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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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Development and Programming of Low Power Cluster
Hradecký, Michal ; Nikl, Vojtěch (referee) ; Jaroš, Jiří (advisor)
This thesis deals with the building and programming of a low power cluster composed of Hardkernel Odroid XU4 kits based on ARM Cortex A15 and Cortex A7 chips. The goal was to design a simple cluster composed of multiple kits and run a set of benchmarks to analyze performance and power consumption. The test set consisted of HPL and Stream benchmarks and various tests for the MPI interface. The overall performance of the cluster composed of four kits in HPL benchmark was measured 23~GFLOP/s in double-precision. During this test, the cluster showed power efficiency about 0.58~GFLOP/W. The work also describes the installation of PBS Torque scheduler and HPC software build and installation framework EasyBuild on 32-bit ARM platform. The comparison with Anselm supercomputer showed that Odroid cluster is as effiecient as large supercomputer but with slightly higher price.
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Physically Based Shading
Matěj, Šimon ; Lysek, Tomáš (referee) ; Starka, Tomáš (advisor)
This thesis deals with imaging of materials in computer graphics, using rendering methods based on physical properties of these materials. Physical principles of light propagation and its interactions with objects are analyzed, several rendering methods based on these principles are described and then analyzed for suitability in implementations. Some of these methods are demonstrated in application.
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Physically Based Rendering
Herrgott, Jiří ; Pečiva, Jan (referee) ; Starka, Tomáš (advisor)
This bachelor thesis is focused on rendering of 3D models in real time, where emphasis is placed on physical properties of simulated light rays. The work is about techniques that deal with this issue and then their use for drawing a physically approximated model.
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Coherent optical communication systems
Štohl, Jakub ; Münster, Petr (referee) ; Kočí, Lukáš (advisor)
This bachelor thesis deals with the possibilities of coherent optical networks. Describes the elements of a coherent network. The practical part deals with the simulation of coherent optical networks using PM-QPSK and PM-16QAM modulation for bandwidth of 112 Gbit/s and 224 Gbit/s.
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Effect of changing ionic strength on the properties of catanionic vesicles from HTMA-DS
Filipová, Lenka ; Klučáková, Martina (referee) ; Mravec, Filip (advisor)
This diploma thesis is focused on evaluating the influence of ionic strength on catanionic vesicules made of ion pair amphiphile (IPA) in the form of HTMA-DS (hexadecyltrimethylammonium-dodecyl sulphate). Catanionic vesicles were stabilized by the addition of cationic surfactant dioctadecyldimethylammonium chloride (DODAC) and cholesterol. The ionic strength was attained by adding CaCl2 and Na2SO4 salts in the concentrations 0–300 mM. The changes influenced by ionic strength were studied by dynamic and electrophoretic light scattering (DLS and ELS), fluorescence anisotropy, generalized polarization (GP), pH measurement, and visual observation. During this experiment, the temperature was set both constant and altering in time. The measurement was performed shortly after adding salts to the catanionic vesicles and in-time measurement was performed as well. This thesis follows a bachelor thesis, where the influence of NaCl on the same type of catanionic vesicles in the same range of ionic strength was studied. The CaCl2 and Na2SO4 influences were then compared to the NaCl according to Hofmeister series. By the DLS and ELS method it was found that the size of vesicles with added CaCl2 and Na2SO4 was decreasing at first and then increasing whereas the -potential was exponentially decreasing with increasing ionic strength. The vesicle size, when the ionic strength was applied, was increasing in time while -potential was almost constant in time. The addition of both salts caused slight dehydration of the external part of the membrane which was examined by the fluorescent probe Laurdan (6-dodecanoyl-2-dimethylamino-naphthalene) and generalized polarization. By fluorescence anisotropy with the probe DPH (1,6-diphenyl-1,3,5-hexatriene), it was detected that both salts caused an increase of the fluidity of an inner part of a membrane. By both of the fluorescent techniques, it was confirmed that the increase in temperature caused a phase transition of the membrane from the solid ordered through the liquid ordered phase to the liquid disordered phase. The pH values also did not show any change with the addition of salts. When comparing the salts’ influence (CaCl2 and Na2SO4 versus NaCl) on catanionic vesicles it was found that in most cases NaCl influenced the observed properties the most. The addition of NaCl caused the largest increase in vesicle size, highest -potential values, initial dehydration of the external part of the membrane, and increased fluidity of the inner part of the membrane at I > 15 mM. These results are in agreement with the Hofmeister series. Based on the visual observation, the samples with ionic strength of more than 150 mM for CaCl2 and 75 mM for Na2SO4 were said to be unstable. This fact is in agreement with the result of ELS. The rest of the samples did not show any visual changes in time (28 days). Additionally, the influence of PBS buffer on catanionic vesicles at the same ionic strength values was studied. PBS buffer simulates the ionic environment of living organisms. Its' influence was characterized by the same methods under the same conditions as mentioned above. The effect of PBS on catanionic vesicles displayed almost the same behaviour in the observed properties. During this experiment, it was also found that the PBS influence on the studied properties was more significant than the influence of CaCl2, Na2SO4, and NaCl salts. Influence of PBS was most similar to the effect of NaCl on catanionic vesicles.
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The content and binding of silver in galena
Němec, Matěj ; Goliáš, Viktor (advisor) ; Zachariáš, Jiří (referee)
Galena as the most important silverbearing ore is found in almost every Ag deposit. If the content of Ag is higher than 0,5 wt. % then is called galena solid solution - PbSss. The galena Ag has two forms of occurrence - inclusions and isomorphic silver. Aboat ninety percent of galena Ag is product of retrograde proces of PbSss cooling. These are matildite (AgBiS2), miargyrite (AgSbS2), diaforite (PbAg3Sb3S8), freislebenite (AgPbSbS3), pyrargyrite (Ag3SbS3) aramayoite (Ag(Sb,Bi)S2), freibergite (Ag12Sb4S13), gustavite (AgPbBi3S6) etc. The smaller amounth of isomorphic Ag is substituted as 2Ag+ = PbII+ . Under the usual conditions of deposition (200 - 300řC) , the solubility of Ag2S is to low. The content of Ag in galena under these conditions is not higher then 0,4 mol. % at 615řC. Most of the isomorphic Ag is bound in coupled substitution Ag+ + Bi III+ /Sb III+ = 2 PbII+ . In this case the content of Ag in PbS can be as high as 9 wt. % at 350 - 400řC. At the deposites where wasn't activated this Bi/Sb - Pb coupled substitution the content of Ag in galena is very low. The content of trace elements of Ag, Bi and Sb can also influence the galena crystal habit. Galena rich on Bi ususaly creates octahedral crystals. Galena with a higher content of Ag and Sb usualy creates cubic crystals.
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Physically Based Rendering
Herrgott, Jiří ; Pečiva, Jan (referee) ; Starka, Tomáš (advisor)
This bachelor thesis is focused on rendering of 3D models in real time, where emphasis is placed on physical properties of simulated light rays. The work is about techniques that deal with this issue and then their use for drawing a physically approximated model.
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Aplikace mesalazinu do peritoneální dutiny potkana
Hönigová, Kateřina
The objective of this diploma thesis was to determine the influence of the application of 5-aminosalicylic acid (5-ASA) in the peritoneal cavity on the initiation and course of the inflammatory reaction. For these purposes, the rat was chosen as the model animal on which the model of intraperitoneal lavage was applied. The rat’s peritoneal cavity is easily accessible and reflects the functions and reactions of the immune system. For the purposes of the experiment, the rats were divided into 3 groups; in the first group, the peritoneal cavity was assessed in its physiological condition, without any prior application of the substance. PBS was applied to the second group of rats, and the evaluation of the absolute numbers of cells followed after 4 and 24 hours using the Bürker counting chamber and optical microscopy. In the last group, mesalazine was applied, the exposure of which was 4 hours for one half of the group and 24 hours for the other. These time intervals were followed by the evaluation of the absolute number of cells. In order to determine the differential numbers of cells for all the samples, the coated glasses were coloured and evaluated. The greatest statistically relevant difference was identified in the case of the neutrophil population, where the neutrophil share increased from 0-5 % in the intact cavity to up to 35 % in the cavity after the PBS application. Out of all the experimental groups, the population of lymphocytes was relatively stable; the share of macrophages was, statistically, considerably lower for the groups after the mesalazine application. These results indicate that the application of PBS as an inert substance did not cause such a major reaction regarding the influx of neutrophils as the application of 5-ASA.
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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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