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General-Purpose Computation Using Graphics Card
Boček, Michal ; Pospíchal, Petr (referee) ; Jaroš, Jiří (advisor)
This thesis describes the programming models OpenCL and CUDA for Parallel Programming adapters and in case of OpenCL even for other computing platforms. There was implemented the application which calculates the electric potential in the crystalline lattice. The algorithm was programmed using two technologies for the GPU - OpenCL and CUDA. Their computational time were compared together with computational time of the CPU.
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Parallel Application Development with Intel Threading Tools
Vadkerti, Ladislav ; Jaroš, Jiří (referee) ; Dvořák, Václav (advisor)
Today's trend in microprocessor design is increasing the number of execution cores within one single chip. Increasing the processor's clock speed reached its limit with growing power consumption. This trend brings new opportunities to software developers, as they can take advantage of real multithreading in their applications. But a lot of new problems to solve appear with threading compared to sequential programming. With proper design, threading can enhance performance by making better use of hardware resources. However, the improper use of threading can lead to performance degradation, unpredictible behavior, or error conditions that are difficult to solve. For this reason Intel developed a suite of tools, that can help software developers to analyze performance and detect coding errors in thread interactions. This thesis focuses on the examination of ways that this tools can be used in multithreaded application development.
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Continuous Integration System for the k-Wave Project
Nečas, Radek ; Kešner, Filip (referee) ; Jaroš, Jiří (advisor)
The main goal of this thesis is to describe the implementation of continuous integration into the k-Wave project. The thesis focuses primarily on the version written in the C/C++ language with the usage of the OpenMP library which typically runs on supercomputers. Accordingly, many of popular workflows and approaches ought to be adapted, a few more created. The outcome of the thesis is a complete solution with real and practical usage. The author provides design, tools selection, runtime environment administration and configuration for each one of the used services. Software implementation of the basic framework is used in order to utilize running tests on the supercomputers. Furthermore, the implementation of chosen types of regression and unit tests are performed. Realisation is based on Gitlab and Jenkis services that are running on separated Docker containers.
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Simulation of Heat Diffusion in the Brain Using High-Level GPGPU Techniques
Krbila, Martin ; Kadlubiak, Kristián (referee) ; Jaroš, Jiří (advisor)
This master's thesis deals with acceleration of heat diffusion simulation using graphics cards. It describes an approach to acceleration of an existing implementation in Matlab, which is a part of k-Wave package. Various high-level as well as low-level libraries for GPU programming are introduced here and their strengths and weaknesses compared. A complete implementation of the simulation on GPU was created as a part of this work. This implementation achieves around hundredfold speedup over the existing CPU solution in Matlab. A module for computation of discrete trigonometric transformations on graphics card was created to accelerate simulation with various boundary conditions. This module achieves around ten times speedup over the best CPU implementation. Another output of this thesis is a performance comparison of several implementations of basic diffusion simulation each using a different GPGPU technique.
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Evulation of the Financial Situation in the Firm and Proposals to its Improvement
Chalásová, Kristína ; Cesnak, Marek (referee) ; Jaroš, Jiří (advisor)
The thesis ‘Evaluation of the financial situation in the firm and proposals to its improvement’ deals with the financial analysis and evaluates the financial situation of the company. The first part defines the theoretical foundations of processing the financial analysis, its tools, methods and ways of using. The subject of the second part is the application of selected methods of financial analysis and proposed recommendations how to solve problem areas, reduce the weaknesses and improve the financial situation of the company.
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The Shortest Graph's Pahts Finding
Jágr, Petr ; Ohlídal, Miloš (referee) ; Jaroš, Jiří (advisor)
The aim of this thesis is finding, comparing and implementation of algorithms for finding the shortest paths between each of pairs of nodes in a graph. For this task I use modifications of existing algorithms to achive the lowest time consumption of the computation. Modifications are established on Dijkstra's and Floyd-Warshall's algorithm. We also familiarize with Bellman-Ford algorithm.
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Parallelisation of Ultrasound Simulations on Multi-GPU Clusters
Dujíček, Aleš ; Kula, Michal (referee) ; Jaroš, Jiří (advisor)
This work is part of the k-Wave project, which is a toolbox designed for time ultrasound simulations in complex and heterogeneous media. The simulation functions are based on the k-space pseudospectral method. The goal of this work is to compute these simulations on graphics cards using local domain decompostion. Thanks to decomposition we could compute these simulations faster, and on larger data grids. The main goal of this work is to achieve efficiency and scalability.
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Optimization of the Distributed I/O Subsystem of the k-Wave Project
Vysocký, Ondřej ; Klepárník, Petr (referee) ; Jaroš, Jiří (advisor)
This thesis deals with an effective solution of the parallel I/O of the k-Wave tool, which is designed for time domain acoustic and ultrasound simulations. k-Wave is a supercomputer application, it runs on a Lustre file system and it requires to be implemented with MPI and stores the data in suitable data format (HDF5). I designed three methods of optimization which fits k-Wave's needs. It uses accumulation and redistribution techniques. In comparison with the native write, every optimization method led to better write speed, up to 13.6GB/s. It is possible to use these methods to optimize every data distributed application with the write speed issue.
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Implementation of 2D Ultrasound Simulations
Šimek, Dominik ; Vaverka, Filip (referee) ; Jaroš, Jiří (advisor)
The work deals with design and implementation of 2D ultrasound simulation. Applications of the ultrasound simulation can be found in medicine, biophysic or image reconstruction. As an example of using the ultrasound simulation we can mention High Intensity Focused Ultrasound that is used for diagnosing and treating cancer. The program is part of the k-Wave toolbox designed for supercomputer systems, specifically for machines with shared memory architecture. The program is implemented in the C++ language and using OpenMP acceleration. Using the designed solution, it is possible to solve large-scale simulations in 2D space. The work also deals with merging and unification of the 2D and 3D simulation using modern C++. A realistic example of use is ultrasound simulation in transcranial neuromodulation and neurostimulation in large domains, which have more than 16384x16384 grid points. Simulation of such size may take several days if we use the original MATLAB 2D k-Wave. Speedup of the new implementation is up to 8 on the Anselm and Salomon supercomputers.
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