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Optimization of Run Configurations of k-Wave Jobs
Sasák, Tomáš ; Jaroš, Marta (referee) ; Jaroš, Jiří (advisor)
This thesis focuses on scheduling, i.e. correct approximation of configurations used to run k-Wave simulations on supercomputers from the IT4Innovations infrastructure. Especially, for clusters Salomon and Anselm. A single work is composed of a set which contains many simulations. Every simulation is executed by some code from the k-Wave toolbox. To calculate the simulation, it is necesarry to select a suitable configuration, which means the amount of supercomputer resources (number of nodes, i.e. cores), and the duration of the rental. Creation of an ideal configuration is complicated and is even harder for an inexperienced user. The approximation is made based on the empiric data, obtained from multiple executions of different sets of simulations on given clusters. This data is stored and used by a set of approximators, which performs the actual approximation by methods of interpolation and regression. The text describes the implementation of the final scheduler. By experimenting, the most efficient methods for this problem has found out to be Akima spline, PCHIP interpolation and cubic spline. The main contribution of this work is creation of a tool which can find suitable configuration for k-Wave simulation without knowing the code or having lots of experience with its usage.
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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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Realization of supercomputer using graphic card
Jasovský, Filip ; Karásek, Jan (referee) ; Mašek, Jan (advisor)
This master´s thesis deals with realization of supercomputer using graphic card with CUDA technology. The theoretical part of this thesis describes the function and the possibility of graphic cards and desktop computers and processes taking place in the proces sof calculations on them. The practical part deals with creation system for calculations on the graphic card using the algorithm of artificial intelligence, more specifically artificial neural networks. Subsequently is the generated program used for data classification of large input data file. Finally the results are compared.
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Scalable machine learning using Hadoop and Mahout tools
Kryške, Lukáš ; Atassi, Hicham (referee) ; Burget, Radim (advisor)
This bachelor’s thesis compares several tools for building a scalable, machine learning platform and describes their advantages and disadvantages. It also practically demonstrates functionality of this scalable platform based on the Apache Hadoop and Apache Mahout tools and measures performance of the K-Means algorithm for total of five computing nodes.
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System for Supercomputer Automation Operation
Strečanský, Peter ; Hrbáček, Radek (referee) ; Jaroš, Jiří (advisor)
The main goal of this thesis is to extend already existing software FabSim by a module, which allows automated supercomputer operation, especially with OpenPBS scheduler. This module was implemented with Python programming language, using Fabric module as its backbone. The scripts, which are executed with OpenPBS are stored as the templates. These templates are dynamically modified to suit users needs. This solution provides a complex set of methods, which allows full--featured operation of supercomputers, integration with git and data management on clusters. The module saves time and makes working with supercomputers much easier.
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Scalable preprocessing of data using Hadoop tool
Marinič, Michal ; Šmirg, Ondřej (referee) ; Burget, Radim (advisor)
The thesis is concerned with scalable pre-processing of data using Hadoop tool which is used for processing of large volumes of data. In the first theoretical part it focuses on explaining of functioning and structure of the basic elements of Hadoop distributed file system and MapReduce methods for parallel processing. The latter practical part of the thesis describes the implementation of basic Hadoop cluster in pseudo-distributed mode for easy program-debugging, and also describes an implementation of Hadoop cluster in fully-distributed mode for simulation in practice.
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Parallelisation of Ultrasound Simulations Using Local Fourier Decomposition
Dohnal, Matěj ; Hrbáček, Radek (referee) ; Jaroš, Jiří (advisor)
This document introduces a brand new method of the 1D, 2D and 3D decomposition with the use of local Fourier basis, its implementation and comparison with the currently used global 1D domain decomposition. The new method was designed, implemented and tested primarily for future use in the simulation software called The k-Wave toolbox, but it can be applied in many other spectral methods. Compared to the global 1D domain decomposition, the Local Fourier decomposition is up to 3 times faster and more efficient thanks to lower inter-process communication, however it is a little inaccurate. The final part of the thesis discusses the limitations of the new method and also introduces best practices to use 3D Local Fourier decomposition to achieve both more speed and accuracy.
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Parallelization of Ultrasound Simulations Using 2D Decomposition
Nikl, Vojtěch ; Dvořák, Václav (referee) ; Jaroš, Jiří (advisor)
This thesis is a part of the k-Wave project, which is a toolbox for the simulation and reconstruction of acoustic wave felds and one of its main contributions is the planning of focused ultrasound surgeries (HIFU). One simulation can take tens of hours and about 60% of the simulation time is taken by the calculation of the 3D Fast Fourier transforms. Up until now the 3D FFT has been calculated purely by the FFTW library and its 1D decomposition, whose major limitation is the maximum number of employable cores. Therefore we introduce a new approach, called the 2D hybrid decomposition of the 3D FFT (HybridFFT), where we combine both MPI processes and OpenMP threads to reach as best performance as possible. On a low number of cores, on the order of a few hundreds, we are about as fast or slightly faster than FFTW and pure MPI 2D decomposition libraries (PFFT and P3DFFT). One of the best results was achieved on a 512^3FFT using 512 cores, where our hybrid version run 31ms, FFTW run 39ms and PFFT run 44ms. The most significant performance advantage should be seen when employing around 8-16 thousand cores, however we haven't had an access to a machine with such resources. Almost a linear scalability has been proven for up to 2048 employed cores.
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Estimation of Algorithm Execution Time Using Machine Learning
Buchta, Martin ; Chlebík, Jakub (referee) ; Jaroš, Jiří (advisor)
This work aims to predict the execution time of k-Wave ultrasound simulations on supercomputers based on a given domain size. The program uses MPI and can be run on multiple nodes. Prediction models were developed using symbolic regression and neural networks, both of which trained on captured data and compared against each other. The results demonstrate that the models outperform existing solutions. Specifically, the symbolic regression model achieved an average error of 5.64% for suitable tasks, while the neural network model achieved an average error of 8.25% on unseen domain sizes and across all tasks, including those not optimized for k-Wave simulations. This work contributes a new, more accurate model for predicting execution time, and compares the effectiveness of neural networks and symbolic regression for this specific type of regression problem. Overall, these findings suggest that new models will have important practical applications in the field of k-Wave ultrasound simulations.
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