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Search results for: peptide profile
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Podstawowe metody integracji aplikacji trójwarstwowych
PublicationW niniejszym rozdziale przedstawiono klasyfikację metod integracji aplikacji trójwarstwowych. Opisano modele i sposoby rozwiązań dla każdej z typowych warstw: bazy danych, pośredniej i GUI oraz przykłady konkretnego ich wykorzystania wraz z diagramami sekwencji. Przeprowadzono analizę jakościową dla każdego z opisanych modeli, zaproponowano metryki dla parametrów jakościowych: modyfikowalności, spójności danych i wydajności wraz...
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Real-Time Multimedia Stream data Processing in a Supercomputer Environment
PublicationRozdział opisuje doświadczenia uzyskane przez autorów podczas pracy w projekcie MAYDAY EURO 2012. Przedstawiono główny cel projektu - stworzenie systemu umożliwiającego rozwijanie i równolegle wykonywanie usług multimedialnych w środowisku klastra obliczeniowego dużej mocy. opisano tematykę przetwarzania dużej liczby strumieni multimedialnych na komputerach dużej mocy. Następnie zaprezentowano możliwości platformy KASKADA: tworzenie...
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Task Allocation and Scalability Evaluation for Real-Time Multimedia Processing in a Cluster Envirinment
PublicationAn allocation algorithm for stream processing tasks is proposed (Modified best Fit Descendent, MBFD). A comparison with another solution (BFD) is provided. Tests of the algorithms in an HPC environment are descrobed and the results are presented. A proper scalability metric is proposed and used for the evaluation of the allocation algorithm.
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The task graph assignment for KASKADA platform
PublicationArtykuł opisuje model obliczeniowy wykorzystany w platformie KASKADA. Opiera się on na dwóch podstawowych elementach: węzłach klastra obliczeniowego oraz grafie zadań. Przeanalizowane zostały algorytmy przydzielania węzłów obliczeniowych dla zadań w zależności od kryteriów: minimalizacja fragmentacji klastra i minimalizacja opóźnienia przetwarzania danych. Zostały przedstawione wyniki symulacji opisanych algorytmów oraz ich...
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Przetwarzanie strumieni multimedialnych z użyciem klastra obliczeniowego
PublicationZaprezentowano docelową funkcjonalność platformy KASKADA oraz sposób konstrukcji kolejnych warstw. Przedstwiono metodę opisu zadań oraz metodę implementacji zadań uzytkowych (framework), których głównym celem jest analiza strumieni multimedialnych dla identyfikacji charakterystycznych obiektów (np. twarzy) oraz niebezpiecznych zdarzeń 9np. bójka0. Zaprezentowano również strategie wykonania tych zadań na komputerze klastrowym w...
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Performance and Power-Aware Modeling of MPI Applications for Cluster Computing
PublicationThe paper presents modeling of performance and power consumption when running parallel applications on modern cluster-based systems. The model includes basic so-called blocks representing either computations or communication. The latter includes both point-to-point and collective communication. Real measurements were performed using MPI applications and routines run on three different clusters with both Infiniband and Gigabit Ethernet...
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Processing of Satellite Data in the Cloud
PublicationThe dynamic development of digital technologies, especially those dedicated to devices generating large data streams, such as all kinds of measurement equipment (temperature and humidity sensors, cameras, radio-telescopes and satellites – Internet of Things) enables more in-depth analysis of the surrounding reality, including better understanding of various natural phenomenon, starting from atomic level reactions, through macroscopic...
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Improving Clairvoyant: reduction algorithm resilient to imbalanced process arrival patterns
PublicationThe Clairvoyant algorithm proposed in “A novel MPI reduction algorithm resilient to imbalances in process arrival times” was analyzed, commented and improved. The comments concern handling certain edge cases in the original pseudocode and description, i.e., adding another state of a process, improved cache friendliness more precise complexity estimations and some other issues improving the robustness of the algorithm implementation....
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Understanding the early-stage release of volatile organic compounds from rapeseed oil during deep-frying of tubers by targeted and omics-inspired approaches using PTR-MS and gas chromatography
PublicationDuring deep-frying, a plethora of volatile products is emitted with the fumes. These compounds could act as oil quality indicators and change the indoor air composition leading to health risks for occupants. The presented experiments focus on deep-frying of different tubers in rapeseed oil at different frying temperatures. Here, two scenarios for real-time monitoring of volatile organic compounds (VOCs) using proton transfer reaction...
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The Importance of Demand and Environment for Defining and Establishing the Role of Data Stewards
PublicationData stewardship is now a central part of FAIR research data management. Although various types of positions called data stewards have been created at academic institutions over the last years, no demand-oriented, formal model of data stewardship and the associated roles exist so far. This workshop report presents the outcomes of the panel discussion “The Importance of Demand and Environment for Defining Data Stewardship” held...
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Shaping the competence of future spatial policymakers for small- and medium-sized towns
PublicationIn this article, the authors aim to present issues addressed within the framework of the architecture and spatial development courses offered by the Faculty of Architecture at Gdańsk University of Technology (FA-GUT), Gdańsk, Poland. These issues concern competence in the education of future spatial planners and their readiness to deal with the development challenges facing small- and medium-sized towns. Within the article, the...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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WPŁYW PARAMETRÓW PROCESU SBM NA DYSTRYBUCJĘ TWORZYWA W BUTELKACH PET – PRZEGLĄD LITERATURY
PublicationZ mechanicznego punktu widzenia profil grubości butelek PET jest uwarunkowany mechaniczno-cieplną odpowiedzią tworzywa rozdmuchiwanej preformy na zadane parametry procesu SBM. Z mikroskopowego punktu widzenia na mechaniczne i termiczne właściwości butelek CSD z PET największy wpływ mają procesy orientowania i krystalizowania tworzywa. Z technologicznego punkty widzenia profil grubości butelek PET po procesie produkcji metodą SBM...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Processing, physico-mechanical and thermal properties of reclaimed GTR and NBR/reclaimed GTR blends as function of various additives
PublicationIn this work, ground tire rubber (GTR) was mechano-chemically reclaimed in the presence of bitumen and various additives. During studies three types of processing and curing additives: (i) peptizer P300; (ii) vulcanization accelerator tetramethylthiuram disulfide (TMTD) and (iii) organic peroxide di(2-tert-butyl-peroxyisopropyl)benzene (BIB1) were applied to enhance reclaiming of GTR. Reclaiming process was evaluated by oscillating...
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Poly-L-Lysine-modified boron-doped diamond electrodes for the amperometric detection of nucleic acid bases
PublicationBoron-doped diamond (BDD) is a very promising supporting material used in the construction of biosensors for molecular recognition. The direct immobilization of structurally-organized huge molecules, such as poly-L-Lysine (PLL) provides the possibility of determining organic molecules, e.g. nucleic acid bases (e.g. adenine, guanine) or peptides and proteins. This paper describes the direct method for chemical and electrochemical...
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Evaluation of a Small Inland Ferry’s Energy Requirements from the Acceleration Stage of Towing Tank Model Tests
PublicationComputing the power required to meet a ship’s operational needs is one of the most important tasks in naval design. The power required to propel a vessel is directly related to the resistance the hull experiences as it moves through the water. The conventional method of determining a ship’s resistance involves towing tank tests of ship models at a fixed speed; however, for short-range vessels, where constant speed is not the primary...
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Time fractional analysis of Casson fluid with application of novel hybrid fractional derivative operator
PublicationA new approach is used to investigate the analytical solutions of the mathematical fractional Casson fluid model that is described by the Constant Proportional Caputo fractional operator having non-local and singular kernel near an infinitely vertical plate. The phenomenon has been expressed in terms of partial differential equations, and the governing equations were then transformed in non-dimensional form. For the sake of generalized...
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Host and pathogen factors in Klebsiella pneumoniae upper urinary tract infections in renal transplant patients
PublicationPurpose . To analyse the role of virulence factors (VFs) and host in Klebsiella pneumoniae upper urinary tract infections (UTIs) in renal transplant (RTx) recipients. Methodology. Clinical and demographic data were registered prospectively. Phylogenetic background of K. pneumoniae isolates was analysed by PCR melting profiles (MP) and the following VFs genes: fimH-1, uge, kpn, ycfM, mrkD, rmpA, magA, hlyA, cnf-1, irp-1, irp-2,...
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A method to synthesise groove cam Geneva mechanisms with increased dwell period
PublicationThe present study develops a method to synthesise the groove cam Geneva mechanism with increased dwell period. The main condition of the synthesis is to provide the desired law of motion of the wheel. Additional synthesis conditions are the limitation of the maximum pressure angle and the limitation of the minimum curvature radius of the cam profile. Unlike the conventional Geneva mechanisms, the synthesised groove cam Geneva mechanisms...
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RDF dataset profiling - a survey of features, methods, vocabularies and applications
PublicationThe Web of Data, and in particular Linked Data, has seen tremendous growth over the past years. However, reuse and take-up of these rich data sources is often limited and focused on a few well-known and established RDF datasets. This can be partially attributed to the lack of reliable and up-to-date information about the characteristics of available datasets. While RDF datasets vary heavily with respect to the features related...
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Interaction of the conserved region 4.2 of sigma(E) with the RseA anti-sigma factor
PublicationEo-E RNA polymerase transcribes a regulon of folding factors for the bacterial envelope and is induced by physical and chemical stresses. The RseA anti-sigma factor inhibits the activity of Esigma(E) RNA, polymerase. It is shown here that the N-terminal portion of sigma(E), residues 1-153, binds core RNA polymerase. RseA interacts with residues 154-191 of sigma(E), a site that is homologous to region 4, the sigma factor binding...
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Accuracy of Trajectory Tracking Based on Nonlinear Guidance Logic for Hydrographic Unmanned Surface Vessels
PublicationA new trend in recent years for hydrographic measurement in water bodies is the use of unmanned surface vehicles (USVs). In the process of navigation by USVs, it is particularly important to control position precisely on the measuring profile. Precise navigation with respect to the measuring profile avoids registration of redundant data and thus saves time and survey costs. This article addresses the issue of precise navigation...
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Scheduling for Industrial Control Traffic Using Massive MIMO and Large Intelligent Surfaces
PublicationIndustry 4.0, with its focus on flexibility and customizability, is pushing in the direction of wireless communication in future smart factories, in particular massive multiple-input multiple-output (MIMO), and its future evolution Large Intelligent Surfaces (LIS), which provide more reliable channel quality than previous technologies. As such, there arises the need to perform efficient scheduling of industrial control traffic...
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Comparison of Average Energy Slope Estimation Formulas for One-dimensional Steady Gradually Varied Flow
PublicationTo find the steady flow water surface profile, it is possible to use Bernoulli’s equation, which is a discrete form of the differential energy equation. Such an approach requires the average energy slope between cross-sections to be estimated. In the literature, many methods are proposed for estimating the average energy slope in this case, such as the arithmetic mean, resulting in the standard step method, the harmonic mean and...
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Badania nośności na zginanie innowacyjnego kształtownika giętego na zimno typu GEB
PublicationLekkie konstrukcje metalowe wytwarzane z kształtowników giętych na zimno to jedna z najszybciej rozwijających się dyscyplin w zakresie budownictwa. Do niedawna profile gięte na zimno stosowano wyłącznie jako elementy drugorzędne, czyli płatwie oraz rygle. Nowo opatentowany przekrój typu GEB ma być wykorzystywany jako element nośny konstrukcji ramowych. Jednak jego zaistnienie na rynku budowlanych konstrukcji metalowych jest uwarunkowane...
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APPLICABILITY OF INLET AIR FOGGING TO MARINE GAS TURBINE
PublicationThe dependency of marine gas turbine on the ambient temperature leads to a decrease of the gas turbine power output in arid areas. Very often gas turbine power output demand is high and the power margins originally designed into the driver , has been exhausted. In such circumstances the inlet air fogging is an effective compensation of gas turbine power. In this paper an analysis of inlet air fogging applicability to marine gas...
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Enzymatic degradation and transport of endothiopeptides into Escherichia coli K12 mutant strains
PublicationZbadano transport trzech otrzymanych na drodze syntezy ditiopeptydów do komórek Escherichia coli K12. Ponadto zbadano szybkość hydrolizy tych związków. Wszystkie peptydy są transportowane przez permeazy, natomiast są bardziej oporne na hydrolizę enzymatyczną w stosunku do naturalnych peptydów.
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Anticandiadal properties of N-acylpeptides containing inhibitor of glucosamine-6-phosphate synthase
PublicationOtrzymano serię N-acylopeptydów zawierających inhibitor syntazy glukozamino-6-fosforanu i zbadano ich aktywność w stosunku do szczepów Candida albicans. Aktywność przeciwgrzybową skorelowano z właściwościami lipofilowymi otrzymanych peptydów. Peptydy zawierające resztę kwasu dekanowego wykazywały najwyższą aktywność przeciwgrzybową.
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WYKORZYSTANIE TESTU MUSHRA W BADANIU KORZYŚCI UŻYTKOWANIA PROTEZ SŁUCHOWYCH
PublicationOcena jakości dopasowania aparatów słuchowych w kontekście korzyści, jakie może przy-nieść proteza jest złożonym zagadnieniem. Obiektywne parametry aparatów, które można wy-znaczyć (np. wzmocnienie czy pasmo przenoszenia) nie zawsze mają bezpośredni i decydujący wpływ w subiektywnej ocenie jakości dopasowania protezy słuchowej przez pacjenta. Pomiary efektywności aparatu słuchowego mogą dotyczyć wielu aspektów, między innymi kompensacji...
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Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series
PublicationIntermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel...
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Interactions of fish gelatin and chitosan in uncrosslinked and crosslinked with EDC films: FT-IR study
PublicationFilms based on fish gelatin, chitosan and blend of fish gelatin and chitosan before and after cross-linking with EDC have been characterized by FT-IR spectroscopy. The FT-IR spectrum of fish gelatin film showed the characteristic amide I, amide II and amide III bands, and the FT-IR spectrum of chitosan film confirmed that the polymer was only a partially deacetylated product, and included CH3-C=O and NH2 groups, the latter both...
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Naturalne związki organiczne
PublicationKsiążka zawiera dwanaście rozdziałów merytorycznych, w których omówiono występowanie, właściwości, otrzymywanie i zastosowanie następujących naturalnych organicznych: aminokwasy, peptydy, białka, cukry, lipidy, alkaloidy, steroidy, kwasy nukleinowe, polifenole i flawonoidy, hormony owadzie i roślinne, terpenoidy i izoterpenoidy oraz związki sygnałowe (feromony).
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On topology optimization of large deformation contact-aided shape morphing compliant mechanisms
PublicationA topology optimization approach for designing large deformation contact-aided shape morphing compliant mechanisms is presented. Such mechanisms can be used in varying operating conditions. Design domains are described by regular hexagonal elements. Negative circular masks are employed to perform dual task, i.e., to decide material states of each element and also, to generate rigid contact surfaces. Each mask is characterized by...
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Combining MUSHRA Test and Fuzzy Logic in the Evaluation of Benefits of Using Hearing Prostheses
PublicationAssessing the effectiveness of hearing aid fittings based on the benefits they provide is crucial but intricate. While objective metrics of hearing aids like gain, frequency response, and distortion are measurable, they do not directly indicate user benefits. Hearing aid performance assessment encompasses various aspects, such as compensating for hearing loss and user satisfaction. The authors suggest enhancing the widely used...
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On Tradeoffs Between Width- and Fill-like Graph Parameters
PublicationIn this work we consider two two-criteria optimization problems: given an input graph, the goal is to find its interval (or chordal) supergraph that minimizes the number of edges and its clique number simultaneously. For the interval supergraph, the problem can be restated as simultaneous minimization of the path width pw(G) and the profile p(G) of the input graph G. We prove that for an arbitrary graph G and an integer t ∈ {1,...
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Data Analysis in Bridge of Data
PublicationThe chapter presents the data analysis aspects of the Bridge of Data project. The software framework used, Jupyter, and its configuration are presented. The solution’s architecture, including the TRYTON supercomputer as the underlying infrastructure, is described. The use case templates provided by the Stat-reducer application are presented, including data analysis related to spatial points’ cloud-, audio- and wind-related research.
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DEPO: A dynamic energy‐performance optimizer tool for automatic power capping for energy efficient high‐performance computing
PublicationIn the article we propose an automatic power capping software tool DEPO that allows one to perform runtime optimization of performance and energy related metrics. For an assumed application model with an initialization phase followed by a running phase with uniform compute and memory intensity, the tool performs automatic tuning engaging one of the two exploration algorithms—linear search (LS) and golden section search (GSS), finds...
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Extended investigation of performance-energy trade-offs under power capping in HPC environments
Publication—In the paper we present investigation of performance-energy trade-offs under power capping using modern processors. The results are presented for systems targeted at both server and client markets and were collected from Intel Xeon E5 and Intel Xeon Phi server processors as well as from desktop and mobile Intel Core i7 processors. The results, when using power capping, show that we can find various interesting combinations of...
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Energy-Aware High-Performance Computing: Survey of State-of-the-Art Tools, Techniques, and Environments
PublicationThe paper presents state of the art of energy-aware high-performance computing (HPC), in particular identification and classification of approaches by system and device types, optimization metrics, and energy/power control methods. System types include single device, clusters, grids, and clouds while considered device types include CPUs, GPUs, multiprocessor, and hybrid systems. Optimization goals include various combinations of...
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GPU Power Capping for Energy-Performance Trade-Offs in Training of Deep Convolutional Neural Networks for Image Recognition
PublicationIn the paper we present performance-energy trade-off investigation of training Deep Convolutional Neural Networks for image recognition. Several representative and widely adopted network models, such as Alexnet, VGG-19, Inception V3, Inception V4, Resnet50 and Resnet152 were tested using systems with Nvidia Quadro RTX 6000 as well as Nvidia V100 GPUs. Using GPU power capping we found other than default configurations minimizing...
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Parallel processing of multimedia streams
PublicationW artykule zaprezentowana jest nowa biblioteka wspierającą tworzenie zadań obliczeniowych, część platformy KASKADA.Przedstawiony został projekt biblioteki, uwzględniający diagram głównych klas oraz diagram sekwencji. Drugi z diagramów ukazuje współpracę głównych klas w procesie przetwarzania strumieni multimedialnych. W dalszej częsci omówione zostały szczegły mechanizmu komunikacji międzyzadawniowej oraz przedstawiony został graf...
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Metody testowania platformy KASKADA
PublicationW rozdziale przedstawiono wykorzystywany iteracyjny i inkrementalny proces wytwarzania oprogramowania, ze szczególnym uwzględnieniem planowania, wykonywania i śledzenia testów oprogramowania platformy KASKADA. Zaprezentowano model V i przykłady testów jednostkowych, systemowych, wydajnościowych i wiarygodnościowych. Przedstawiono wybrane wyniki testów oraz ich wpływ na konstrukcję platformy.
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Systemy monitorowania na platformie KASKADA
PublicationW artykule znajduje się opis projektu pt. „MAYDAY EURO 2012” Superkomputerowa platforma kontekstowej analizy strumieni danych multimedialnych do identyfikacji wyspecyfikowanych obiektów lub niebezpiecznych zdarzeń. Projekt jest współfinansowany z Europejskiego Funduszu Rozwoju Regionalnego i Budżetu Państwa w ramach Programu Operacyjnego Innowacyjna Gospodarka. KASKADA jest platformą na klastrze komputerowym (superkomputer Galera)...
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Dystrybucja, archiwizacja i przetwarzanie strumieni multimedialnych na platformie KASKADA
PublicationZaprezentowano metody przetwarzania strumieni multimedialnych na platformie KASKADA. Przedstawiono koncepcję dystrybucji strumieni do zadań obliczeniowych wykonywanych na poszczególnych węzłach klastra komputerowego. Zaprezentowano w jaki sposób dane strumieni są konwertowane i dostosowywane do wykorzystywania przez algorytmy obudowane w tzw. Ramkę KASKADA. Przedstawiono projekt i implementację archiwum strumieni multimedialnych...
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Energy-Aware Scheduling for High-Performance Computing Systems: A Survey
PublicationHigh-performance computing (HPC), according to its name, is traditionally oriented toward performance, especially the execution time and scalability of the computations. However, due to the high cost and environmental issues, energy consumption has already become a very important factor that needs to be considered. The paper presents a survey of energy-aware scheduling methods used in a modern HPC environment, starting with the...
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Dynamic GPU power capping with online performance tracing for energy efficient GPU computing using DEPO tool
PublicationGPU accelerators have become essential to the recent advance in computational power of high- performance computing (HPC) systems. Current HPC systems’ reaching an approximately 20–30 mega-watt power demand has resulted in increasing CO2 emissions, energy costs and necessitate increasingly complex cooling systems. This is a very real challenge. To address this, new mechanisms of software power control could be employed. In this...
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KASKADA Platform in Cloud Environment
PublicationKASKADA is a computing platform for developing and running services and applications oriented to multimedia processing and data streaming. A solution for serving the platform in the PaaS model is presented. The paper briefly describes the software for creating the private cloud environment based on the OpenStack software. The coud has been deployed to a supercomputer working in C2 NIWA at the Gdansk University of technology. This...
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Tryton Supercomputer Capabilities for Analysis of Massive Data Streams
PublicationThe recently deployed supercomputer Tryton, located in the Academic Computer Center of Gdansk University of Technology, provides great means for massive parallel processing. Moreover, the status of the Center as one of the main network nodes in the PIONIER network enables the fast and reliable transfer of data produced by miscellaneous devices scattered in the area of the whole country. The typical examples of such data are streams...
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Integracja usług multimedialnych na przykładzie platformy KASKADA
PublicationOpisano metody integracji wykorzystywane podczas tworzenia aplikacji na platformie KASKADA. Przedstawiono trzy podstawowe elementy podlegające integracji: aplikacje, usługi i urządzenia zewnętrzne. Zaproponowano metody współpracy między nimi, jak również przedstawiono szczegóły techniczne komunikacji: usługi sieciowe dla synchronicznego wykonywania usług, system kolejkowy dla asynchronicznej wymiany wiadomości oraz specjalnie zaprojektowany...