GridICE: a monitoring service for Grid systems Andreozzi, Sergio; De Bortoli, Natascia; Fantinel, Sergio ...
Future generation computer systems,
04/2005, Letnik:
21, Številka:
4
Journal Article
Recenzirano
Grid systems follow a new paradigm of distributed computing that enables the coordination of resources and services that are not subject to centralized control, can dynamically join and leave virtual ...pools, and are assigned to users by means of an explicit assignment functionality. The monitoring of a Grid is a multi-institutional and Virtual Organization (VO)-oriented service. It must deal with the dynamics, diversity, and geographical distribution of the resources available to Virtual Organizations, and the various levels of abstraction for modeling them. This paper presents the requirements, architecture and implementation of GridICE, a monitoring service for Grid systems. The suitability of this tool in real-life scenarios is analyzed and discussed.
Distributed Computing Infrastructures have dedicated mechanisms to provide user communities with computational environments. While in the last decade the Grid has demonstrated to be a powerful ...paradigm in supporting scientific research, the complexity of the user experience still limits its adoption by unskilled user communities. Command line interfaces, X.509 certificates, template customization for job submission and data access tools require end-users to dedicate significant learning effort and thus represent a barrier to access Grid computing facilities. In this paper, we present a Web portal that solves the aforementioned limitations by providing simplified access to Grid and Cloud computing services. The portal provides a set of interfaces that support federated authentication mechanisms, storage discovery and job description templates, enabling user communities to run specific use cases. We developed the portal framework within the Italian Grid Infrastructure where the major national user representatives drove its design, the implemented solutions and its validation by testing some specific use cases.
In the prospect of employing 10 Gigabit Ethernet as networking technology for online systems and offline data analysis centers of High Energy Physics experiments, we performed a series of ...measurements on the performance of 10 Gigabit Ethernet, using the network interface cards mounted on the PCI-Express bus of commodity PCs both as transmitters and receivers. In real operating conditions, the achievable maximum transfer rate through a network link is not only limited by the capacity of the link itself, but also by that of the memory and peripheral buses and by the ability of the CPUs and of the Operating System to handle packet processing and interrupts raised by the network interface cards in due time. Besides the TCP and UDP maximum data transfer throughputs, we also measured the CPU loads of the sender/receiver processes and of the interrupt and soft-interrupt handlers as a function of the packet size, either using standard or ¿jumbo¿ Ethernet frames. In addition, we also performed the same measurements by simultaneously reading data from Fibre Channel links and forwarding them through a 10 Gigabit Ethernet link, hence emulating the behavior of a disk server in a Storage Area Network exporting data to client machines via 10 Gigabit Ethernet.
Although agonists and antagonists of muscarinic receptors have been known for long time, there is renewed interest in compounds (such as allosteric or bitopic ligands, or biased agonists) able to ...differently and selectively modulate these receptors. As a continuation of our previous research, we designed a new series of dimers of the well-known cholinergic agonist carbachol. The new compounds were tested on the five cloned human muscarinic receptors (hM1–5) expressed in CHO cells by means of equilibrium binding experiments, showing a dependence of the binding affinity on the length and position of the linker connecting the two monomers. Kinetic binding studies revealed that some of the tested compounds were able to slow the rate of NMS dissociation, suggesting allosteric behavior, also supported by docking simulations. Assessment of ERK1/2 phosphorylation on hM1, hM2 and hM3 activation showed that the new compounds are endowed with muscarinic antagonist properties. At hM2 receptors, some compounds were able to stimulate GTPγS binding but not cAMP accumulation, suggesting a biased behavior.
Classification, Molecular and cellular pharmacology.
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CHEP 06 Computing in High Energy and Nuclear Physics (Grid
middleware and e-Infrastructure operation), Mumbai India, 2006 Moving from a National Grid Testbed to a Production quality Grid service for
...the HEP applications requires an effective operations structure and
organization, proper user and operations support, flexible and efficient
management and monitoring tools. Moreover the middleware releases should be
easily deployable using flexible configuration tools, suitable for various and
different local computing farms. The organizational model, the available tools
and the agreed procedures for operating the national/regional grid
infrastructures that are part of the world-wide EGEE grid as well as the
interconnection of the regional operations structures with the global
management, control and support structure play a key role for the success of a
real production grid. In this paper we describe the operations structure that
we are currently using at the Italian Grid Operation and Support Center. The
activities described cover monitoring, management and support for the
INFN-GRID/Grid.It production grid (spread over more than 30 sites) and its
interconnection with the EGEE/LCG structure as well as the roadmap to improve
the global support quality, stability and reliability of the Grid service.
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A series of homodimers of the well-known cholinergic agonist carbachol have been synthesized, showing the two agonist units symmetrically connected through a methylene chain of ...variable length. The new compounds have been tested on the five cloned muscarinic receptors (hM1–5) expressed in CHO cells by means of equilibrium binding studies, showing an increase in affinity by rising the number of methylene units up to 7 and 9. Functional experiments on guinea-pig ileum and assessment of ERK1/2 phosphorylation on hM1, hM2 and hM3 on CHO cells have shown that the new compounds are endowed with muscarinic antagonistic properties. Kinetic binding studies have revealed that some of the tested compounds are able to slow the rate of dissociation of NMS, suggesting a bitopic behavior. Docking simulations, performed on the hM1 and hM2 receptors, give a sound rationalization of the experimental data revealing how these compounds are able to interact with both orthosteric and allosteric binding sites depending on the length of their connecting chain.
Moving from a National Grid Testbed to a Production quality Grid service for the HEP applications requires an effective operations structure and organization, proper user and operations support, ...flexible and efficient management and monitoring tools. Moreover the middleware releases should be easily deployable using flexible configuration tools, suitable for various and different local computing farms. The organizational model, the available tools and the agreed procedures for operating the national/regional grid infrastructures that are part of the world-wide EGEE grid as well as the interconnection of the regional operations structures with the global management, control and support structure play a key role for the success of a real production grid. In this paper we describe the operations structure that we are currently using at the Italian Grid Operation and Support Center. The activities described cover monitoring, management and support for the INFN-GRID/Grid.It production grid (spread over more than 30 sites) and its interconnection with the EGEE/LCG structure as well as the roadmap to improve the global support quality, stability and reliability of the Grid service.
The study presents a docking analysis for the interaction capabilities of some muscarinic receptors (i.e., M
1, M
2, and M
5) whose full-length models were previously generated by us. In detail, the ...docking simulations involved a dataset of 30 agonists, taken from the literature, including a first series of oxathiolane/dioxolane congeners and a second subset of more heterogeneous ligands. The obtained results unveil that it is possible to discriminate among the binding modes of considered muscarinic receptors, developing specific interaction patterns which are significantly different for the arrangement of both polar and hydrophobic interactions. Thus, the M
1 subtype possesses the widest binding site, while the M
2 receptor is characterized by a large but asymmetric region that accommodates the ligand’s ammonium head and finally the M
5 binding site is quite similar to that of M
2 subtype being univocally characterized by a second aspartate residue which interacts with the ammonium head. The significant correlations between docking scores and affinity values afford an encouraging validation for the reported binding modes and confirm the key role of molecular flexibility in the ligand recognition of muscarinic receptors.
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