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Use of ICT infrastructure for teaching HPC
PublikacjaIn this paper we look at modern ICT infrastructure as well as curriculum used for conducting a contemporary course on high performance computing taught over several years at the Faculty of Electronics Telecommunications and Informatics, Gdansk University of Technology, Poland. We describe the infrastructure in the context of teaching parallel programming at the cluster level using MPI, node level using OpenMP and CUDA. We present...
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Electrochemical Characterization of Gelatine Derived Ceramics
PublikacjaNew materials obtained by pyrolysis of gelatine (G) and poly(1,2-dimethylsilazane) (PSN) (weight ratio: G/PSN 70/30) at temperatures 700 and 900 °C were characterized by SEM and Raman spectroscopy. The presence of ceramics influences on the cluster size of the materials. Electrochemical tests were performed by cyclic voltammetry and galvanostatic cyclic polarization. The capacity of G/PSN was 464 and 527 mAh/g for materials pyrolysed...
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Shoreline Extraction Based on LiDAR Data Obtained Using an USV
PublikacjaThis article explores the use of Light Detection And Ranging (LiDAR) derived point clouds to extract the shoreline of the Lake Kłodno (Poland), based on their geometry properties. The data collection was performed using the Velodyne VLP‐16 laser scanner, which was mounted on the HydroDron Unmanned Surface Vehicle (USV). A modified version of the shoreline extraction method proposed by Xu et al. was employed, comprising of the following...
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A Fail-Safe NVRAM Based Mechanism for Efficient Creation and Recovery of Data Copies in Parallel MPI Applications
PublikacjaThe paper presents a fail-safe NVRAM based mechanism for creation and recovery of data copies during parallel MPI application runtime. Specifically, we target a cluster environment in which each node has an NVRAM installed in it. Our previously developed extension to the MPI I/O API can take advantage of NVRAM regions in order to provide an NVRAM based cache like mechanism to significantly speed up I/O operations and allow to preload...
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HMSE: A tool for coupling MODFLOW and HYDRUS-1D computer programs
PublikacjaA new software HMSE has been developed to facilitate external coupling between two well-known programs for subsurface flow modeling: MODFLOW-2005 (saturated zone flow) and HYDRUS-1D (unsaturated zone flow). Two coupling schemes have been implemented. In the first case the groundwater recharge flux is calculated by HYDRUS-1D assuming a fixed water table position and then passed to MODFLOW input files. In the second case the water...
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Li nucleation on the graphite anode under potential control in Li-ion batteries
PublikacjaApplication of Li-ion batteries in electric vehicles requires improved safety, increased lifetime and high charging rates. One of the most commonly used intercalation anode material for Li-ion batteries, graphite, is vulnerable to Li nucleation, a side reaction which competes with the intercalation process and leads to loss of reversible capacity of the battery, ageing and short-circuits. In this study, we deploy a combined grand...
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Theoretical study of the structure, energetics and vibrational frequencies of water-acetone and water-2-butanone complexes
PublikacjaKompleksy acetonu i 2-butanonu z 0-2 cząsteczkami wody połączonymi wiązaniem wodorowym z tlenem karbonylowym zbadano z wykorzystaniem teorii funkcjonału gęstości (DFT) na poziomie B3LYP/6-311++G(d,p). Obliczenia w fazie gazowej uzupełniono o optymalizacje w otoczeniu rozpuszczalnika, symulowanego za pomocą modelu polaryzowalnego kontinuum (PCM). Częstości drgań oscylacyjnych otrzymane na podstawie zależności empirycznej sa zgodne...
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Modeling energy consumption of parallel applications
PublikacjaThe paper presents modeling and simulation of energy consumption of two types of parallel applications: geometric Single Program Multiple Data (SPMD) and divide-and-conquer (DAC). Simulation is performed in a new MERPSYS environment. Model of an application uses the Java language with extension representing message exchange between processes working in parallel. Simulation is performed by running threads representing distinct process...
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Valence and lowest Rydberg electronic states of phenol investigated by synchrotron radiation and theoretical methods
PublikacjaWe present the experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectra of phenol covering for the first time the full 4.3–10.8 eV energy-range, with absolute cross sections determined. Theoretical calculations on the vertical excitation energies and oscillator strengths were performed using time-dependent density functional theory and the equation-of-motion coupled cluster method restricted to single and double...
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On a matching distance between rooted phylogenetic trees
PublikacjaThe Robinson–Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach...
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Theoretical study of the photoelectron spectrum of ethyl formate: Ab initio and density functional theory investigation
PublikacjaThe first ionization energy and associated photoelectron spectrum of ethyl formate are investigated with quantum chemistry calculations. The geometries, harmonic vibrational frequencies and first ionization energy are computed at the Hartree-Fock (HF) and at the second order Moller-Plesset perturbation theory (MP2). Moreover, accurate ionization energies are obtained with the Coupled-Cluster theory including singles and doubles...
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Multi-state vibronic interactions in the fluorobenzene radical cation: The importance of quadratic coupling terms
PublikacjaThe multi-mode multi-state vibronic interactions in the set of X^2B_1 - D^2A_1 electronic states of the monofluoro benzene radical cation are investigated theoretically, based on a quadratic vibronic coupling approach. The underlying ionization potentials and coupling constants are obtained from ab initio coupled-cluster calculations. Previous investigations (relying on the linear coupling approach) are extended by including all...
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Project-Based Collaborative Research and Training Roadmap for Manufacturing Based on Industry 4.0
PublikacjaThe importance of the economy being up to date with the latest developments, such as Industry 4.0, is more evident than ever before. Successful implementation of Industry 4.0 principles requires close cooperation of industry and state authorities with universities. A paradigm of such cooperation is described in this paper stemming from university partners with partly overlapping and partly complementary areas of expertise in manufacturing....
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Information Retrieval in Wikipedia with Conceptual Directions
PublikacjaThe paper describes our algorithm used for retrieval of textual information from Wikipedia. The experiments show that the algorithm allows to improve typical evaluation measures of retrieval quality. The improvement of the retrieval results was achieved by two phase usage approach. In first the algorithm extends the set of content that has been indexed by the specified keywords and thus increases the Recall value. Then, using the...
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Three levels of fail-safe mode in MPI I/O NVRAM distributed cache
PublikacjaThe paper presents architecture and design of three versions for fail-safe data storage in a distributed cache using NVRAM in cluster nodes. In the first one, cache consistency is assured through additional buffering write requests. The second one is based on additional write log managers running on different nodes. The third one benefits from synchronization with a Parallel File System (PFS) for saving data into a new file which...
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Configurations of H 3 + (H2)n clusters and their energies
PublikacjaThe H-3(+) ion plays an important role in low temperature astrophysical and laboratory plasmas. It is considered as the initiator of many ion-molecule chemistries. Also its clusters with H-2 are quite interesting. We study configurations of the H-3(+)(H-2)(n) clusters for n = 1 up to n = 12 as a simple test system. Total energies for these structures, with zero point vibration corrections have been calculated. Stabilization energies...
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Finger Vein Presentation Attack Detection Method Using a Hybridized Gray-Level Co-Occurrence Matrix Feature with Light-Gradient Boosting Machine Model
PublikacjaPresentation Attack Detection (PAD) is crucial in biometric finger vein recognition. The susceptibility of these systems to forged finger vein images is a significant challenge. Existing approaches to mitigate presentation attacks have computational complexity limitations and limited data availability. This study proposed a novel method for identifying presentation attacks in finger vein biometric systems. We have used optimal...
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Evaluation of Machine Learning Methods for the Experimental Classification and Clustering of Higher Education Institutions
PublikacjaHigher education institutions have a big impact on the future of skills supplied on the labour market. It means that depending on the changes in labour market, higher education institutions are making changes to fields of study or adding new ones to fulfil the demand on labour market. The significant changes on labour market caused by digital transformation, resulted in new jobs and new skills. Because of the necessity of computer...
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Aggregation properties of some zirconium phosphate loaded with dirhenium(III) complexes
PublikacjaOne of the important areas of modern science is the selection of the right forms of drug delivery. Layered inorganic nanoparticles, such as zirconium phosphate, have proven themselves well in this area. The study of the properties of these systems and methods of their preparation makes it possible to determine a rational technology of their manufacture, storage conditions as well as suggest a possible mechanism of therapeutic action....
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A Parallel MPI I/O Solution Supported by Byte-addressable Non-volatile RAM Distributed Cache
PublikacjaWhile many scientific, large-scale applications are data-intensive, fast and efficient I/O operations have become of key importance for HPC environments. We propose an MPI I/O extension based on in-system distributed cache with data located in Non-volatile Random Access Memory (NVRAM) available in each cluster node. The presented architecture makes effective use of NVRAM properties such as persistence and byte-level access behind...
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Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
PublikacjaThe thermally induced self-healing mechanisms in metallopolymers based on bisterpyridine complexes of iron(II) sulfate and cadmium(II) bromide, respectively, were studied by means of combined quantum mechanical/molecular mechanical (QM/MM) simulations and Raman spectroscopy. Two possible healing schemes, one based on a decomplexation of the cross-linking complexes and a second one relying on the dissociation of ionic clusters,...
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All-gather Algorithms Resilient to Imbalanced Process Arrival Patterns
PublikacjaTwo novel algorithms for the all-gather operation resilient to imbalanced process arrival patterns (PATs) are presented. The first one, Background Disseminated Ring (BDR), is based on the regular parallel ring algorithm often supplied in MPI implementations and exploits an auxiliary background thread for early data exchange from faster processes to accelerate the performed all-gather operation. The other algorithm, Background Sorted...
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Adaptive system for recognition of sounds indicating threats to security of people and property employing parallel processing of audio data streams
PublikacjaA system for recognition of threatening acoustic events employing parallel processing on a supercomputing cluster is featured. The methods for detection, parameterization and classication of acoustic events are introduced. The recognition engine is based onthreshold-based detection with adaptive threshold and Support Vector Machine classifcation. Spectral, temporal and mel-frequency descriptors are used as signal features. The...
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Personalized nutrition in ageing society: redox control of major-age related diseases through the NutRedOx Network (COST Action CA16112)
PublikacjaA healthy ageing process is important when it is considered that one-third of the population of Europe is already over 50 years old, although there are regional variations. This proportion is likely to increase in the future, and maintenance of vitality at an older age is not only an important measure of the quality of life but also key to participation and productivity. So, the binomial “nutrition and ageing” has different aspects...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublikacjaCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublikacjaIn this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects...
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The electronic excited states of dichloromethane in the 5.8-10.8 eV energy range investigated by experimental and theoretical methods
PublikacjaWe present a comprehensive experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectrum of dichloromethane, CH 2 Cl 2 , with absolute cross sections determined for the full 5.8–10.8 eV energy-range. The calculations on the vertical excitation energies and oscillator strengths were performed using the equation-of-motion coupled cluster method, restricted to the single and double excitations level (EOM-CCSD), and...
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Homoleptic mono-, di-, and tetra-iron complexes featuring phosphido ligands: a synthetic, structural, and spectroscopic study
PublikacjaWe report the first series of homoleptic phosphido iron complexes synthesized by treating either the β-diketiminato complex [(Dippnacnac)FeCl2Li(dme)2] (Dippnacnac = HC[(CMe)N(C6H3-2,6-iPr2)]2) or [FeBr2(thf )2] with an excess of phosphides R2PLi (R = tBu, tBuPh, Cy, iPr). Reaction outcomes depend strongly on the bulkiness of the phosphido ligands. The use of tBu2PLi precursor led to an anionic diiron complex 1 encompassing a planar...
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Collision‐Aware Routing Using Multi‐Objective Seagull Optimization Algorithm for WSN‐Based IoT
PublikacjaIn recent trends, wireless sensor networks (WSNs) have become popular because of their cost, simple structure, reliability, and developments in the communication field. The Internet of Things (IoT) refers to the interconnection of everyday objects and sharing of information through the Internet. Congestion in networks leads to transmission delays and packet loss and causes wastage of time and energy on recovery. The routing protocols...
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Distributed System For Noise Threat Evaluation Based On Psychoacoustic Measurements
PublikacjaAn innovative system designed for the continuous monitoring of acoustic climate of urban areas was presentedin the paper. The assessment of environmental threats is performed using online data, acquired through a grid ofengineered monitoring stations collecting comprehensive information about the acoustic climate of urban areas.The grid of proposed devices provides valuable data for the purpose of long and short time acoustic climateanalysis....
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Approximation algorithms for job scheduling with block-type conflict graphs
PublikacjaThe problem of scheduling jobs on parallel machines (identical, uniform, or unrelated), under incompatibility relation modeled as a block graph, under the makespan optimality criterion, is considered in this paper. No two jobs that are in the relation (equivalently in the same block) may be scheduled on the same machine in this model. The presented model stems from a well-established line of research combining scheduling theory...
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Understanding the kinetics and atmospheric degradation mechanism of chlorotrifluoroethylene (CF2=CFCl) initiated by OH radicals
PublikacjaThe atmospheric degradation of chlorotrifluoroethylene (CTFE) by OH˙ was investigated using density functional theory (DFT). The potential energy surfaces were also defined in terms of single-point energies derived from the linked cluster CCSD(T) theory. With an energy barrier of −2.62 to −0.99 kcal mol−1 using the M06-2x method, the negative temperature dependence was determined. The OH˙ attack on Cα and Cβ atoms (labeled pathways...
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Fuzzy Divisive Hierarchical Clustering of Solvents According to Their Experimentally and Theoretically Predicted Descriptors
PublikacjaThe present study describes a simple procedure to separate into patterns of similarity a large group of solvents, 259 in total, presented by 15 specific descriptors (experimentally found and theoretically predicted physicochemical parameters). Solvent data is usually characterized by its high variability, dierent molecular symmetry, and spatial orientation. Methods of chemometrics can usefully be used to extract and explore accurately...
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublikacjaCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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A multithreaded CUDA and OpenMP based power‐aware programming framework for multi‐node GPU systems
PublikacjaIn the paper, we have proposed a framework that allows programming a parallel application for a multi-node system, with one or more GPUs per node, using an OpenMP+extended CUDA API. OpenMP is used for launching threads responsible for management of particular GPUs and extended CUDA calls allow to manage CUDA objects, data and launch kernels. The framework hides inter-node MPI communication from the programmer who can benefit from...
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Scheduling of compatible jobs on parallel machines
PublikacjaThe dissertation discusses the problems of scheduling compatible jobs on parallel machines. Some jobs are incompatible, which is modeled as a binary relation on the set of jobs; the relation is often modeled by an incompatibility graph. We consider two models of machines. The first model, more emphasized in the thesis, is a classical model of scheduling, where each machine does one job at time. The second one is a model of p-batching...
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An algorithm for selecting a machine learning method for predicting nitrous oxide emissions in municipal wastewater treatment plants
PublikacjaThis study presents an advanced algorithm for selecting machine learning (ML) models for nitrous oxide (N2O) emission prediction in wastewater treatment plants (WWTPs) employing the activated sludge process. The examined ML models comprised multivariate adaptive regression spline (MARS), support vector machines (SVM), and extreme gradient boosting (XGboost). The study explores the concept that involves new criteria to select the...