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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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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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Efficient Communication in Multi-GPU Systems
Špeťko, Matej ; Jaroš, Jiří (referee) ; Vaverka, Filip (advisor)
After the introduction of CUDA by Nvidia, the GPUs became devices capable of accelerating any general purpose computation. GPUs are designed as parallel processors which posses huge computation power. Modern supercomputers are often equipped with GPU accelerators. Sometimes single GPU performance is not enough for a scientific application and it needs to scale over multiple GPUs. During the computation, there is a need for the GPUs to exchange partial results. This communication represents computation overhead and it is important to research methods of the effective communication between GPUs. This means less CPU involvement, lower latency and shared system buffers. This thesis is focused on inter-node and intra-node GPU-to-GPU communication using GPUDirect technologies from Nvidia and CUDA-Aware MPI. Subsequently, k-Wave toolbox for simulating the propagation of acoustic waves is introduced. This application is accelerated by using CUDA-Aware MPI. Peer-to-peer transfer support is also integrated to k-Wave using CUDA Inter-process Communication.
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Efficient Communication in Multi-GPU Systems
Špeťko, Matej ; Jaroš, Jiří (referee) ; Vaverka, Filip (advisor)
After the introduction of CUDA by Nvidia, the GPUs became devices capable of accelerating any general purpose computation. GPUs are designed as parallel processors which posses huge computation power. Modern supercomputers are often equipped with GPU accelerators. Sometimes the performance or the memory capacity of a single GPU is not enough for a scientific application. The application needs to be scaled into multiple GPUs. During the computation there is need for the GPUs to exchange partial results. This communication represents computation overhead. For this reason it is important to research the methods of the effective communication between GPUs. This means less CPU involvement, lower latency, shared system buffers. Inter-node and intra-node communication is examined. The main focus is on GPUDirect technologies from Nvidia and CUDA-Aware MPI. Subsequently k-Wave toolbox for simulating the propagation of acoustic waves is introduced. This application is accelerated by using CUDA-Aware MPI.
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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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Political activity of Anselm of Canterbury
Kalina, Jan ; Suchánek, Drahomír (advisor) ; Drška, Václav (referee)
The thesis aims to describe Anselm's years as prior and abbot and his archiepiscopal career. Analyzing the years spent in the Norman monastery of Bec as a missionary and teacher in its school, the thesis notes the amount of knowledge and experiences which prepared Anselm for his archiepiscopal career. His intellectual qualities and theories are examined as well as some of his highly influential theological texts. Anselm also strove to spread the reforms of his teacher and mentor at Bec and his predecessor at Canterbury, Archbishop Lanfranc. Anselm's following archiepiscopal career spanned the reigns of two kings: William Rufus and Henry I. The study proves that the policies and attitudes of both rulers were quite different. Under the reign of William Rufus, Anselm tried to bring his ideal theoretical state of things into actuality, but the king resisted everything he attempted to do. With his death, Anselm's position changed rapidly and dramatically. Henry, on the other hand, excelled in the ability to work out a compromise. In the end, Anselm's archiepiscopal career concluded with cooperation between king and archbishop.
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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.
|
|
|
Efficient Communication in Multi-GPU Systems
Špeťko, Matej ; Jaroš, Jiří (referee) ; Vaverka, Filip (advisor)
After the introduction of CUDA by Nvidia, the GPUs became devices capable of accelerating any general purpose computation. GPUs are designed as parallel processors which posses huge computation power. Modern supercomputers are often equipped with GPU accelerators. Sometimes the performance or the memory capacity of a single GPU is not enough for a scientific application. The application needs to be scaled into multiple GPUs. During the computation there is need for the GPUs to exchange partial results. This communication represents computation overhead. For this reason it is important to research the methods of the effective communication between GPUs. This means less CPU involvement, lower latency, shared system buffers. Inter-node and intra-node communication is examined. The main focus is on GPUDirect technologies from Nvidia and CUDA-Aware MPI. Subsequently k-Wave toolbox for simulating the propagation of acoustic waves is introduced. This application is accelerated by using CUDA-Aware MPI.
|
|
|
Efficient Communication in Multi-GPU Systems
Špeťko, Matej ; Jaroš, Jiří (referee) ; Vaverka, Filip (advisor)
After the introduction of CUDA by Nvidia, the GPUs became devices capable of accelerating any general purpose computation. GPUs are designed as parallel processors which posses huge computation power. Modern supercomputers are often equipped with GPU accelerators. Sometimes single GPU performance is not enough for a scientific application and it needs to scale over multiple GPUs. During the computation, there is a need for the GPUs to exchange partial results. This communication represents computation overhead and it is important to research methods of the effective communication between GPUs. This means less CPU involvement, lower latency and shared system buffers. This thesis is focused on inter-node and intra-node GPU-to-GPU communication using GPUDirect technologies from Nvidia and CUDA-Aware MPI. Subsequently, k-Wave toolbox for simulating the propagation of acoustic waves is introduced. This application is accelerated by using CUDA-Aware MPI. Peer-to-peer transfer support is also integrated to k-Wave using CUDA Inter-process Communication.
|
|
|
Political activity of Anselm of Canterbury
Kalina, Jan ; Suchánek, Drahomír (advisor) ; Drška, Václav (referee)
The thesis aims to describe Anselm's years as prior and abbot and his archiepiscopal career. Analyzing the years spent in the Norman monastery of Bec as a missionary and teacher in its school, the thesis notes the amount of knowledge and experiences which prepared Anselm for his archiepiscopal career. His intellectual qualities and theories are examined as well as some of his highly influential theological texts. Anselm also strove to spread the reforms of his teacher and mentor at Bec and his predecessor at Canterbury, Archbishop Lanfranc. Anselm's following archiepiscopal career spanned the reigns of two kings: William Rufus and Henry I. The study proves that the policies and attitudes of both rulers were quite different. Under the reign of William Rufus, Anselm tried to bring his ideal theoretical state of things into actuality, but the king resisted everything he attempted to do. With his death, Anselm's position changed rapidly and dramatically. Henry, on the other hand, excelled in the ability to work out a compromise. In the end, Anselm's archiepiscopal career concluded with cooperation between king and archbishop.
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