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6,452 results for “Application”
Exascale Potholes for HPC: Execution Performance and Variability Analysis of the Flagship Application Code HemeLB
<p>Performance measurement and analysis of parallel applications is often challenging, despite many excellent commercial and open-source tools being available. Currently envisaged exascale computer systems exacerbate matters by requiring extremely high scalability to effectively exploit millions of processor cores. Unfortunately, significant application execution performance variability arising from increasingly complex interactions between hardware and system software makes this situation much more difficult for application developers and performance analysts alike.<br> </p> <p>This work considers the performance assessment of the HemeLB exascale flagship application code from the EU HPC Centre of Excellence (CoE) for Computational Biomedicine (CompBioMed) running on the SuperMUC-NG Tier-0 leadership system, using the methodology of the Performance Optimisation and Productivity (POP) CoE. Although 80% scaling efficiency is maintained to over 100,000 MPI processes, disappointing initial performance with more processes and corresponding poor strong scaling was identified to originate from the same few compute nodes in multiple runs, which later system diagnostic checks found had faulty DIMMs and lacklustre performance. Excluding these compute nodes from subsequent runs improved performance of executions with over 300,000 MPI processes by a factor of five, resulting in 190x speed-up compared to 864 MPI processes. While communication efficiency remains very good up to the largest scale, parallel efficiency is primarily limited by load balance found to be largely due to core-to-core and run-to-run variability from excessive stalls for memory accesses, that affect many HPC systems with Intel Xeon Scalable processors. The POP methodology for this performance diagnosis is demonstrated via a detailed exposition with widely deployed `standard' measurement and analysis tools.</p>
Rapid synthesis and characterization of silver-loaded graphene oxide nanomaterials and their antibacterial applications
<p>All original data used in figures and tables of the manuscript are available in the dataset, which includes the X-ray diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy with energy dispersion spectroscopy, zeta potential analysis and antibacterial properties measurement. Ultrasound was practically used in large-scale production of water-soluble silver/graphene oxide (Ag/GO) by reducing the silver ions (Ag+) attached to graphene oxide into silver nanoparticles. The infrared and X-ray photoelectron spectra indicated that there is a strong interaction between Ag and GO. The morphology analysis showed that AgNPs having a monodisperse size was well dispersed on the surface of the GO nanosheet. The zeta potential analysis showed that the Ag/GO nanomaterials suspension has high stability. In addition, the Ag/GO nanomaterials exhibited an effective antibacterial activity against Escherichia coli and Staphylococcus aureus.</p>
The dataset of figures for "The GPU version of LICOM3 under HIP framework and its large-scale application"
<p>A high-resolution (1/20°) global ocean general circulation model with Graphics processing units (GPUs) code implementations is developed based on the LASG/IAP Climate system Ocean Model version 3 (LICOM3) under Heterogeneous-compute Interface for Portability (HIP) framework. The dynamic core and physics package of LICOM3 are both ported to the GPU, and 3-dimensional parallelization is applied. The HIP version of the LICOM3 (LICOM3-HIP) is 42 times faster than what the same number of CPU cores dose, when 384 AMD GPUs and CPU cores are used. The LICOM3-HIP has excellent scalability; it can still obtain speedup of more than four on 9216 GPUs comparing to 384 GPUs. In this phase, we successfully performed a test of 1/20° LICOM3-HIP using 6550 nodes and 26200 GPUs, and at the grand scale, the model’s time to solution can still obtain an increasing, about 2.72 simulated years per day (SYPD). The high performance was due to putting almost all of computation processes inside GPUs, and thus greatly reduces the time cost of data transfer between CPUs and GPUs. At the same time, a 14-year spin-up integration following the phase 2 of Ocean Model Intercomparison Project (OMIP-2) protocol of surface forcing has been conducted, and the preliminary results have been evaluated. We found that the model results have little differences from the CPU version. Further comparison with observations and lower-resolution LICOM3 results suggests that the 1/20° LICOM3-HIP can not only reproduce the observations, but also produce much smaller scale activities, such as submesoscale eddies and frontal scales structures.</p>
Dataset for: Trust Assessment in 32 KiB of RAM: Multi-application Trust-based Task Offloading for Resource-constrained IoT Nodes
<p>The dataset used to generate graphs for: Matthew Bradbury, Arshad Jhumka and Tim Watson. Trust Assessment in 32 KiB of RAM: Multi-application Trust-based Task Offloading for Resource-constrained IoT Nodes. Proceedings of the Symposium on Applied Computing, ACM, 2021, 1-10.</p> <p>Also includes instructions for experiment setup.</p> <p>Scripts from https://github.com/MBradbury/iot-trust-task-alloc are required to analyse and graph these results.</p>
RNA Ensembles From Solvent Accessibility Data: Application to the SAM-I Riboswitch Aptamer Domain
<p>SASA-derived ensembles of the -SAM and +SAM states of the SAM-responsive riboswitch.</p>
Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule
<p>Allometric trends in the degree of sexual dimorphism with body size have long fascinated evolutionary biologists. Many male-biased clades display more prominent sexual dimorphism in larger taxa (Rensch's rule), with most examples documenting this pattern for body size dimorphism. While sexual dimorphism in traits other than body size is equally functionally relevant, characterizing allometric patterns of sexual dimorphism in such traits is hampered by lack of an analytical framework that can accommodate multivariate phenotypes. In this paper we derive a multivariate equivalency for investigating trends in sexual dimorphism – relative to overall body size – across taxa and provide a generalized test to determine whether such allometric patterns correspond with Rensch's rule. For univariate linear traits like body size, our approach yields equivalent results to those from standard procedures, but our test is also capable of detecting trends in multivariate datasets like shape. Computer simulations reveal the method displays appropriate statistical properties, and an empirical example in Mediterranean lizards provides the first demonstration of Rensch's rule in a multivariate phenotype (head shape). Our generalized procedure substantially extends the analytical toolkit for investigating macroevolutionary patterns of sexual dimorphism and seeking a better understanding of the processes that underlie them.</p>
Endurance and Avoidance Response Patterns in Pain Patients: Application of Action Control Theory in Pain Research
<p>Identifying pain-related response patterns and understanding underlying functional mechanisms of symptom formation and recovery are essential steps for tailoring interventions to increase the effectiveness of treatment. The focus of this study thus was to replicate pain-related avoidance and endurance response patterns associated with the Fear-Avoidance Model (FAM) and Avoidance-Endurance Model (AEM) by means of latent profile analysis. Apart from the analysis of primary and other secondary characteristics of the pain response profiles, we especially analyzed the influence of stress and action control as covariates in accordance with Action Control Theory (ACT).</p>
Synthesis of a novel amphoteric copolymer and its application as a dispersant for coal water slurry preparation
<p>In this work, a novel amphoteric copolymer was synthesized via free radical polymerization, named Poly(sodium p-styrenesulfonate–co-acrylic acid-co-diallyldimethylammonium chloride) (P(SS-co-AA-co-DMDAAC)). Afterwards, P(SS-co-AA-co-DMDAAC) was explored for use as a dispersant in coal water slurry (CWS) preparation. The structure of P(SS-co-AA-co-DMDAAC) was verified by Fourier transform infrared spectroscopy (FTIR) and Nuclear magnetic resonance (NMR). The synthetic conditions were optimized as the feed ratio of AA to SS was 1:1 (for Yulin coal) or 1.5:1 (for Yili coal), and DMDAAC dosage was 4.0 wt% (for Yulin coal) and 6.0 wt% (for Yili coal) toward total monomers. The performances of P(SS-co-AA-co-DMDAAC) as a dispersant for CWS were evaluated by various technologies, such as apparent viscosity, Zeta potential, static stability and contact angle measurements. The results revealed that the optimized dosage of P(SS-co-AA-co-DMDAAC) in CWS preparation was 0.3 wt% and 0.4 wt% for Yulin coal and Yili coal respectively. In this optimum condition, CWS prepared using P(SS-co-AA-co-DMDAAC) as dispersant showed a typical shear thinning behavior and excellent stability, which are desired in industry. The rheological models also confirmed the pseudo-plastic characteristics of CWS. Finally, as compared to the widespread used anionic dispersant Poly(sodium p-styrenesulfonate) (PSS), P(SS-co-AA-co-DMDAAC) developed in this work exhibited better slurry making performance. Introduction of cationic functional groups promoted the adsorption of dispersant, which further enhanced the electrostatic repulsion among coal particles. Accordingly, the viscosity of CWS decreased and static stability enhanced.</p>
Supplementary Information for "Resolution and the Detection of Cultural Dispersals: development and application of spatiotemporal methods in Lowland South America"
<p>Data and code to reproduce the analyses in "Resolution and the Detection of Cultural Dispersals: development and application of spatiotemporal methods in Lowland South America"</p> <p> </p> <p><strong>Abstract</strong></p> <p>Inferring episodes of expansion, admixture, diffusion, and/or migration in prehistory is at present undergoing a resurgence in macro-scale archaeological interpretation. In parallel to this renewed popularity, expanding access to computational tools and datasets has seen the use of aggregated radiocarbon datasets for the study of dispersals also increasing. This paper advocates for developing reflexive practice in the application of radiocarbon dates to prehistoric dispersals, by reflecting on the quality and qualities of the underlying data, particularly chronometric uncertainty, and framing dispersals explicitly in terms of hypothesis testing. This paper draws on cultural expansions within South America and employs two emblematic examples, the Arauquinoid and Tupiguarani traditions, to develop an analytical solution that not only incorporates chronometric uncertainty in bivariate regression but, importantly, tests whether the datasets provide statistically significant evidence for a dispersal process. The analysis, which the paper provides the means to replicate, identifies fundamental issues with resolution and data quality that impede identification of pre-Columbian cultural dispersals through simple spatial gradients of radiocarbon data. The results suggest that reflexivity must be fed back into theoretical frameworks of prehistoric mobility for the study of dispersals, in turn informing the construction of more critical statistical null models. As a first step, alternative models of cultural expansion should be formally considered alongside demographic models.Inferring episodes of expansion, admixture, diffusion, and/or migration in prehistory is at present undergoing a resurgence in macro-scale archaeological interpretation. In parallel to this renewed popularity, expanding access to computational tools and datasets has seen the use of aggregated radiocarbon datasets for the study of dispersals also increasing. This paper advocates for developing reflexive practice in the application of radiocarbon dates to prehistoric dispersals, by reflecting on the quality and qualities of the underlying data, particularly chronometric uncertainty, and framing dispersals explicitly in terms of hypothesis testing. This paper draws on cultural expansions within South America and employs two emblematic examples, the Arauquinoid and Tupiguarani traditions, to develop an analytical solution that not only incorporates chronometric uncertainty in bivariate regression but, importantly, tests whether the datasets provide statistically significant evidence for a dispersal process. The analysis, which the paper provides the means to replicate, identifies fundamental issues with resolution and data quality that impede identification of pre-Columbian cultural dispersals through simple spatial gradients of radiocarbon data. The results suggest that reflexivity must be fed back into theoretical frameworks of prehistoric mobility for the study of dispersals, in turn informing the construction of more critical statistical null models. As a first step, alternative models of cultural expansion should be formally considered alongside demographic models.</p>
Supplementary Data for Remote soil moisture measurement from drone-borne reflectance spectroscopy: Applications to hydroperiod measurement in desert playas
<p>This supporting dataset includes:</p> <p>• Ground-based reflectance measurements for the two plume-crossing transects (AHT3 and AHT4). Data show reflectance by wavelength at each scan position.</p> <p>• Reduced data records (RDR) showing GPS position data for the drone and the associated reflectance measurement, by wavelength, averaged over 1 second intervals for the three mapping sorties, AHS4, 5, and 7.</p> <p>• The sample datasheet showing ground-based and lab-base measurements of the sampling transects.</p>
Data from: Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil
Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Secondly, we applied the hABC models to a dataset of 7 squamate and 4 amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in Northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the expansion of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.
Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters
<p>Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and evaluates the utility of microfluidic droplets, also termed ultraminiaturized bioreactors, for rapid detection of viable Salmonella enterica ser. Typhimurium in a shredded lettuce wash water acquired from a major Mid-Atlantic produce processing facility (denoted as Producer) in the U.S. Using a fluorescentlylabeled anti- S. Typhimurium antibody and relative fluorescence intensities, paired with in-droplet incubation, S. Typhimurium was detected and identified with 100% specificity in less than 5 h. In initial optimization experiments using S. Typhimuriumspiked sterile water, the relative fluorescence intensity of S. Typhimurium was approximately two times that of the observed relative intensities of five non- S. Typhimurium negative controls at 4-h incubation in droplets containing Rappaport-Vasiliadis (RV) broth at 37 ° C: relative fluorescence intensity for S. Typhimurium = 2.36 (95% CI: 2.15-2.58), Enterobacter aerogens 1.12 (95% CI: 1.09-1.16), Escherichia coli 700609 = 1.13 (95% CI: 1.09-1.17), E. coli 13706 1.13 (95% CI: 1.07-1.19), E. coli 700891 1.05 (95% CI: 1.03-1.07) and Citrobacter freundii 1.04 (95% CI: 1.03-1.05). S. Typhimurium - and E. aerogens -spiked shredded lettuce wash waters acquired from the Producer were then incubated 4 h in-droplet at 37 ° C with RV broth. The observed relative fluorescence of S. Typhimurium was significantly higher than that of E. aerogens , 1.56 (95% CI: 1.42-1.71) and 1.10 (95% CI: 1.08-1.12), respectively. While further optimization focusing on compatible concentration methodologies for highly-dilute produce water samples is needed, this application of droplet microfluidics shows great promise in dramatically shortening the time necessary – from days to hours – to confirm viable bacterial contamination in ready-to-eat produce wash waters used throughout the domestic and international food industry.</p>
150 stacks for autofocus testing applications
<p>This dataset includes 150 stacks of images meant to be a testing resource for autofocus applications. The staks were taken over the z axis of the samples, being the best approximation to a sweep of all the possible fields of view in a sample.</p> <p>The images have a resolution of 1388x1040 pixels, and were taken from four different tissue samples (adipose, intestine, kidney, and stomach). For each tissue sample we used two magnifications, 5x and 10x, and each magnification was applied with two bit depths, 8 bits and 16 bits, resulting in a total of 16 categories. </p> <p>Each category contains 10 stacks, except for adipose tissue 10x 8 bits and 16 bits, which contain 5 stacks each.This results in a total of 150 stacks</p>
New application of strontium isotopes reveals evidence of limited migratory behaviour in Late Cretaceous hadrosaurs
<p>Dinosaur migration patterns are very difficult to determine, often relying solely on the geographic distribution of fossils. Unfortunately, it is generally not possible to determine if a fossil taxon's geographic distribution is the result of migration or simply a wide distribution. Whereas some attempts have been made to use isotopic systems to determine migratory patterns in dinosaurs, these methods have yet to achieve wider usage in the study of dinosaur ecology.</p> <p>Here we have used strontium isotope ratios from fossil enamel to reconstruct the movements of an individual hadrosaur from Dinosaur Provincial Park in Alberta, Canada. Results from this study are consistent with a range or migratory pattern between Dinosaur Provincial Park and a contemporaneous locality in the South Saskatchewan River area, Alberta Canada. This represents a minimum distance of approximately 80 km, which is consistent with migrations seen in modern elephants. These results suggest the continent-wide distribution of some hadrosaur species in the Late Cretaceous of North America is not the result of extremely long-range migratory behaviours.</p>
The ‘SAR Matrix’ method and its extensions for applications in medicinal chemistry and chemogenomics
<p>SD files of data sets reported in the manuscript that are used to generate the SARMs and CSMs are uploaded. The given data sets are represented by the corresponding figure numbers (as reported in the publication). The file format is provided in the file 'description.txt'.</p>
Data for: Elastic Application-Level Monitoring for Large Software Landscapes in the Cloud
<p>Application-level monitoring provides valuable, detailed insights into running applications. However, many approaches often only employ a single analysis application. This analysis application may become a performance bottleneck when monitoring several programs resulting in reduced monitoring quality or violated service level agreements of the monitored applications.</p> <p>We present an approach for elastic, distributed application-level monitoring for large software landscapes consisting of several hundreds of applications by utilizing cloud computing. Our approach dynamically inserts and removes worker levels to circumvent overloading the analysis master application without interrupting or pausing the actual live analysis of the monitored data. To evaluate our approach, we conduct an experiment in which we generate load - following a real workload pattern - on web applications in a 24 hour experiment.</p> <p>In our experiment, 160 monitored JPetStore instances generate roughly 20 million analyzed method calls per second in the peak. Furthermore, two worker levels are dynamically started and removed in line with the imposed workload on the monitored applications. The experiment shows that our monitoring approach is capable of live analyzing several millions of monitored method calls per second without overloading the analysis master application.</p> <p>This package provides our supplementary data.</p>
Data and plotting scripts used in "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"
<p>Raw performance data and plotting scripts used to generate the figures in the paper "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"</p>
WESSBAS: Extraction of Probabilistic Workload Specifications for Load Testing and Performance Prediction - A Model-Driven Approach for Session-Based Application Systems.
<p>Supplementary material for the paper: "WESSBAS: Extraction of Probabilistic Workload Specifications for Load Testing and Performance Prediction".</p> <p>Included in the supplementary material are the evaluation results.</p> <p>The WESSBAS software relevant to the paper is available via https://github.com/Wessbas/</p> <p>The WESSBAS UI is available as a password-protected (password: wessbasui) ZIP file:</p> <p>https://dl.dropboxusercontent.com/u/81621779/wessbas.ui.zip (--- WESSBAS GUI (license confirmation pending, i.e., not on GitHub, yet))</p>
Towards the formal verification of data-intensive applications through metric temporal logic
p>The dataset consists of a set of model descriptions representingnbsp;span>Storm topologies. It is designed on purpose to show the approach presented in the paper quot;/span>span>Towards the formal verification of data-intensive applications through m/span>span>etric/span>span>nbsp;temporalnbsp;/span>span>logicquot; (F. Marconi, M.M. Bersani, M. Erascu and M. Rossi) which focuses on the analysisnbsp;/span>span>of bottleneck nodes of data intensive applications implemented with Storm./span>/p>
Data and plotting scripts used in "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"
<p>Raw performance data and plotting scripts used to generate the figures in the paper "High level implementation of geometric multigrid solvers for finite element problems: applications in atmospheric modelling"</p> <p>A previous version of this dataset (corresponding to an earlier revision of the paper) is available as https://doi.org/10.5281/zenodo.50533.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.