and the rural site. The data analysis, including a principal component analysis (PCA) on the size-resolved dataset of chemical concentrations, indicated that the photochemical oxidation of inorganic and organic gaseous precursors was an important mechanism of secondary aerosol formation at both sites. In addition, at the rural site a second formation process, explaining the largest fraction (22 %) of the total variance, was active at nighttime, especially under stagnant conditions. Nocturnal chemistry in the rural Po Valley was associated with the formation of ammonium nitrate in large accumulation-mode (0.42–1.2 µm) aerosols favored by local thermodynamic conditions (higher relative humidity and lower temperature compared to the urban site). Nocturnal concentrations of fine nitrate were, in fact, on average 5 times higher at the rural site than in Bologna. The water uptake by this highly hygroscopic compound under high RH conditions provided the medium for increased nocturnal aerosol uptake of water-soluble organic gases and possibly also for aqueous chemistry, as revealed by the shifting of peak concentrations of secondary compounds (water-soluble organic carbon (WSOC) and sulfate) toward the large accumulation mode (0.42–1.2 µm). Contrarily, the diurnal production of WSOC (proxy for secondary organic aerosol) by photochemistry was similar at the two sites but mostly affected the small accumulation mode of particles (0.14–0.42 µm) in Bologna, while a shift to larger accumulation mode was observed at the rural site. A significant increment in carbonaceous aerosol concentration (for both WSOC and water-insoluble carbon) at the urban site was recorded mainly in the quasi-ultrafine fraction (size range 0.05–0.14 µm), indicating a direct influence of traffic emissions on the mass concentrations of this range of particles

ESTUDIOS BRASILEÑOS SOBRE EL DEPORTE: ÉNFASIS EN LO DEPORTE-EDUCACIÓN

Essa resenha descreve e analisa Estudos brasileiros sobre o esporte: ênfase no esporte-educação, de Manoel José Gomes Tubino. A obra evidencia o esporte contemporâneo e o processo de consolidação efetiva de seus princípios. Por meio de um abrangente relato histórico dos movimentos esportivos internacionais que influenciaram as políticas públicas do esporte brasileiro, o autor propõe ações para a consolidação dos princípios do esporte-educação, os quais considera o alicerce fundamental para a estrutura esportiva brasileira.This review describes and analyzes the book Brazilian studies about sport: the sport education emphasis, by Manoel José Gomes Tubino. The work marks the contemporary sport practice and the process of effective consolidation of its principles. Through a wide historical description of the international sports movements which influenced Brazilian sports public policies, the author proposes actions for sports-education principles consolidation, which he considers to be the key basis to Brazilian sports structure.  Esa reseña describe y analiza Estudios brasileños sobre el deporte: énfasis en lo deporte-educación, de Manoel José Gomes Tubino. El obra pone en evidencia el deporte contemporáneo y el proceso de consolidación efectiva de sus  principios. A través de un amplio relato histórico de los movimientos deportivos internacionales que influyeron en las políticas públicas del deporte brasileño, el autor propone acciones para la consolidación de los principios del deporte-educación, que considera la base fundamental para la estructura del deporte brasileño.

Deficient spermiogenesis in mice lacking Rlim

The X-linked gene Rlim plays major roles in female mouse development and reproduction, where it is crucial for the maintenance of imprinted X chromosome inactivation in extraembryonic tissues of embryos. However, while females carrying a systemic Rlim knockout (KO) die around implantation, male Rlim KO mice appear healthy and are fertile. Here, we report an important role for Rlim in testis where it is highly expressed in post-meiotic round spermatids as well as in Sertoli cells. Systemic deletion of the Rlim gene results in lower numbers of mature sperm that contains excess cytoplasm, leading to decreased sperm motility and in vitro fertilization rates. Targeting the conditional Rlim cKO specifically to the spermatogenic cell lineage largely recapitulates this phenotype. These results reveal functions of Rlim in male reproduction specifically in round spermatids during spermiogenesis

Non-classical ProIL-1beta activation during mammary gland infection is pathogen-dependent but caspase-1 independent

Infection of the mammary gland with live bacteria elicits a pathogen-specific host inflammatory response. To study these host-pathogen interactions wild type mice, NF-kappaB reporter mice as well as caspase-1 and IL-1beta knockout mice were intramammarily challenged with Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). The murine mastitis model allowed to compare the kinetics of the induced cytokine protein profiles and their underlying pathways. In vivo and ex vivo imaging showed that E. coli rapidly induced NF-kappaB inflammatory signaling concomitant with high mammary levels of TNF-alpha, IL-1 alpha and MCP-1 as determined by multiplex analysis. In contrast, an equal number of S. aureus bacteria induced a low NF-kappaB activity concomitant with high mammary levels of the classical IL-1beta fragment. These quantitative and qualitative differences in local inflammatory mediators resulted in an earlier neutrophil influx and in a more extensive alveolar damage post-infection with E. coli compared to S. aureus. Western blot analysis revealed that the inactive proIL-1beta precursor was processed into pathogen-specific IL-1beta fragmentation patterns as confirmed with IL-1beta knockout animals. Additionally, caspase-1 knockout animals allowed to investigate whether IL-1beta maturation depended on the conventional inflammasome pathway. The lack of caspase-1 did not prevent extensive proIL-1beta fragmentation by either of S. aureus or E. coli. These non-classical IL-1beta patterns were likely caused by different proteases and suggest a sentinel function of IL-1beta during mammary gland infection. Thus, a key signaling nodule can be defined in the differential host innate immune defense upon E. coli versus S. aureus mammary gland infection, which is independent of caspase-1

Metals distribution in colorectal biopsies: New insight on the elemental fingerprint of tumour tissue

International audienceBackground: Colorectal cancer is considered to be an environmental disease. In this context, the study of environmental risk factors associated with the presence of chemical elements is important, as well as improving our knowledge of the elemental fingerprint of tumor tissuecompared to non-cancer tissue.Aims: The objective was to evaluate the element distribution in colorectal adenocarcinoma biopsies, adjacent non-tumor tissues, and healthy controls (non-cancer colorectal biopsies including occlusion or ischemic colons).Methods: The study is a case-control study which compared the element distribution in colon biopsies from two groups of patients: with colorectal cancer and without colorectal cancer. Patients with colorectal cancer provided 2 different groups of samples: colorectal cancer biopsies and adjacent non-tumor tissues. 15 metal concentrations (Al, B, Cd, Cr, Cu, Fe, Mg, Mn, Ni, Pb, Se, Si, Ti, V, and Zn) in colorectal biopsies were quantified by using acid digestion procedures and then inductively coupled plasma (ICP) atomic emission spectrometry.Results: A total of 104 patients were included. 76 patients in the colorectal cancer group (i.e. tumor and adjacent non-tumor tissues) and 28 patients in the healthy control group (i.e. noncancer colorectal biopsies). Among the 15 elements analyzed by ICP spectrometry, only boron, chromium, zinc, silicon, and magnesium were found in colorectal tissue at clearly detectable concentrations. Our data indicated that colorectal tumor biopsies have significantly elevated concentrations of magnesium as compared to adjacent non-tumor or healthy tissues. Zinc concentration followed the same trend but differences were not statistically significant. In addition, silicon appears to be more accumulated in colorectal cancer tissue than in healthy non-cancer tissue, while chromium was mostly found in adjacent non-tumor tissue. Conclusion: Magnesium, chromium, zinc and silicon were found in noteworthy concentrations in colorectal tumor. Their potential role in colorectal carcinogenesis should be explored