|
|
Acceleration of Axisymetric Ultrasound Simulations
Kukliš, Filip ; Vaverka, Filip (referee) ; Jaroš, Jiří (advisor)
Simulácia šírenia ultrazvuku prostredníctvom mäkkých biologických tkanív má širokú škálu praktických aplikácií. Patria sem dizajn prevodníkov pre diagnostický a terapeutický ultrazvuk, vývoj nových metód spracovania signálov a zobrazovacích techník, štúdium anomálií ultrazvukových lúčov v heterogénnych médiách, ultrazvuková klasifikácia tkanív, učenie rádiológov používať ultrazvukové zariadenia a interpretáciu ultrazvukových obrazov, modelové vrstvenie medicínskeho obrazu a plánovanie liečby pre ultrazvuk s vysokou intenzitou. Ultrazvuková simulácia však predstavuje výpočtovo zložitý problém, pretože simulačné domény sú veľmi veľké v porovnaní s akustickými vlnovými dĺžkami, ktoré sú predmetom záujmu. Ale ak je problém osovo symetrický, problém môže byť riešený v 2D.To umožňuje spúšťanie simulácií na mriežke s väčším počtom bodov, s menším využitím výpoč- tových zdrojov za kratšiu dobu. Táto práca modeluje a implementuje zrýchlenie vlnovej nelineárnej ultrazvukovej simulácie v axisymetrickom súradnicovom systéme realizovanom v Matlabe pomocou Mex súborov pre diskrétne sínové a kosínové transformácie. Axisymetrická simulácia bola implementovaná v C++ ako open source rozšírenie K-WAVE toolboxu. Kód je optimalizovaný na beh na jednom uzle superpočítaču Salomon (IT4Innovations, Ostrava, Česká republika) s dvoma dvanásť-jadrovými procesormi Intel Xeon E5-2680v3. Na maximalizáciu výpočtovej efektívnosti boli vykonané viaceré optimalizácie kódu. Po prvé, fourierové tramsformácie boli vypočítané pomocou real-to-complex FFT z knižnice FFTW. V porovnaní s complex-to-complex FFT to znížilo čas výpočtu a pamäť spojenú s výpočtom FFT o takmer 50%. Taktiež diskrétne sínové a kosínové transformácie sa počítali pomocou knižnice FFTW, ktoré v Matlab verzii museli byť vyvolané z dynamicky načítaných MEX súborov. Po druhé, aby sa znížilo zaťaženie priepustnosti pamäte, boli všetky operácie počítané jednoduchej presnosti pohyblivej rádovej čiarky. Po tretie, elementárne operá- cie boli paralelizované pomocou OpenMP a potom vektorizované pomocou rozšírení SIMD (SSE). Celkový výpočet C++ verzie je až do 34-násobne rýchlejší a využíva menej ako tretinu pamäte ako Matlab verzia simulácie. Simulácia ktorá by trvala takmer dva dni tak môže byť vypočítaná za jeden a pol hodinu. Toto všetko umožňuje počítať simuláciu na výpočetnej mriežke s veľkosťou 16384 × 8192 bodov v primeranom čase.
|
|
|
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.
|
|
|
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.
|
|
|
Simulation of Fracture Tests in Civil Engineering
Bordovský, Gabriel ; Vaverka, Filip (referee) ; Jaroš, Jiří (advisor)
In this thesis, a program for fracture test in civil engineering has been optimized. The simulation is used for a validation of the fracture characteristics for blocks of construct material used for historic buildings reconstructure. This thesis illustrates the possibilities of an effective usage of the processor’s potential without the loss of the output quality. The individual parts of the simulation are analyzed and this thesis proposes for the critical sections some possible optimizations such as vectorization or parallel processing. The techniques used in this thesis may be used on similar computing problems and help shorten the required runtime. The prototype of the simulation was able to process the simulation in 7.7 hours. Optimized version is capable to process the same simulation in 2.1 hours on one core or 21 minutes on eight cores. The parallel optimized version is 21 times faster than the prototype.
|
|
|
Simulation of Ultrasound Propagation in Bones
Kadlubiak, Kristián ; Vaverka, Filip (referee) ; Jaroš, Jiří (advisor)
It is estimated that mind-boggling 14.1 million new cases of cancer occurred worldwide in 2012 alone. This number is alarming. Although healthy lifestyle may reduce a risk of developing cancer, there is always some probability that cancer would develop even in an absolutely fit individual. There are two main conditions for successful treatment of cancer. Firstly, early diagnostic is absolutely crucial. Secondly, there is a need for suitable surgical methods for affected tissue removal. Ultrasound has a great potential to be used for both purposes as a non-invasive method. Photoacoustic spectroscopy is imaging method for tumor detection of great properties making the use of ultrasound while High-Intensity Focused Ultrasound (HIFU) is non-invasive surgical method. These methods would be impossible without precise ultrasound propagation simulations. The k-Wave is an open source MATLAB toolbox implementing such simulations. So, why are not these methods already deployed in treatment? Unfortunately, the simulation of ultrasound propagation is a very time consuming task, which makes it ineffective for medical purposes. However, there are a few options how to accelerate these simulations. The use of GPU is a very promising way to accelerate simulation. The main topic of this thesis is the acceleration of the simulation of soundwaves propagation in bones and hard tissue. The implementation developed as a part of this thesis was benchmarked on various supercomputers including Anselm in Ostrava and Piz Daint in Lugano. The implemented solution provides remarkable acceleration compared to the original MATLAB prototype. It was able to accelerate the simulation around 160 times in the best case. It means that the simulation, which would otherwise last for 6.5 days, can be now computed in one hour. This acceleration was achieved using an NVIDIA Tesla P100 to run the simulation with the domain size of 416x416x416 grid points. The thesis includes performance benchmarks on different GPUs to provide complex image acceleration capabilities of developed implementation and provides discussion about memory usage and numerical accuracy. Thanks to the implemented solution harnessing the power of modern GPUs, doctors and researchers all around the world have a powerful tool in hands.
|
|
|
Water Simulation Using GPU
Hanzlíček, Jiří ; Jaroš, Jiří (referee) ; Vaverka, Filip (advisor)
The goal of this thesis is to find a suitable model of fluids, the numerical simulation of which can be realized as interactive program. This requirement leads to a solution based on highly parallel algorithm. The implementation is built not only for CPU, but also GPU in a way, that allows to compare computational performance of each device on selected model.
|
|
|
Overclocking of Modern Processors with an Emphasis on Performance, Power Consumption and Temperature
Kelečéni, Jakub ; Vaverka, Filip (referee) ; Nikl, Vojtěch (advisor)
This thesis analyzes the dependency of performance, power consumption and temperature on processor frequency. Theoretical part discusses the processor architecture, benchmarks and algorithm types. Experimental part is focused on benchmarks - matrix multiplication, Quicksort, PI number calculation, Ackermann function, LAMMPS, PMBW, Linpack. This set of benchmarks includes both single-threaded and multi-threaded algorithms. Testing consist of three different settings of processor frequency. Multi-threaded benchmarks using different number of threads. Informations regarding the power consumption of CPU and RAM were recorded during these tests. Every test logs his running time. The impact of parallelization on power consumption and runtime is also reflected. Results from the tests are shown in charts and tables. The proper configuration of CPU for each given algorithm is analyzed in conclusion.
|
|
|
GPU-Accelerated Design of Optically Generated Ultrasound Using Binary Amplitude Holograms
Knotek, Martin ; Vaverka, Filip (referee) ; Jaroš, Jiří (advisor)
In this thesis, we deal with the possibilities of the acceleration of scientific computations using the graphical processing unit. The term scientific computation in this context means an algorithm, which computes binary holograms that are used to generate ultrasound. We will concentrate specifically on the design of the hologram, focusing at the speed we can achieve when computing the surface of the hologram. For this purpose, we will use two popular parallel data processing platforms - CUDA and OpenMP. The surface design pattern of the hologram is important due to the fact, that it determines the hologram’s specific physical characteristics.
|
|
|
Digital Filter Design on GPU
Vaverka, Filip ; Maršík, Lukáš (referee) ; Polok, Lukáš (advisor)
This thesis shows one of the approaches to the design of ditigal filters with infinite impulse response and specified order. The proposed solution is based on an evolutionary genetic algorithm and therefore allows for direct filter design from its specification. Its main contribution to this subject is that the implementation is parallel and it is acceleraded by GPU. The filters are designed in cascade representation. It also allows to specify both, the desired frequency and phase characteristics of filters.
|
|
|
Mobile Robot Localization Using Camera
Vaverka, Filip ; Orság, Filip (referee) ; Rozman, Jaroslav (advisor)
This thesis describes design and implementation of an approach to the mobile robot localization. The proposed method is based purely on images taken by a monocular camera. The described solution handles localization as an association problem and, therefore, falls in the category of topological localization methods. The method is based on a generative probabilistic model of the environment appearance. The proposed solution is capable to eliminate some of the difficulties which are common in traditional localization approaches.
|
guest ::
RSS feed.