Grids with multiple batch systems for performance enhancement of multi-component and parameter sweep parallel applications

In this work, we evaluate the benefits of using Grids with multiple batch systems to improve the performance of multi-component and parameter sweep parallel applications by reduction in queue waiting times. Using different job traces of different loads, job distributions and queue waiting times corresponding to three different queuing policies(FCFS, conservative and EASY backfilling), we conducted a large number of experiments using simulators of two important classes of applications. The first simulator models Community Climate System Model (CCSM), a prominent multi-component application and the second simulator models parameter sweep applications. We compare the performance of the applications when executed on multiple batch systems and on a single batch system for different system and application configurations. We show that there are a large number of configurations for which application execution using multiple batch systems can give improved performance over execution on a single system.

Uplift resistance of buried pipelines in blocky clay backfill

This paper presents the results from 10 minidrum centrifuge tests conducted at the Schofield Centre, compiled with 4 additional test results from Thusyanthan et al., 2008. All these tests were designed to measure the uplift resistance of a pipeline installed into stiff clay by trenching and backfilling, then uplifted approximately 3 months after installation. All tests were conducted at 1:30 scale using soil obtained from offshore clay samples. Experimental results show that clay blocks remained intact after 3 prototype months of consolidation, and were lifted rather than sheared during pipe pullout. The uplift resistance therefore depends on the weight of the soil cover and the shearing resistance mobilised at the softening contact points between the intact blocks and within the interstitial slurry. Slow drained pullout led to lower resistance than fast pullout, indicating that the drained response is critical for design. The varying scatter shows that peak uplift resistance is very sensitive to the arrangement of the backfill blocks when the cover and pipe diameter are comparable to the block size. Copyright © 2009 by The International Society of Offshore and Polar Engineers (ISOPE).

Multiplexed DNA-mediated electrochemistry

The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of π-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the π-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA π-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.

First, Methylene Blue (MB′) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB′ was reduced through DNA-mediated charge transport. The redox signal intensity for MB′-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB′ on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.

Next, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening π-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA. Further gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.

Finally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.

n-type Ge-SiGe quantum cascade structure utilizing quantum wells for electrons in the L and Gamma valleys

In this letter, we propose an n-type vertical transition bound-to-continuum Ge-SiGe quantum cascade structure utilizing electronic quantum wells in the L and F valleys of the Ge layers. The optical transition levels are located in the quantum wells in the L valley. Under a bias of 80 kV/cm, the carriers in the lower level are extracted by miniband transport and L - Gamma tunneling into the subband in the Gamma well of the next period. And then the electrons are injected into the upper level by ultrafast intervalley scattering, which not only effectively increases the tunneling rate and suppresses the thermal backfilling of electrons, but also enhances the injection efficiency of the upper level. The performance of the laser is discussed.

Characterisation of the performance of sustainable grout containing bentonite for geotechnical applications

The grouts used in sealing or backfilling boreholes should ideally be selected to be compatible with the insitu field instruments installed in the borehole and also be engineered to match closely the geotechnical properties of the parent soils. A stable grout can be made using cement with various proportions of bentonite. The grout stability is very important during both the liquid and set conditions. The liquid grout fluidity should be as viscous as possible to avoid segregation, yet fluid enough to be easily pumpable and fill voids and over-break in the borehole. This paper investigates the effect of bentonite on the fresh and rheological properties of cement-based grouts in order to develop a stable grout to be used in these geotechnical situations. These properties were evaluated by the mini-slump flow, marsh cone flow time, Lombardi plate cohesion meter, static bleeding, yield stress and plastic viscosity values. Additionally, the compressive strength at 3 days, 7 days and 28 days were also investigated. The key parameters investigated were the dosages of bentonite and water-to-binder ratio (W/B). Test results showed that the dosage of bentonite had a significant effect on the fluidity, rheological properties and compressive strength of grout. The increase in the dosage of bentonite led to increasing the values of flow time, plate cohesion meter, yield stress and plastic viscosity, and reducing the mini-slump results, the static bleeding and the compressive strength at 3 days, 7 days and 28 days. Conversely, the increase in W/B led to decreasing the values of flow time, plate cohesion meter, yield stress, and plastic viscosity and the compressive strength, while increasing the mini-slump results and bleeding. Some recommendations for suitable mix proportions for use in soil boreholes are made.

Concerning the length of time slots for efficient gang scheduling

Applying gang scheduling can alleviate the blockade problem caused by exclusively used space-sharing strategies for parallel processing. However, the original form of gang scheduling is not practical as there are several fundamental problems associated with it. Recently many researchers have developed new strategies to alleviate some of these problems. Unfortunately, one important problem has not been so far seriously addressed, that is, how to set the length of time slots to obtain a good performance of gang scheduling. In this paper we present a strategy to deal with this important issue for efficient gang scheduling.

Gang scheduling with a queue for large jobs

Applying gang scheduling can alleviate the blockade problem caused by exclusively space-sharing scheduling. To simply allow jobs to run simultaneously on the same processors as in conventional gang scheduling, however, may introduce a large number of time slots in the system. In consequence the cost of context switches will be greatly increased, and each running job can only obtain a small portion of resources including memory space and processor utilisation and so no jobs can finish their computations quickly. Therefore, the number of jobs allowed to run in the system should be limited. In this paper we present some experimental results to show that by limiting real large jobs time-sharing the same processors and applying the backfilling technique we can greatly reduce the average number of time slots in the system and significantly improve the performance of both small and large jobs.

Evaluating the EASY-backfill job scheduling of static workloads on clusters

This research aims at improving our understanding of backfilling job scheduling algorithms. The most frequently used algorithm, EASY-backfilling, was selected for a performance evaluation by scheduling static workloads of parallel jobs on a computer cluster. To achieve the aim, we have developed a batch job scheduler for Linux clusters, implemented several scheduling algorithms including ARCA and EASY-Backfilling, and carried out their performance evaluation by running well known MPI applications on a real cluster. Our performance evaluation carried out for EASY-Backfilling serves two purposes. First, the performance results obtained from our evaluation can be used to validate other researcherspsila results generated by simulation, and second, the methodology used in our evaluation has alleviated many problems existed in the simulations presented in the current literature.

The impact of under-estimated length of jobs on EASY-backfill scheduling

The issue of under-estimated length of jobs (parallel applications) on backfill-based scheduling is ignored in the current literature because users want to avoid their jobs to be killed when the requested time expires. Therefore, users prefer to over-estimate the length of their jobs. This paper shows the impact of underestimated length of jobs on their execution performance in an EASY-backfill scheduling-based system. We have developed a batch job scheduler for Linux clusters that implements an enhanced EASY- backfilling algorithm in such a way that a job with an under-estimated execution time would not be killed unless it would delay other jobs. We have carried out performance evaluation by scheduling static workloads of well known MPI parallel applications on a real cluster. Our results show that most of the jobs do not have to be aborted even though their job lengths are under-estimated whereas the slowdown of jobs and the throughput of the system are only slightly degraded.

La Rocca di Castiglione del Lago (PG) Campagna di scavo 2014

The archaeological study took into account a very important part of Castiglione del Lago urban unit, where the presence of stratification, probably from the Classical period, had been pointed out, on which military and religious units were over-lapped. More specifically, the area with a small church inside the arms courtyard of the castle, could have suggested the presence of archaeological realities,especially from the sporadic finding of Etruscan pottery. The archaeological investigation was first launched in the area of the small chapel, where at least two construction phases were highlighted, although with no appreciable result regarding Classical period phases. The excavation led to the discovery of underground structures, a number of Renaissance tombs placed around the church, and the identification of other structures related to military use over a cistern-well. At the end of the excavation, the structures were consolidated and protected before the backfilling; the materials recovered during the investigation have been registered at the Municipality of Castiglione del Lago, after bein examined by the Soprintendenza per i Beni Archeologi dell’Umbria and the Soprintendenza per i Beni Storico, Artistici ed Etnoantropologici dell’Umbria.