Fault Tolerance in Multicore Clusters. Techniques to Balance Performance and Dependability

In High Performance Computing (HPC) the demand for more performance is satisfied by increasing the number of components. With the growing scale of HPC applications has came an increase in the number of interruptions as a consequence of hardware failures. The remarkable decrease of Mean Times Between Failures (MTBF) in current systems encourages the research of suitable Fault Tolerance (FT) solutions which makes it possible to guarantee the successful completion of parallel applications. By executing applications on HPC systems, we aim to improve the performance despite the failures that may affect systems. Our research focuses on analyzing and reducing the impact of scalable FT techniques based on rollback-recovery (e.g. uncoordinated checkpoint). As message logging is normally the main source of overhead when using uncoordinated checkpoint approaches, our research focuses on analyzing and reducing the impact of current pessimistic receiver-based message logging techniques. Taking into account the advent of multicore machines, our main contributions aim to make an efficient use of the parallel environment considering the interaction between applications processes and fault tolerance tasks. The main contributions of this research are described below.Facultad de Informátic

An analysis of the decision-making process for single implant treatment in general practice

Background: There is little information on the decision-making process for single implant treatment in general practice. Aim: To study the incidence of and the factors associated with the decision to perform single implant treatment after tooth extraction by general practitioners in a private, fee-for-service setting. Methods: One hundred practitioners with a general dental practice in Ghent were randomly selected from an official list received by the Belgian Social Security Institute. Clinicians were asked to fill in a study form for every single extraction they performed during an 8-week period. The study form related to the treatment decision as discussed with the patient and a number of patient- and clinician-related factors. The association of these factors with single implant treatment was evaluated using univariate tests and logistic regression. A decision-tree was also constructed with the predictors from the regression analysis as independent variables. Results: Ninety-four general dentists (52 males, 42 females; mean age 49; range 24–68)agreed to participate and extracted 1180 single teeth in an equal number of patients (50% males, 50% females; mean age 53; range 18–90). The main reasons for tooth loss were caries (48%) and periodontal disease (28%). At the time of extraction tooth replacement was deemed necessary in half of the patients and are movable partial denture was chosen in 55% of them. Similar frequencies were found for fixed partial denture (23%) and single implant treatment (21%). Although the vast majority of patient- and clinician-related factors showed a significant association with the latter on the basis of univariate tests, logistic regression only identified seven predictors. These included location of the extracted tooth, number of missing teeth, regular supportive care, bone loss at adjacent teeth, restoration level of adjacent teeth, gender of the clinician and dentists’ experience in implant prosthetics. The decision tree identified bone loss at adjacent teeth and number of missing teeth as the most important predictors for single implant treatment. Conclusions and clinical implications: If tooth replacement was deemed necessary at the time of extraction, a single implant was the treatment of choice in only one-fifth of the patients. Mainly oral factors had an impact on the decision-making process in contrast to patients’ background and medical factors. Dentists’ experience in implant prosthetics also showed a positive association with single implant treatment as opposed to dentists’ experience in implant surgery

DimLightSim: optical/electrical network simulator for HPC applications

Optical Packet Switches (OPS) and Optical Circuit Switches (OCS) provide the needed low latency transmissions in today large data centers and HPC systems. These switches can deliver lower latency and higher bandwidth than traditional electrical-based switches. Although light-based transmission has its advantages over electrical-based transmissions, in optical devices packet collisions are possible and this can generate retransmissions. In this work we present an optical network simulator called DimLightSim. DimLightSim models communication events in optical devices at packet level by replaying real application traces. Different experimental evaluations have been made using DimLightSim in order to compare current datacenter networks with the fully optical Architecture-on-Demand (AoD) proposed in the Lightness project. Initial results helped to foresee the impact in HPC applications execution time. In terms of performance improvement, the AoD architecture can outperform Infiniband-based network up to 19%

Carotenoid triplet state formation in Rhodobacter sphaeroides R-26 reaction centers exchanged with modified bacteriochlorophyll pigments and reconstituted with spheroidene

Triplet state electron paramagnetic resonance (EPR) experiments have been carried out at X-band on Rb. sphaeroides R-26 reaction centers that have been reconstituted with the carotenoid, spheroidene, and exchanged with 132-OH-Zn-bacteriochlorophyll a and [3-vinyl]-132-OH-bacteriochlorophyll a at the monomeric, lsquoaccessoryrsquo bacteriochlorophyll sites BA,B or with pheophytin a at the bacteriopheophytin sites HA,B. The primary donor and carotenoid triplet state EPR signals in the temperature range 95–150 K are compared and contrasted with those from native Rb. sphaeroides wild type and Rb. sphaeroides R-26 reaction centers reconstituted with spheroidene. The temperature dependencies of the EPR signals are strikingly different for the various samples. The data prove that triplet energy transfer from the primary donor to the carotenoid is mediated by the monomeric, BChlB molecule. Furthermore, the data show that triplet energy transfer from the primary donor to the carotenoid is an activated process, the efficiency of which correlates with the estimated triplet state energies of the modified pigments

Regulation of the upstream petroleum industry. A comparative analysis and evaluation of the regulatory frameworks of South Africa and Namibia

Includes bibliographical referencesControversy surrounds the upstream petroleum industry. Although the benefit of petroleum resources is beyond dispute, the exploitation of petroleum resources comes at a price, as history has shown time and again. Not only does petroleum exploitation have detrimental effects on the environment, but host countries often are worse off than countries with little or no petroleum resources. This "resource curse" is partially the result of flawed regulatory frameworks for petroleum resource extraction in host countries. This thesis identifies three elements that must be present in a country's regulatory framework for petroleum extraction if the resource curse phenomenon is to be avoided and benefit s from petroleum are to be maximised. These elements are: transparency, accountability and a balance of interests between the petroleum companies and the host nation. Namibia and South Africa are not yet major players in the international upstream petroleum industry. There is accordingly not much academic engagement with petroleum law in these two jurisdictions. The courts have also not yet had the opportunity to scrutinise the legislation regulating the upstream petroleum industries of South Africa and Namibia. There are, however, indications that both countries may possess viable quantities of petroleum resources. In anticipation of the possibility of finding commercially viable quantities of petroleum, South Africa and Namibia have enacted legislation to regulate the upstream petroleum industry, but the efficiency of the legislation, specifically how it reflects the elements of transparency, accountability and balance of interest, have not yet been considered. The research for this thesis is driven by the question of how the regulatory framework for petroleum exploitation in South Africa and Namibia embraces the elements of transparency, accountability and balance of interest. The purpose of this thesis is to examine the regulatory frameworks for upstream petroleum resources in South Africa and Namibia in anticipation of the demands that will be placed on law as the sectors grow. In doing so, this thesis scrutinises the legislation in South Africa and Namibia to determine the extent to which the three crucial elements of transparency, accountability and balance of interest between the petroleum company and the host nation are reflected in the regulatory frameworks for petroleum resources

Diluting the Scalability Boundaries: Exploring the Use of Disaggregated Architectures for High-Level Network Data Analysis

Traditional data centers are designed with a rigid architecture of fit-for-purpose servers that provision resources beyond the average workload in order to deal with occasional peaks of data. Heterogeneous data centers are pushing towards more cost-efficient architectures with better resource provisioning. In this paper we study the feasibility of using disaggregated architectures for intensive data applications, in contrast to the monolithic approach of server-oriented architectures. Particularly, we have tested a proactive network analysis system in which the workload demands are highly variable. In the context of the dReDBox disaggregated architecture, the results show that the overhead caused by using remote memory resources is significant, between 66\% and 80\%, but we have also observed that the memory usage is one order of magnitude higher for the stress case with respect to average workloads. Therefore, dimensioning memory for the worst case in conventional systems will result in a notable waste of resources. Finally, we found that, for the selected use case, parallelism is limited by memory. Therefore, using a disaggregated architecture will allow for increased parallelism, which, at the same time, will mitigate the overhead caused by remote memory.Comment: 8 pages, 6 figures, 2 tables, 32 references. Pre-print. The paper will be presented during the IEEE International Conference on High Performance Computing and Communications in Bangkok, Thailand. 18 - 20 December, 2017. To be published in the conference proceeding

The accessory bacteriochlorophyll

The primary electron transfer in reaction centers of Rhodobacter sphaeroides is studied by subpicosecond absorption spectroscopy with polarized light in the spectral range of 920-1040 nm. Here the bacteriochlorophyll anion radical has an absorption band while the other pigments of the reaction center have vanishing ground-state absorption. The transient absorption data exhibit a pronounced 0.9-ps kinetic component which shows a strong dichroism. Evaluation of the data yields an angle between the transition moments of the special pair and the species related with the 0.9-ps kinetic component of 26 +/- 8 degrees. This angle compares favorably with the value of 29 degrees expected for the reduced accessory bacteriochlorophyll. Extensive transient absorbance data are fully consistent with a stepwise electron transfer via the accessory bacteriochlorophyll