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Year 2024
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Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
PublicationGraphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended...
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Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales
PublicationCoarse-grained models are nowadays extensively used in biomolecular simulations owing to the tremendous extension of size- and time-scale of simulations. The physics-based UNRES (UNited RESidue) model of proteins developed in our laboratory has only two interaction sites per amino-acid residue (united peptide groups and united side chains) and implicit solvent. However, owing to rigorous physics-based derivation, which enabled...
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Teaching High–performance Computing Systems – A Case Study with Parallel Programming APIs: MPI, OpenMP and CUDA
PublicationHigh performance computing (HPC) education has become essential in recent years, especially that parallel computing on high performance computing systems enables modern machine learning models to grow in scale. This significant increase in the computational power of modern supercomputers relies on a large number of cores in modern CPUs and GPUs. As a consequence, parallel program development based on parallel thinking has become...
Year 2023
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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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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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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
Year 2022
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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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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...
Year 2021
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
Year 2020
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Performance/energy aware optimization of parallel applications on GPUs under power capping
PublicationIn the paper we present an approach and results from application of the modern power capping mechanism available for NVIDIA GPUs to the bench- marks such as NAS Parallel Benchmarks BT, SP and LU as well as cublasgemm- benchmark which are widely used for assessment of high performance computing systems’ performance. Specifically, depending on the benchmarks, various power cap configurations are best for desired trade-off of performance...
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Survey of Methodologies, Approaches, and Challenges in Parallel Programming Using High-Performance Computing Systems
PublicationThis paper provides a review of contemporary methodologies and APIs for parallel programming, with representative technologies selected in terms of target system type (shared memory, distributed, and hybrid), communication patterns (one-sided and two-sided), and programming abstraction level. We analyze representatives in terms of many aspects including programming model, languages, supported platforms, license, optimization goals,...
Year 2019
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Detection of the Oocyte Orientation for the ICSI Method Automation
PublicationAutomation or even computer assistance of the popular infertility treatment method: ICSI (Intracytoplasmic Sperm Injection) would speed up the whole process and improve the control of the results. This paper introduces a preliminary research for automatic spermatozoon injection into the oocyte cytoplasm. Here, the method for detection a correct orientation of the polar body of the oocyte is presented. Proposed method uses deep...
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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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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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Influence of YARN Schedulers on Power Consumption and Processing Time for Various Big Data Benchmarks
PublicationClimate change caused by human activities can influence the lives of everybody onthe planet. The environmental concerns must be taken into consideration by all fields of studyincludingICT. Green Computing aims to reduce negative effects of IT on the environment while,at the same time, maintaining all of the possible benefits it provides. Several Big Data platformslike Apache Spark orYARNhave become widely used in analytics and...
Year 2018
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Analyzing energy/performance trade-offs with power capping for parallel applications on modern multi and many core processors
PublicationIn the paper we present extensive results from analyzing energy/performance trade-offs with power capping observed on four different modern CPUs, for three different parallel applications such as 2D heat distribution, numerical integration and Fast Fourier Transform. The CPU tested represent both multi-core type CPUs such as Intel⃝R Xeon⃝R E5, desktop and mobile i7 as well as many-core Intel⃝R Xeon PhiTM x200 but also server, desktop...
Year 2017
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Multidimensional GIS for satellite imagery analysis
PublicationMultidimensional Geographical Information System allows storing, querying and processing of multidimensional query data. It is able to process satellite imagery and provide tools for its analysis. In the article authors present the developed system that analyzes a time series of SENTINEL - 1 mission satellite imagery acquired over the coast of Poland. The algorithm used finds and detects changes in the shape...
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Parallelization of Selected Algorithms on Multi-core CPUs, a Cluster and in a Hybrid CPU+Xeon Phi Environment
PublicationIn the paper we present parallel implementations as well as execution times and speed-ups of three different algorithms run in various environments such as on a workstation with multi-core CPUs and a cluster. The parallel codes, implementing the master-slave model in C+MPI, differ in computation to communication ratios. The considered problems include: a genetic algorithm with various ratios of master processing time to communication...
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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...
Year 2016
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SOLAP GIS in maritime research
PublicationMultidimensional Geographical Information System is a system especially designed to acquire, distribute, analyze and visualize complicated spatio-temporal data. Modern Geographical Information System technology can provide easy-to-use, near real-time solutions to many problems from different areas of research. In the article, authors summarize recent works on Spatial Online Analytical Processing (SOLAP) and multidimensional Geographical...
Year 2015
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DESIGN OF THE DUAL CONSTELLATION GPS/GALILEO MOBILE DEVICE FOR IMPROVING NAVIGATION OF THE VISUALLY IMPAIRED IN AN URBAN AREA
PublicationIt is well known by users of Personal Navigation Device (PND) and other GPS-based devices that positioning suffers from (local) significant decreases of accuracy in partially obscured environments like urbanized areas, where buildings (especially high buildings), trees or terrain block large portions of the sky. In such areas, GPS receiver performance is usually deteriorated by the reduced number of currently available satellite...
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DESIGN OF THE DUAL CONSTELLATION GPS/GALILEO MOBILE DEVICE FOR IMPROVING NAVIGATION OF THE VISUALLY IMPAIRED IN AN URBAN AREA, POLISH MARITIME RESEARCH
PublicationThe article discusses damages of essential tribological associations in crankshaft and piston systems of large power two-stroke engines used as main engines, which take place during transport tasks performed by those ships. Difficulties are named which make preventing those damages impossible, despite the fact that the technical state of engines of this type is identified with the aid of complex diagnostic systems making use of...
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DUAL CONSTELLATION GPS/GALILEO MOBILE SYSTEM FOR IMPROVING NAVIGATION OF THE VISUALLY IMPAIRED IN AN URBAN AREA
PublicationIt is well known by users of Portable Navigation Device (PND) and other GPS-based devices that positioning suffers from (local) significant decreases of accuracy in partially obscured environments like urbanized areas, where buildings (especially high buildings), trees or terrain block large portions of the sky. In such areas, GPS receiver performance is usually deteriorated by the reduced number of currently available satellite...
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METHOD TO EXTEND OPERATIONABILITY OF WEB-GIS BASED MARINE SERVICES USING SSE PLATFORM
PublicationEarth Observation (EO) products are widely used by geospatial society. Over the last years a number of new applications of satellite imagery were proposed. This led to an increased interest in EO products, not only from researchers but also from companies and individuals. The authors constitute the essential part of the team that created the marine, web-GIS system - SafeCity GIS - for dissemination of data obtained from a 1.5...
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SSE PLATFORM APPLICATION TO EXTEND OPERATIONABILITY OF WEB-GIS BASED MARINE SERVICES OF AN HRPT-METOP SATELLITE GROUND STATION
PublicationEarth Observation (EO) products are widely used by geospatial society. Over the last years a number of new applications of satellite imagery were proposed. This led to an increased interest in EO products, not only from researchers but also from companies and individuals. The authors constitute the essential part of the team that created the marine, web-GIS system - SafeCity GIS - for dissemination of data obtained from a 1.5 metre...
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Using Rule-Based System for Monitoring Marine Navigation Data Processing
PublicationProcessing marine navigational data requires sophisticated software solutions. Typically, specialized tools called processors are analyzing raw data from different sensors. It becomes important to create the monitoring software that is able to validate and verify processing components integrated into the final system. Drools®business rule management platform provides a core business rules engine, web authoring and rules management...
Year 2014
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Using EO satellite data in Safe City and Coastal Zone web-GIS
PublicationThe paper presents a novel design of a web-based Safe City & Coastal Zone GIS (SCCZ-GIS) which integrates data acquired from different remote sensing and geospatial data sources for monitoring the security of the coastal zone, its inhabitants and Critical Infrastructure. The system utilizes several innovative technologies and directly co-operates with different remote sensing data sources and services, like a satellite ground station...
Year 2013
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Application development for Android, iOS and BlackBerry mobile platforms
PublicationMobile devices, along with dedicated operating systems, have become a substantial and rising trend in software development. Computer industry has significantly changed in order to fulfil the needs of this new segment of the market. Authors have participated in projects, which involved programming on Android, iOS and BlackBerry operating systems. In this paper the most popular mobile platforms (and multiplatform Unity3D environment)...
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Client-server Approach in the Navigation System for the Blind
PublicationThe article presents the client‐server approach in the navigation system for the blind ‐ “Voice Maps”. The authors were among the main creators of the prototype and currently the commercialization phase is being finished. In the implemented prototype only exemplary, limited spatial data were used, therefore they could be stored and analysed (for path-finding process) in the mobile device’s memory without any difficulties. The...
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GIS for processing multidimensional marine data in SAAS model
PublicationGeographic Information Systems (GIS) have always been a useful tool for visualization and processing of geospatial data. However, their capabilities of analysis non-standard information such as hydroacoustic soundings has thus far been very limited. This paper proposes a general-purpose GIS which uses techniques such as OLAP, WCS and WCPS for processing of multidimensional spatio-temporal data. The versatility of the GIS is exemplified...
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GIS Solution for Weather Forecast Data Analysis
PublicationIn this paper authors present the GIS system for the analysis of the numerical weather prediction data. This kind of data has multidimensional character (three dimensions and time) and its analysis should consider all the available factors. Proposed GIS system consists of RASDAMAN application with implemented OLAP cube mechanism, which enables the user to process data in the spatial-time domain. It also simplifies the meteorological...
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Methods of navigation in the mobile application supporting movement of the blind
PublicationThis paper presents conclusions from the last development phase of the “Voice Maps” project. Authors specify newly found available options for navigation in affordable system for the blind with all their related aspects. System uses dedicated geographical data, built-in smartphone GPS receivers and DGPS external device in order to assist blind users in their everyday travelling. Authors also discuss new methods to improve positioning...
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Operational Enhancement of Numerical Weather Prediction with Data from Real-time Satellite Images
PublicationNumerical weather prediction (NWP) is a rapidly expanding field of science, which is related to meteorology, remote sensing and computer science. Authors present methods of enhancing WRF EMS (Weather Research and Forecast Environmental Modeling System) weather prediction system using data from satellites equipped with AMSU sensor (Advanced Microwave Sounding Unit). The data is acquired with Department of Geoinformatics’ ground...
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Remote Spatial Database Access in the Navigation System for the Blind
PublicationThe article presents the problem of a database access in the navigation systems. The authors were among the main creators of the prototype navigation system for the blind - “Voice Maps”. In the implemented prototype only exemplary, limited spatial data were used, therefore they could be stored in the mobile device’s memory without any difficulties. Currently the aforementioned system is being prepared for commercialization - the...
Year 2012
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Architektura rozproszonego systemu udostępniającego wyniki numerycznych prognoz pogody
PublicationW artykule przedstawiono architekturę systemu udostępniania wyników numerycznych prognoz pogody do którego należą m.in. serwer, portal internetowy oraz mobilne aplikacje klienckie, które wizualizują na różne sposoby dane pogodowe pobrane z serwera. Oprogramowanie mobilne przeznaczone jest na najpopularniejsze platformy mobilne, czyli iOS (min. iPhone, iPad, iPod) oraz Android. Prototyp systemu funkcjonuje operacyjnie w ramach...
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System numerycznej prognozy pogody oparty na pakiecie WRF EMS
PublicationW artykule przedstawiono zagadnienia dotyczące wykorzystania systemów numerycznego prognozowania pogody przy pomocy oprogramowania wchodzącego w skład pakietu WRF EMS (ang. Weather Research and Forecast Environmental Modeling System). Artykuł opisuje podstawowe równania modelujące procesy w atmosferze oraz architekturę systemu numerycznego prognozowania pogody WRF EMS. Przedstawiono także architekturę prototypu systemu informacji...