The D-Grid Integration Project: How to Build a Grid for Different Communities

The Grid world is highly dynamic due to the appearance of new resources, easier access and new Grid applications. Moreover, an increasing number of scientific communities begins to realize that Grids will become an indispensable tool for modern science. However, the requirements of those communities often differ significantly from each other. Therefore, it is a particularly di±cult challenge to establish a national Grid infrastructure that serves as many communities as possible. To address this challenge, the German D-Grid has developed a concept that is based on development of independent Community Grids that are connected with a single integration project. Further, the process will involve several steps to consider dependencies between the various projects and their tasks. Presently, we are still at the beginning of the realization of a German Grid. Therefore in this paper, we first briefly explain this concept in this paper. Then we focus on the integration project and describe its tasks in more detail. This includes some first results and experiences that were achieved within the first year of the project. Finally, some plans for future steps are presented

Actin Dynamics Regulate Multiple Endosomal Steps during Kaposi's Sarcoma-Associated Herpesvirus Entry and Trafficking in Endothelial Cells

The role of actin dynamics in clathrin-mediated endocytosis in mammalian cells is unclear. In this study, we define the role of actin cytoskeleton in Kaposi's sarcoma-associated herpesvirus (KSHV) entry and trafficking in endothelial cells using an immunofluorescence-based assay to visualize viral capsids and the associated cellular components. In contrast to infectivity or reporter assays, this method does not rely on the expression of any viral and reporter genes, but instead directly tracks the accumulation of individual viral particles at the nuclear membrane as an indicator of successful viral entry and trafficking in cells. Inhibitors of endosomal acidification reduced both the percentage of nuclei with viral particles and the total number of viral particles docking at the perinuclear region, indicating endocytosis, rather than plasma membrane fusion, as the primary route for KSHV entry into endothelial cells. Accordingly, a viral envelope protein was only detected on internalized KSHV particles at the early but not late stage of infection. Inhibitors of clathrin- but not caveolae/lipid raft-mediated endocytosis blocked KSHV entry, indicating that clathrin-mediated endocytosis is the major route of KSHV entry into endothelial cells. KSHV particles were colocalized not only with markers of early and recycling endosomes, and lysosomes, but also with actin filaments at the early time points of infection. Consistent with these observations, transferrin, which enters cells by clathrin-mediated endocytosis, was found to be associated with actin filaments together with early and recycling endosomes, and to a lesser degree, with late endosomes and lysosomes. KSHV infection induced dynamic actin cytoskeleton rearrangements. Disruption of the actin cytoskeleton and inhibition of regulators of actin nucleation such as Rho GTPases and Arp2/3 complex profoundly blocked KSHV entry and trafficking. Together, these results indicate an important role for actin dynamics in the internalization and endosomal sorting/trafficking of KSHV and clathrin-mediated endocytosis in endothelial cells

On the Design and Evaluation of Job Scheduling Algorithms

In this paper we suggest a strategy to design job scheduling systems. To this end, we first split a scheduling system into three components: Scheduling policy, objective function and scheduling algorithm. After discussing the relationship between those components we explain our strategy with the help of a simple example. The main focus of this example is the selection and the evaluation of several scheduling algorithms.

Analysis of Smith's rule in stochastic machine scheduling

In a landmark paper from 1986, Kawaguchi and Kyan show that scheduling jobs according to ratios weight over processing time–also known as Smith’s rule–has a tight performance guarantee of approximately 1.207 for minimizing the weighted sum of completion times in parallel machine scheduling. We prove the counterintuitive result that the performance guarantee of Smith’s rule is not better than 1.243 when processing times are exponentially distributed

Preemption based backfill

Recent advances in DNA analysis, global climate modeling and computational fluid dynamics have increased the demand for supercomputing resources. Through increasing the efficiency and throughput of existing supercomputing centers, additional computational power can be provided for these applications. Backfill has been shown to increase the efficiency of supercomputer schedulers for large, homogenous machines[3]. Utilizations can still be as low as 60 % for machines with heterogeneous resources and strict administrative requirements. Preemption based backfill allows the scheduler to be more aggressive in filling up the schedule for a supercomputer[2]. Utilization can be increased and administrative requirements relaxed if it is possible to preempt a running job to allow a higher priority task to run.