Constraint Programming-based Job Dispatching for Modern HPC Applications

A High-Performance Computing job dispatcher is a critical software that assigns the finite computing resources to submitted jobs. This resource assignment over time is known as the on-line job dispatching problem in HPC systems. The fact the problem is on-line means that solutions must be computed in real-time, and their required time cannot exceed some threshold to do not affect the normal system functioning. In addition, a job dispatcher must deal with a lot of uncertainty: submission times, the number of requested resources, and duration of jobs. Heuristic-based techniques have been broadly used in HPC systems, at the cost of achieving (sub-)optimal solutions in a short time. However, the scheduling and resource allocation components are separated, thus generates a decoupled decision that may cause a performance loss. Optimization-based techniques are less used for this problem, although they can significantly improve the performance of HPC systems at the expense of higher computation time. Nowadays, HPC systems are being used for modern applications, such as big data analytics and predictive model building, that employ, in general, many short jobs. However, this information is unknown at dispatching time, and job dispatchers need to process large numbers of them quickly while ensuring high Quality-of-Service (QoS) levels. Constraint Programming (CP) has been shown to be an effective approach to tackle job dispatching problems. However, state-of-the-art CP-based job dispatchers are unable to satisfy the challenges of on-line dispatching, such as generate dispatching decisions in a brief period and integrate current and past information of the housing system. Given the previous reasons, we propose CP-based dispatchers that are more suitable for HPC systems running modern applications, generating on-line dispatching decisions in a proper time and are able to make effective use of job duration predictions to improve QoS levels, especially for workloads dominated by short jobs.

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.

Geometrico-static modelling of continuum parallel robots

In this thesis, we explore three methods for the geometrico-static modelling of continuum parallel robots. Inspired by biological trunks, tentacles and snakes, continuum robot designs can reach confined spaces, manipulate objects in complex environments and conform to curvilinear paths in space. In addition, parallel continuum manipulators have the potential to inherit some of the compactness and compliance of continuum robots while retaining some of the precision, stability and strength of rigid-links parallel robots. Subsequently, the foundation of our work is performed on slender beam by applying the Cosserat rod theory, appropriate to model continuum robots. After that, three different approaches are developed on a case study of a planar parallel continuum robot constituted of two connected flexible links. We solve the forward and inverse geometrico-static problem namely by using (a) shooting methods to obtain a numerical solution, (b) an elliptic method to find a quasi-analytical solution, and (c) the Corde model to perform further model analysis. The performances of each of the studied methods are evaluated and their limits are highlighted. This thesis is divided as follows. Chapter one gives the introduction on the field of the continuum robotics and introduce the parallel continuum robots that is studied in this work. Chapter two describe the geometrico-static problem and gives the mathematical description of this problem. Chapter three explains the numerical approach with the shooting method and chapter four introduce the quasi-analytical solution. Then, Chapter five introduce the analytic method inspired by the Corde model and chapter six gives the conclusions of this work.

Feedback control of underactuated cable-driven parallel robots

In this work an Underactuated Cable-Driven Parallel Robot (UACDPR) that operates in the three dimensional Euclidean space is considered. The End-Effector has 6 degrees of freedom and is actuated by 4 cables, therefore from a mechanical point of view the robot is defined underconstrained. However, considering only three controlled pose variables, the degree of redundancy for the control theory can be considered one. The aim of this thesis is to design a feedback controller for a point-to-point motion that satisfies the transient requirements, and is capable of reducing oscillations that derive from the reduced number of constraints. A force control is chosen for the positioning of the End-Effector, and error with respect to the reference is computed through data measure of several sensors (load cells, encoders and inclinometers) such as cable lengths, tension and orientation of the platform. In order to express the relation between pose and cable tension, the inverse model is derived from the kinematic and dynamic model of the parallel robot. The intrinsic non-linear nature of UACDPRs systems introduces an additional level of complexity in the development of the controller, as a result the control law is composed by a partial feedback linearization, and damping injection to reduce orientation instability. The fourth cable allows to satisfy a further tension distribution constraint, ensuring positive tension during all the instants of motion. Then simulations with different initial conditions are presented in order to optimize control parameters, and lastly an experimental validation of the model is carried out, the results are analysed and limits of the presented approach are defined.

Machine Learning in Automatic Tabulation for Constraint Model Reformulation

Combinatorial decision and optimization problems belong to numerous applications, such as logistics and scheduling, and can be solved with various approaches. Boolean Satisfiability and Constraint Programming solvers are some of the most used ones and their performance is significantly influenced by the model chosen to represent a given problem. This has led to the study of model reformulation methods, one of which is tabulation, that consists in rewriting the expression of a constraint in terms of a table constraint. To apply it, one should identify which constraints can help and which can hinder the solving process. So far this has been performed by hand, for example in MiniZinc, or automatically with manually designed heuristics, in Savile Row. Though, it has been shown that the performances of these heuristics differ across problems and solvers, in some cases helping and in others hindering the solving procedure. However, recent works in the field of combinatorial optimization have shown that Machine Learning (ML) can be increasingly useful in the model reformulation steps. This thesis aims to design a ML approach to identify the instances for which Savile Row’s heuristics should be activated. Additionally, it is possible that the heuristics miss some good tabulation opportunities, so we perform an exploratory analysis for the creation of a ML classifier able to predict whether or not a constraint should be tabulated. The results reached towards the first goal show that a random forest classifier leads to an increase in the performances of 4 different solvers. The experimental results in the second task show that a ML approach could improve the performance of a solver for some problem classes.

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.

Integrated Proteomics Identified Up-regulated Focal Adhesion-mediated Proteins In Human Squamous Cell Carcinoma In An Orthotopic Murine Model.

Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.

The Soluble Guanylyl Cyclase Activator Bay 60-2770 Potently Relaxes The Pulmonary Artery On Congenital Diaphragmatic Hernia Rabbit Model.

Congenital diaphragmatic hernia (CDH) is associated with pulmonary hypertension which is often difficult to manage, and a significant cause of morbidity and mortality. In this study, we have used a rabbit model of CDH to evaluate the effects of BAY 60-2770 on the in vitro reactivity of left pulmonary artery. CDH was performed in New Zealand rabbit fetuses (n = 10 per group) and compared to controls. Measurements of body, total and left lung weights (BW, TLW, LLW) were done. Pulmonary artery rings were pre-contracted with phenylephrine (10 μM), after which cumulative concentration-response curves to glyceryl trinitrate (GTN; NO donor), tadalafil (PDE5 inhibitor) and BAY 60-2770 (sGC activator) were obtained as well as the levels of NO (NO3/NO2). LLW, TLW and LBR were decreased in CDH (p < 0.05). In left pulmonary artery, the potency (pEC50) for GTN was markedly lower in CDH (8.25 ± 0.02 versus 9.27 ± 0.03; p < 0.01). In contrast, the potency for BAY 60-2770 was markedly greater in CDH (11.7 ± 0.03 versus 10.5 ± 0.06; p < 0.01). The NO2/NO3 levels were 62 % higher in CDH (p < 0.05). BAY 60-2770 exhibits a greater potency to relax the pulmonary artery in CDH, indicating a potential use for pulmonary hypertension in this disease.

Bay 41-2272, A Soluble Guanylate Cyclase Stimulator, Relaxes Isolated Human Ureter In A Standardized In Vitro Model.

To characterize the relaxation induced by BAY 41-2272 in human ureteral segments. Ureter specimens (n = 17) from multiple organ human deceased donors (mean age 40 ± 3.2 years, male/female ratio 2:1) were used to characterize the relaxing response of BAY 41-2272. Immunohistochemical analysis for endothelial and neuronal nitric oxide synthase, guanylate cyclase stimulator (sGC) and type 5 phosphodiesterase was also performed. The potency values were determined as the negative log of the molar to produce 50% of the maximal relaxation in potassium chloride-precontracted specimens. The unpaired Student t test was used for the comparisons. Immunohistochemistry revealed the presence of endothelial nitric oxide synthase in vessel endothelia and neuronal nitric oxide synthase in urothelium and nerve structures. sGC was expressed in the smooth muscle and urothelium layer, and type 5 phosphodiesterase was present in the smooth muscle only. BAY 41-2272 (0.001-100 μM) relaxed the isolated ureter in a concentration dependent manner, with a potency and maximal relaxation value of 5.82 ± 0.14 and 84% ± 5%, respectively. The addition of nitric oxide synthase and sGC inhibitors reduced the maximal relaxation values by 21% and 45%, respectively. However, the presence of sildenafil (100 nM) significantly potentiated (6.47 ± 0.10, P <.05) this response. Neither glibenclamide or tetraethylammonium nor ureteral urothelium removal influenced the relaxation response by BAY 41-2272. BAY 41-2272 relaxes the human isolated ureter in a concentration-dependent manner, mainly by activating the sGC enzyme in smooth muscle cells rather than in the urothelium, although a cyclic guanosine monophosphate-independent mechanism might have a role. The potassium channels do not seem to be involved.

Photoelastic Analysis Of All-on-four Concept Using Different Implants Angulations For Maxilla.

Conventional tilted implants are used in oral rehabilitation for heavily absorbed maxilla to avoid bone grafts; however, few research studies evaluate the biomechanical behavior when different angulations of the implants are used. The aim of this study was evaluate, trough photoelastic method, two different angulations and length of the cantilever in fixed implant-supported maxillary complete dentures. Two groups were evaluated: G15 (distal tilted implants 15°) and G35 (distal tilted implants 35°) n = 6. For each model, 2 distal tilted implants (3.5 x 15 mm long cylindrical cone) and 2 parallel tilted implants in the anterior region (3.5 x 10 mm) were installed. Photoelastic models were submitted to three vertical load tests: in the end of cantilever, in the last pillar and in the all pillars at the same time. We obtained the shear stress by Fringes software and found values for total, cervical and apical stress. The quantitative analysis was performed using the Student tests and Mann-Whitney test; p ≥ 0.05. There is no difference between G15 and G35 for total stress regardless of load type. Analyzing the apical region, G35 reduced strain values considering the distal loads (in the cantilever p = 0.03 and in the last pillar p = 0.02), without increasing the stress level in the cervical region. Considering the load in all pillars, G35 showed higher stress concentration in the cervical region (p = 0.04). For distal loads, G15 showed increase of tension in the apical region, while for load in all pillars, G35 inclination increases stress values in the cervical region.

Atomic Charge Transfer-counter Polarization Effects Determine Infrared Ch Intensities Of Hydrocarbons: A Quantum Theory Of Atoms In Molecules Model.

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

Mesenchymal Stromal Cells From Adipose Tissue Attached To Suture Material Enhance The Closure Of Enterocutaneous Fistulas In A Rat Model.

Surgical treatment for enterocutaneous fistulas (EF) frequently fails. Cell therapy may represent a new approach to treatment. Mesenchymal stromal cells (MSCs) have high proliferative and differentiation capacity. This study aimed to investigate whether MSCs could adhere to suture filament (SF), promoting better EF healing. MSCs, 1 × 10(6), from adipose tissue (ATMSCs) were adhered to a Polyvicryl SF by adding a specific fibrin glue formulation. Adhesion was confirmed by confocal and scanning electron microscopy (SEM). A cecal fistula was created in 22 Wistar rats by incising the cecum and suturing the opening to the surgical wound subcutaneously with four separate stitches. The animals were randomly allocated to three groups: control (CG)-five animals, EF performed; injection (IG)-eight animals 1 × 10(6) ATMSCs injected around EF borders; and suture filament (SG): nine animals, sutured with 1 × 10(6) ATMSCs attached to the filaments with fibrin glue. Fistulas were photographed on the operation day and every 3 days until the 21st day and analyzed by two observers using ImageJ Software. Confocal and SEM results demonstrated ATMSCs adhered to SF (ATMSCs-SF). The average reduction size of the fistula area at 21st day was greater for the SG group (90.34%, P < 0.05) than the IG (71.80%) and CG (46.54%) groups. ATMSCs adhered to SF maintain viability and proliferative capacity. EF submitted to ATMSCs-SF procedure showed greater recovery and healing. This approach might be a new and effective tool for EF treatment.

Urothelial Carcinogen Resistance Driven By Stronger Toll-like Receptor 2 (tlr2) And Uroplakin Iii (up Iii) Defense Mechanisms: A New Model.

The objective of the study was to illustrate the applicability and significance of the novel Lewis urothelial cancer model compared to the classic Fisher 344. Fischer 344 and Lewis females rats, 7 weeks old, were intravesical instilled N-methyl-N-nitrosourea 1.5 mg/kg every other week for a total of four doses. After 15 weeks, animals were sacrificed and bladders analyzed: histopathology (tumor grade and stage), immunohistochemistry (apoptotic and proliferative indices) and blotting (Toll-like receptor 2-TLR2, Uroplakin III-UP III and C-Myc). Control groups received placebo. There were macroscopic neoplastic lesions in 20 % of Lewis strain and 70 % of Fischer 344 strain. Lewis showed hyperplasia in 50 % of animals, normal bladders in 50 %. All Fischer 344 had lesions, 20 % papillary hyperplasia, 30 % dysplasia, 40 % neoplasia and 10 % squamous metaplasia. Proliferative and apoptotic indices were significantly lower in the Lewis strain (p < 0.01). The TLR2 and UP III protein levels were significantly higher in Lewis compared to Fischer 344 strain (70.8 and 46.5 % vs. 49.5 and 16.9 %, respectively). In contrast, C-Myc protein levels were significantly higher in Fischer 344 (22.5 %) compared to Lewis strain (13.7 %). The innovative Lewis carcinogen resistance urothelial model represents a new strategy for translational research. Preservation of TLR2 and UP III defense mechanisms might drive diverse urothelial phenotypes during carcinogenesis in differently susceptible individuals.

Prostatic Angiogenic Responses In Late Life: Antiangiogenic Therapy Influences And Relation With The Glandular Microenvironment In The Transgenic Adenocarcinoma Of Mouse Prostate (tramp) Model.

Aging is considered one of the main predisposing factors for the development of prostate malignancies. Angiogenesis is fundamental for tumor growth and its inhibition represents a promising therapeutic approach in cancer treatment. Thus, we sought to determine angiogenic responses and the effects of antiangiogenic therapy in the mouse prostate during late life, comparing these findings with the prostatic microenvironment in the Transgenic Adenocarcinoma of Mouse Prostate (TRAMP) model. Male mice (52 week-old FVB) were submitted to treatments with SU5416 (6 mg/kg; i.p.) and/or TNP-470 (15 mg/kg; s.c.). Finasteride was administered (20 mg/kg; s.c.), alone or in association to both inhibitors. The dorsolateral prostate was collected for VEGF, HIF-1α, FGF-2 and endostatin immunohistochemical and Western Blotting analyses and for microvessel density (MVD) count. Senescence led to increased MVD and VEGF, HIF-1α and FGF-2 protein levels in the prostatic microenvironment, similarly to what was observed in TRAMP mice prostate. The angiogenic process was impaired in all the treated groups, demonstrating significantly decreased MVD. Antiangiogenic and/or finasteride treatments resulted in decreased VEGF and HIF-1α levels, especially following TNP-470 administration, either alone or associated to SU5416. The combination of these agents resulted in increased endostatin levels, regardless of the presence of finasteride. Prostatic angiogenesis stimulation during senescence favored the development of neoplastic lesions, considering the pro-angiogenic microenvironment as a common aspect also observed during cancer progression in TRAMP mice. The combined antiangiogenic therapy was more efficient, leading to enhanced imbalance towards angiogenic inhibition in the organ. Finally, finasteride administration might secondarily upregulate the expression of pro-angiogenic factors, pointing to the harmful effects of this therapy. Prostate 75: 484-499, 2015. © 2014 Wiley Periodicals, Inc.