LOGOS: Enabling Local Resource Managers for the Efficient Support of Data-Intensive Workflows within Grid Sites

In this study we discuss how to enable grid sites for the support of data-intensive workflows. Usually, within grid sites, tasks and resources are administrated by local resource managers (LRMs). Many of LRMs have been designed for managing compute-intensive applications. Therefore, data-intensive workflow applications might not perform well on such environments due to the number and size of data transfers between tasks. To improve the performance of such kind of applications it is necessary to redefine the scheduling policies integrated on LRMs. This paper proposes a novel scheme for efficiently supporting data-intensive workflows in LRMs within grid sites. Such scheme is partially implemented in our grid middleware LOGOS and used to improve the performance of a well known LRM: HTCondor. The core of LOGOS is a novel communication-aware scheduling algorithm (PPSA) capable of finding near-optimal solutions. Experiments conducted in this study showed that our approach leads to performance improvements up to 52 % in the management of data-intensive workflow applications

FaaSter, better, cheaper : the prospect of serverless scientific computing and HPC

The adoption of cloud computing facilities and programming models differs vastly between different application domains. Scalable web applications, low-latency mobile backends and on-demand provisioned databases are typical cases for which cloud services on the platform or infrastructure level exist and are convincing when considering technical and economical arguments. Applications with specific processing demands, including high-performance computing, high-throughput computing and certain flavours of scientific computing, have historically required special configurations such as compute- or memory-optimised virtual machine instances. With the rise of function-level compute instances through Function-as-a-Service (FaaS) models, the fitness of generic configurations needs to be re-evaluated for these applications. We analyse several demanding computing tasks with regards to how FaaS models compare against conventional monolithic algorithm execution. Beside the comparison, we contribute a refined FaaSification process for legacy software and provide a roadmap for future work

Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics

The most common cause of death in cystic fibrosis (CF) patients is progressive lung function decline, which is punctuated by acute pulmonary exacerbations (APEs). A major challenge is to discover biomarkers for detecting an oncoming APE and allow for pre-emptive clinical interventions. Metabolic profiling of exhaled breath condensate (EBC) samples collected from CF patients before, during, and after APEs and under stable conditions (n = 210) was performed using ultraperformance liquid chromatography (UPLC) coupled to Orbitrap mass spectrometry (MS). Negative ion mode MS data showed that classification between metabolic profiles from "pre-APE" (pending APE before the CF patient had any signs of illness) and stable CF samples was possible with good sensitivities (85.7 and 89.5%), specificities (88.4 and 84.1%), and accuracies (87.7 and 85.7%) for pediatric and adult patients, respectively. Improved classification performance was achieved by combining positive with negative ion mode data. Discriminant metabolites included two potential biomarkers identified in a previous pilot study: Lactic acid and 4-hydroxycyclohexylcarboxylic acid. Some of the discriminant metabolites had microbial origins, indicating a possible role of bacterial metabolism in APE progression. The results show promise for detecting an oncoming APE using EBC metabolites, thus permitting early intervention to abort such an event.Fil: Zang, Xiaoling. Georgia Institute of Techology; Estados UnidosFil: Monge, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; ArgentinaFil: Gaul, David A.. Georgia Institute of Techology; Estados UnidosFil: McCarty, Nael A.. University of Emory; Estados UnidosFil: Stecenko, Arlene. University of Emory; Estados UnidosFil: Fernández, Facundo M.. Georgia Institute of Techology; Estados Unido

An accurate calculation of the nucleon axial charge with lattice QCD

We report on a lattice QCD calculation of the nucleon axial charge, $g_A$, using M\"{o}bius Domain-Wall fermions solved on the dynamical $N_f=2+1+1$ HISQ ensembles after they are smeared using the gradient-flow algorithm. The calculation is performed with three pion masses, $m_\pi\sim\{310,220,130\}$ MeV. Three lattice spacings ($a\sim\{0.15,0.12,0.09\}$ fm) are used with the heaviest pion mass, while the coarsest two spacings are used on the middle pion mass and only the coarsest spacing is used with the near physical pion mass. On the $m_\pi\sim220$ MeV, $a\sim0.12$ fm point, a dedicated volume study is performed with $m_\pi L \sim \{3.22,4.29,5.36\}$. Using a new strategy motivated by the Feynman-Hellmann Theorem, we achieve a precise determination of $g_A$ with relatively low statistics, and demonstrable control over the excited state, continuum, infinite volume and chiral extrapolation systematic uncertainties, the latter of which remains the dominant uncertainty. Our final determination at 2.6\% total uncertainty is $g_A = 1.278(21)(26)$, with the first uncertainty including statistical and systematic uncertainties from fitting and the second including model selection systematics related to the chiral and continuum extrapolation. The largest reduction of the second uncertainty will come from a greater number of pion mass points as well as more precise lattice QCD results near the physical pion mass.Comment: 17 pages + 11 pages of references and appendices. 15 figures. Interested readers can download the Python analysis scripts and an hdf5 data file at https://github.com/callat-qcd/project_gA_v

Bias of damped Lyman--α systems from their cross-correlation with CMB lensing

We cross-correlate the positions of damped Lyman-α systems (DLAs) and their parent quasar catalog with a convergence map derived from the Planck cosmic microwave background (CMB) temperature data. We make consistent measurements of the lensing signal of both samples in both Fourier and configuration space. By interpreting the excess signal present in the DLA catalog with respect to the parent quasar catalog as caused by the large scale structure traced by DLAs, we are able to infer the bias of these objects: bDLA=2.6±0.9. These results are consistent with previous measurements made in cross-correlation with the Lyman-α forest, although the current noise in the lensing data and the low number density of DLAs limits the constraining power of this measurement. We discuss the robustness of the analysis with respect to a number different systematic effects and forecast prospects of carrying out this measurement with data from future experiments