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Search results for: HPC
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Use of ICT infrastructure for teaching HPC
PublicationIn 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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Using Redis supported by NVRAM in HPC applications
PublicationNowadays, the efficiency of storage systems is a bottleneck in many modern HPC clusters. High performance in the traditional approach – processing using files – is often difficult to obtain because of a model’s complexity and its read/write patterns. An alternative approach is to apply a key-value database, which usually has low latency and scales well. On the other hand, many key-value stores suffer from a limitation of memory...
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Network-aware Data Prefetching Optimization of Computations in a Heterogeneous HPC Framework
PublicationRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublicationIn 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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A Regular Expression Matching Application with Configurable Data Intensity for Testing Heterogeneous HPC Systems
PublicationModern High Performance Computing (HPC) systems are becoming increasingly heterogeneous in terms of utilized hardware, as well as software solutions. The problems, that we wish to efficiently solve using those systems have different complexity, not only considering magnitude, but also the type of complexity: computation, data or communication intensity. Developing new mechanisms for dealing with those complexities or choosing an...
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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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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Dynamic Data Management Among Multiple Databases for Optimization of Parallel Computations in Heterogeneous HPC Systems
PublicationRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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Simulation of Parallel Applications on Large-scale Distributed Systems
PublicationThis chapter has a form of a review article in the field of simulating High-Performance Computing systems. We justify the need for a new versatile simulator considering heterogeneity, energy efficiency and reliability of HPC systems. We sketch the problems that need to be solved by such simulator and rationalize using discrete-event simulation for this purpose. Based on a review of existing discrete-event HPC simulation solutions...
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Higher platelet counts correlate to tumour progression and can be induced by intratumoural stroma in non-metastatic breast carcinomas
PublicationBackground Platelets support tumour progression. However, their prognostic significance and relation to circulating tumour cells (CTCs) in operable breast cancer (BrCa) are still scarcely known and, thus, merit further investigation. Methods Preoperative platelet counts (PCs) were compared with clinical data, CTCs, 65 serum cytokines and 770 immune-related transcripts obtained using the NanoString technology. Results High normal...
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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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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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Efficiency Evaluation of High Performance Computing Systems Using Data Envelopment Analysis
PublicationThe paper presents an evaluation method of high performance computing (HPC) systems using multicriteria efficiency analysis. The Data Envelopment Analysis approach was applied and adapted to the specifics of HPC, which enabled us to compare relative efficiency of systems considering simultaneously multiple parameters. The analysis is based on the TOP500 list of world largest supercomputers and their parameters such as: the number...
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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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Optimization of hybrid parallel application execution in heterogeneous high performance computing systems considering execution time and power consumption
PublicationMany important computational problems require utilization of high performance computing (HPC) systems that consist of multi-level structures combining higher and higher numbers of devices with various characteristics. Utilizing full power of such systems requires programming parallel applications that are hybrid in two meanings: they can utilize parallelism on multiple levels at the same time and combine together programming interfaces...
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Process arrival pattern aware algorithms for acceleration of scatter and gather operations
PublicationImbalanced process arrival patterns (PAPs) are ubiquitous in many parallel and distributed systems, especially in HPC ones. The collective operations, e.g. in MPI, are designed for equal process arrival times (PATs), and are not optimized for deviations in their appearance. We propose eight new PAP-aware algorithms for the scatter and gather operations. They are binomial or linear tree adaptations introducing additional process...
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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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Superkomputery do wspomagania procesów gospodarczych ze szczególnym uwzględnieniem sektora bankowego
PublicationW artykule omówiono wykorzystanie superkomputerów do wspomagania procesów gospodarczych ze szczególnym uwzględnieniem sektora bankowego. Odniesiono się do wybranych projektów wspierających rozwój gospodarczy w oparciu o superkomputery. W szczególności zaproponowano zastosowanie HPC do implementacji wybranych metod sztucznej inteligencji w bankowości, w tym oceny ryzyka wybranych przedsięwzięć. Zaproponowane podejście umożliwia...
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Modifiers for Medical Grade Polymeric Systems used in FDM 3D Printing - Short Review
PublicationFDM 3D printing could find an application in the wide range of biomedical applications. Unfortunately, the quantity of polymeric biomaterials suitable to processing into filaments is limited. The most frequently used biomaterials for medical constructs such as bone grafts, soft tissue scaffolds or another DDS include PCL, PLA, PVA, HPC, EVA copolymer, EC and TPUs. Various modifiers such as TCP, HA, TEC, MMC could be applicated...
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All-gather Algorithms Resilient to Imbalanced Process Arrival Patterns
PublicationTwo 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...