High-performance parallel systems for data-intensive computing

Thesis (Ph.D.)--University of Washington, 2016-08

'The application of Bayesian Optimization and Classifier Systems in Nurse Scheduling'

Abstract. Two ideas taken from Bayesian optimization and classifier systems are presented for personnel scheduling based on choosing a suitable scheduling rule from a set for each person's assignment. Unlike our previous work of using genetic algorithms whose learning is implicit, the learning in both approaches is explicit, i.e. we are able to identify building blocks directly. To achieve this target, the Bayesian optimization algorithm builds a Bayesian network of the joint probability distribution of the rules used to construct solutions, while the adapted classifier system assigns each rule a strength value that is constantly updated according to its usefulness in the current situation. Computational results from 52 real data instances of nurse scheduling demonstrate the success of both approaches. It is also suggested that the learning mechanism in the proposed approaches might be suitable for other scheduling problems.

'The application of Bayesian Optimization and Classifier Systems in Nurse Scheduling'

Abstract. Two ideas taken from Bayesian optimization and classifier systems are presented for personnel scheduling based on choosing a suitable scheduling rule from a set for each person's assignment. Unlike our previous work of using genetic algorithms whose learning is implicit, the learning in both approaches is explicit, i.e. we are able to identify building blocks directly. To achieve this target, the Bayesian optimization algorithm builds a Bayesian network of the joint probability distribution of the rules used to construct solutions, while the adapted classifier system assigns each rule a strength value that is constantly updated according to its usefulness in the current situation. Computational results from 52 real data instances of nurse scheduling demonstrate the success of both approaches. It is also suggested that the learning mechanism in the proposed approaches might be suitable for other scheduling problems.

Characterization of a biodegradable starch based film. Application on the preservation of fresh spinach

Mestrado em Engenharia Alimentar - Instituto Superior de Agronomia - UL

A structure design method for compliant parallel manipulators with actuation isolation

Since precise linear actuators of a compliant parallel manipulator suffer from their inability to tolerate the transverse motion/load in the multi-axis motion, actuation isolation should be considered in the compliant manipulator design to eliminate the transverse motion at the point of actuation. This paper presents an effective design method for constructing compliant parallel manipulators with actuation isolation, by adding the same number of actuation legs as the number of the DOF (degree of freedom) of the original mechanism. The method is demonstrated by two design case studies, one of which is quantitatively studied by analytical modelling. The modelling results confirm possible inherent issues of the proposed structure design method such as increased primary stiffness, introduced extra parasitic motions and cross-axis coupling motions.

Design and application of experimental methods for steel sheet shearing

Shearing is the process where sheet metal is mechanically cut between two tools. Various shearing technologies are commonly used in the sheet metal industry, for example, in cut to length lines, slitting lines, end cropping etc. Shearing has speed and cost advantages over competing cutting methods like laser and plasma cutting, but involves large forces on the equipment and large strains in the sheet material. The constant development of sheet metals toward higher strength and formability leads to increased forces on the shearing equipment and tools. Shearing of new sheet materials imply new suitable shearing parameters. Investigations of the shearing parameters through live tests in the production are expensive and separate experiments are time consuming and requires specialized equipment. Studies involving a large number of parameters and coupled effects are therefore preferably performed by finite element based simulations. Accurate experimental data is still a prerequisite to validate such simulations. There is, however, a shortage of accurate experimental data to validate such simulations. In industrial shearing processes, measured forces are always larger than the actual forces acting on the sheet, due to friction losses. Shearing also generates a force that attempts to separate the two tools with changed shearing conditions through increased clearance between the tools as result. Tool clearance is also the most common shearing parameter to adjust, depending on material grade and sheet thickness, to moderate the required force and to control the final sheared edge geometry. In this work, an experimental procedure that provides a stable tool clearance together with accurate measurements of tool forces and tool displacements, was designed, built and evaluated. Important shearing parameters and demands on the experimental set-up were identified in a sensitivity analysis performed with finite element simulations under the assumption of plane strain. With respect to large tool clearance stability and accurate force measurements, a symmetric experiment with two simultaneous shears and internal balancing of forces attempting to separate the tools was constructed. Steel sheets of different strength levels were sheared using the above mentioned experimental set-up, with various tool clearances, sheet clamping and rake angles. Results showed that tool penetration before fracture decreased with increased material strength. When one side of the sheet was left unclamped and free to move, the required shearing force decreased but instead the force attempting to separate the two tools increased. Further, the maximum shearing force decreased and the rollover increased with increased tool clearance. Digital image correlation was applied to measure strains on the sheet surface. The obtained strain fields, together with a material model, were used to compute the stress state in the sheet. A comparison, up to crack initiation, of these experimental results with corresponding results from finite element simulations in three dimensions and at a plane strain approximation showed that effective strains on the surface are representative also for the bulk material. A simple model was successfully applied to calculate the tool forces in shearing with angled tools from forces measured with parallel tools. These results suggest that, with respect to tool forces, a plane strain approximation is valid also at angled tools, at least for small rake angles. In general terms, this study provide a stable symmetric experimental set-up with internal balancing of lateral forces, for accurate measurements of tool forces, tool displacements, and sheet deformations, to study the effects of important shearing parameters. The results give further insight to the strain and stress conditions at crack initiation during shearing, and can also be used to validate models of the shearing process.

Dynamics of undeactuated cable-driven parallel robots

This thesis focuses on the dynamics of underactuated cable-driven parallel robots (UACDPRs), including various aspects of robotic theory and practice, such as workspace computation, parameter identification, and trajectory planning. After a brief introduction to CDPRs, UACDPR kinematic and dynamic models are analyzed, under the relevant assumption of inextensible cables. The free oscillatory motion of the end-effector (EE), which is a unique feature of underactuated mechanisms, is studied in detail, from both a kinematic and a dynamic perspective. The free (small) oscillations of the EE around equilibria are proved to be harmonic and the corresponding natural oscillation frequencies are analytically computed. UACDPR workspace computation and analysis are then performed. A new performance index is proposed for the analysis of the influence of actuator errors on cable tensions around equilibrium configurations, and a new type of workspace, called tension-error-insensitive, is defined as the set of poses that a UACDPR EE can statically attain even in presence of actuation errors, while preserving tensions between assigned (positive) bounds. EE free oscillations are then employed to conceive a novel procedure aimed at identifying the EE inertial parameters. This approach does not require the use of force or torque measurements. Moreover, a self-calibration procedure for the experimental determination of UACDPR initial cable lengths is developed, which consequently enables the robot to automatically infer the EE initial pose at machine start-up. Lastly, trajectory planning of UACDPRs is investigated. Two alternative methods are proposed, which aim at (i) reducing EE oscillations even when model parameters are uncertain or (ii) eliminate EE oscillations in case model parameters are perfectly known. EE oscillations are reduced in real-time by dynamically scaling a nominal trajectory and filtering it with an input shaper, whereas they can be eliminated if an off-line trajectory is computed that accounts for the system internal dynamics.

Direct Kinematics of Underactuated Cable-Driven Parallel Robots: Sensitivity to Redundant Measurements

Underactuated cable-driven parallel robots (UACDPRs) shift a 6-degree-of-freedom end-effector (EE) with fewer than 6 cables. This thesis proposes a new automatic calibration technique that is applicable for under-actuated cable-driven parallel robots. The purpose of this work is to develop a method that uses free motion as an exciting trajectory for the acquisition of calibration data. The key point of this approach is to find a relationship between the unknown parameters to be calibrated (the lengths of the cables) and the parameters that could be measured by sensors (the swivel pulley angles measured by the encoders and roll-and-pitch angles measured by inclinometers on the platform). The equations involved are the geometrical-closure equations and the finite-difference velocity equations, solved using the least-squares algorithm. Simulations are performed on a parallel robot driven by 4 cables for validation. The final purpose of the calibration method is, still, the determination of the platform initial pose. As a consequence of underactuation, the EE is underconstrained and, for assigned cable lengths, the EE pose cannot be obtained by means of forward kinematics only. Hence, a direct-kinematics algorithm for a 4-cable UACDPR using redundant sensor measurements is proposed. The proposed method measures two orientation parameters of the EE besides cable lengths, in order to determine the other four pose variables, namely 3 position coordinates and one additional orientation parameter. Then, we study the performance of the direct-kinematics algorithm through the computation of the sensitivity of the direct-kinematics solution to measurement errors. Furthermore, position and orientation error upper limits are computed for bounded cable lengths errors resulting from the calibration procedure, and roll and pitch angles errors which are due to inclinometer inaccuracies.

Mechanical design and hybrid control strategies for overconstrained cable-driven parallel robots

Cable-driven parallel robots offer significant advantages in terms of workspace dimensions and payload capability. They are attractive for many industrial tasks to be performed on a large scale, such as handling and manufacturing, without a substantial increase in costs and mechanical complexity with respect to a small-scale application. However, since cables can only sustain tensile stresses, cable tensions must be kept within positive limits during the end-effector motion. This problem can be managed by overconstraining the end-effector and controlling cable tensions. Tension control is typically achieved by mounting a load sensor on all cables, and using specific control algorithms to avoid cable slackness or breakage while the end-effector is controlled in a desired position. These algorithms require multiple cascade control loops and they can be complex and computationally demanding. To simplify the control of overconstrained cable-driven parallel robots, this Thesis proposes suitable mechanical design and hybrid control strategies. It is shown how a convenient design of the cable guidance system allows kinematic modeling to be simplified, without introducing geometric approximations. This guidance system employs swiveling pulleys equipped with position and tension sensors and provides a parallelogram arrangement of cables. Furthermore, a hybrid force/position control in the robot joint space is adopted. According to this strategy, a particular set of cables is chosen to be tension-controlled, whereas the other cables are length-controlled. The force-controlled cables are selected based on the computation of a novel index called force-distribution sensitivity to cable-tension errors. This index aims to evaluate the maximum expected cable-tension error in the length-controlled cables if a unit tension error is committed in the force-controlled cables. In practice, the computation of the force-distribution sensitivity allows determining which cables are best to be force-controlled, to ensure the lowest error in the overall force distribution when a hybrid force/position joint-space strategy is used.

Contributions to the performance analysis of continuum parallel robots

Continuum parallel robots (CPRs) are manipulators employing multiple flexible beams arranged in parallel and connected to a rigid end-effector. CPRs promise higher payload and accuracy than serial CRs while keeping great flexibility. As the risk of injury during accidental contacts between a human and a CPR should be reduced, CPRs may be used in large-scale collaborative tasks or assisted robotic surgery. There exist various CPR designs, but the prototype conception is rarely based on performance considerations, and the CPRs realization in mainly based on intuitions or rigid-link parallel manipulators architectures. This thesis focuses on the performance analysis of CPRs, and the tools needed for such evaluation, such as workspace computation algorithms. In particular, workspace computation strategies for CPRs are essential for the performance assessment, since the CPRs workspace may be used as a performance index or it can serve for optimal-design tools. Two new workspace computation algorithms are proposed in this manuscript, the former focusing on the workspace volume computation and the certification of its numerical results, while the latter aims at computing the workspace boundary only. Due to the elastic nature of CPRs, a key performance indicator for these robots is the stability of their equilibrium configurations. This thesis proposes the experimental validation of the equilibrium stability assessment on a real prototype, demonstrating limitations of some commonly used assumptions. Additionally, a performance index measuring the distance to instability is originally proposed in this manuscript. Differently from the majority of the existing approaches, the clear advantage of the proposed index is a sound physical meaning; accordingly, the index can be used for a more straightforward performance quantification, and to derive robot specifications.

Energy consumption of parallel algorithms for solving linear systems on HPC architecture

Modern High-Performance Computing HPC systems are gradually increasing in size and complexity due to the correspondent demand of larger simulations requiring more complicated tasks and higher accuracy. However, as side effects of the Dennard’s scaling approaching its ultimate power limit, the efficiency of software plays also an important role in increasing the overall performance of a computation. Tools to measure application performance in these increasingly complex environments provide insights into the intricate ways in which software and hardware interact. The monitoring of the power consumption in order to save energy is possible through processors interfaces like Intel Running Average Power Limit RAPL. Given the low level of these interfaces, they are often paired with an application-level tool like Performance Application Programming Interface PAPI. Since several problems in many heterogeneous fields can be represented as a complex linear system, an optimized and scalable linear system solver algorithm can decrease significantly the time spent to compute its resolution. One of the most widely used algorithms deployed for the resolution of large simulation is the Gaussian Elimination, which has its most popular implementation for HPC systems in the Scalable Linear Algebra PACKage ScaLAPACK library. However, another relevant algorithm, which is increasing in popularity in the academic field, is the Inhibition Method. This thesis compares the energy consumption of the Inhibition Method and Gaussian Elimination from ScaLAPACK to profile their execution during the resolution of linear systems above the HPC architecture offered by CINECA. Moreover, it also collates the energy and power values for different ranks, nodes, and sockets configurations. The monitoring tools employed to track the energy consumption of these algorithms are PAPI and RAPL, that will be integrated with the parallel execution of the algorithms managed with the Message Passing Interface MPI.

Propylthiouracil Quantification In Human Plasma By High-performance Liquid Chromatography Coupled With Electrospray Tandem Mass Spectrometry: Application In A Bioequivalence Study.

A rapid, sensitive and specific method for quantifying propylthiouracil in human plasma using methylthiouracil as the internal standard (IS) is described. The analyte and the IS were extracted from plasma by liquid-liquid extraction using an organic solvent (ethyl acetate). The extracts were analyzed by high performance liquid chromatography coupled with electrospray tandem mass spectrometry (HPLC-MS/MS) in negative mode (ES-). Chromatography was performed using a Phenomenex Gemini C18 5μm analytical column (4.6mm×150mm i.d.) and a mobile phase consisting of methanol/water/acetonitrile (40/40/20, v/v/v)+0.1% of formic acid. For propylthiouracil and I.S., the optimized parameters of the declustering potential, collision energy and collision exit potential were -60 (V), -26 (eV) and -5 (V), respectively. The method had a chromatographic run time of 2.5min and a linear calibration curve over the range 20-5000ng/mL. The limit of quantification was 20ng/mL. The stability tests indicated no significant degradation. This HPLC-MS/MS procedure was used to assess the bioequivalence of two propylthiouracil 100mg tablet formulations in healthy volunteers of both sexes in fasted and fed state. The geometric mean and 90% confidence interval CI of Test/Reference percent ratios were, without and with food, respectively: 109.28% (103.63-115.25%) and 115.60% (109.03-122.58%) for Cmax, 103.31% (100.74-105.96%) and 103.40% (101.03-105.84) for AUClast. This method offers advantages over those previously reported, in terms of both a simple liquid-liquid extraction without clean-up procedures, as well as a faster run time (2.5min). The LOQ of 20ng/mL is well suited for pharmacokinetic studies. The assay performance results indicate that the method is precise and accurate enough for the routine determination of the propylthiouracil in human plasma. The test formulation with and without food was bioequivalent to reference formulation. Food administration increased the Tmax and decreased the bioavailability (Cmax and AUC).

Effect Of Aloe Vera Application On The Content And Molecular Arrangement Of Glycosaminoglycans During Calcaneal Tendon Healing.

Although several treatments for tendon lesions have been proposed, successful tendon repair remains a great challenge for orthopedics, especially considering the high incidence of re-rupture of injured tendons. Our aim was to evaluate the pharmacological potential of Aloe vera on the content and arrangement of glycosaminoglycans (GAGs) during tendon healing, which was based on the effectiveness of A. vera on collagen organization previously observed by our group. In rats, a partial calcaneal tendon transection was performed with subsequent topical A. vera application at the injury site. The tendons were treated with A. vera ointment for 7 days and excised on the 7(th) , 14(th) , or 21(st) day post-surgery. Control rats received ointment without A. vera. A higher content of GAGs and a lower amount of dermatan sulfate were detected in the A. vera-treated group on the 14(th) day compared with the control. Also at 14 days post-surgery, a lower dichroic ratio in toluidine blue stained sections was observed in A. vera-treated tendons compared with the control. No differences were observed in the chondroitin-6-sulfate and TGF-β1 levels between the groups, and higher amount of non-collagenous proteins was detected in the A. vera-treated group on the 21(st) day, compared with the control group. No differences were observed in the number of fibroblasts, inflammatory cells and blood vessels between the groups. The application of A. vera during tendon healing modified the arrangement of GAGs and increased the content of GAGs and non-collagenous proteins.

Chemo-, Regio- And Stereoselective Heck Arylation Of Allylated Malonates: Mechanistic Insights By Esi-ms And Synthetic Application Toward 5-arylmethyl-γ-lactones.

We describe herein a general method for the controlled Heck arylation of allylated malonates. Both electron-rich and electron-poor aryldiazonium salts were readily employed as the aryl-transfer agents in good yields and in high chemo-, regio-, and stereoselectivity without formation of decarboxylated byproducts. Reaction monitoring via ESI-MS was used to support the formation of chelated Pd species through the catalytic cycle. Additionally, some Heck adducts were successfully used in the total synthesis of pharmacologically active γ-lactones.

Recolonization Of Mutans Streptococci After Application Of Chlorhexidine Gel.

Streptococcus mutans is specifically suppressed by intensive treatment with chlorhexidine gel, but the time for recolonization and the effect on other oral bacteria are not totally clear. In this study, recolonization of mutans streptococci was evaluated in nine healthy adult volunteers, who were highly colonized with this microorganism. Stimulated saliva was collected before (baseline) and at 1, 7, 14, 21 and 28 days after application of 1% chlorhexidine gel on volunteers' teeth for two consecutive days. On each day, the gel was applied using disposable trays for 3 x 5 min with intervals of 5 min between each application. Saliva was plated on blood agar to determine total microorganisms (TM); on mitis salivarius agar to determine total streptococci (TS) and on mitis salivarius agar plus bacitracin to determine mutans streptococci (MS). Chlorhexidine was capable of reducing the counts of MS and the proportion of MS with regard to total microorganisms (%MS/TM) (p<0.05), but these values did not differ statistically from baseline (p>0.05) after 14 days for MS and 21 days for %MS/TM. The counts of TM and TS and the proportion of MS to total streptococci did not differ statistically from baseline (p>0.05) after chlorhexidine treatment. The results suggest that the effect of chlorhexidine gel treatment on suppression of mutans streptococci is limited to less than a month in highly colonized individuals.