A REST Model for High Throughput Scheduling in Computational Grids

Current grid computing architectures have been based on cluster management and batch queuing systems, extended to a distributed, federated domain. These have shown shortcomings in terms of scalability, stability, and modularity. To address these problems, this dissertation applies architectural styles from the Internet and Web to the domain of generic computational grids. Using the REST style, a flexible model for grid resource interaction is developed which removes the need for any centralised services or specific protocols, thereby allowing a range of implementations and layering of further functionality. The context for resource interaction is a generalisation and formalisation of the Condor ClassAd match-making mechanism. This set theoretic model is described in depth, including the advantages and features which it realises. This RESTful style is also motivated by operational experience with existing grid infrastructures, and the design, operation, and performance of a proto-RESTful grid middleware package named DIRAC. This package was designed to provide for the LHCb particle physics experiment's âﾜoff-lineâ computational infrastructure, and was first exercised during a 6 month data challenge which utilised over 670 years of CPU time and produced 98 TB of data through 300,000 tasks executed at computing centres around the world. The design of DIRAC and performance measures from the data challenge are reported. The main contribution of this work is the development of a REST model for grid resource interaction. In particular, it allows resource templating for scheduling queues which provide a novel distributed and scalable approach to resource scheduling on the grid

Non-Coding RNA Features Critical to the Replication of HIV-1

The HIV-1 genome contains RNA sequences and structures that control many aspects of viral replication including, but not limited to transcription, splicing, nuclear export, translation, packaging and reverse transcription. Despite this extensive existing catalogue of RNA sequences that are critical to its replication, chemical probing and targeting mutagenesis studies suggest that the HIV-1 genome may contain many more RNA elements of unknown important function. To determine whether there are additional, undiscovered cis-acting RNA elements in the HIV-1 genome that are important for viral replication, we conducted a global synonymous mutagenesis experiment. Sixteen mutant proviruses containing clusters of ~50 to ~200 synonymous mutations covering nearly the entire HIV-1 protein coding sequence were designed and synthesized. Analyses of these mutant viruses resulted in their division into three phenotypic groups. Group 1 mutants exhibited near wild-type replication, Group 2 mutants exhibited replication defects accompanied by perturbed RNA splicing, and Group 3 mutants had replication defects in the absence of obvious splicing perturbation. The three phenotypes were caused by mutations that exhibited a clear regional bias in their distribution along the viral genome, and those that caused replication defects all caused reductions in the level of unspliced RNA. We characterized in detail the underlying defects for Group 2 mutants. Second-site revertants that enabled viral replication could be derived for Group 2 mutants, and generally contained point mutations that reduced the utilization of proximal splice sites. Mapping of the changes responsible for splicing perturbations in Group 2 viruses revealed the presence of several RNA sequences that apparently suppressed the use of cryptic or canonical splice sites. Some sequences that affected splicing were diffusely distributed, while others could be mapped to discrete elements, proximal or distal to the affected splice sites. This data from the Group 2 mutants indicates complex negative regulation of HIV-1 splicing by RNA elements in various regions of the HIV-1 genome that enable balanced splicing and viral replication. In silico analysis of the Group 3 mutants revealed that our mutagenesis had significantly increased the frequency of CG dinucleotides in sections of the viral genome to that of random sequence. This is important due to the remarkable CG suppression in both the HIV-1 and human genomes, and we had therefore disrupted the dinucleotide congruence that exists between HIV-1 and the genome of its host. We recoded these mutants to selectively remove either only the CG dinucleotides or only remove the mutations that did not encode a CG dinucleotide. Analysis of these mutants clearly demonstrated that the addition of CG dinucleotides were the causative mutations entirely responsible for the observed replication defects. qPCR analysis and smFISH microscopy revealed that the addition of CG dinucleotides to HIV-1 resulted in a depletion of the cytoplasmic mRNA molecules where the CG-dinucleotides were encoded as exons. A targeted siRNA screen for proteins that destabilize cytoplasmic RNA identified the Zinc-finger Antiviral Protein (ZAP) as responsible for the restriction of the CG-high HIV-1, specifically by targeting CGhigh viral RNA. CLIP-Seq experiments demonstrate that ZAP binds directly to CG dinucleotides in both cellular and viral RNA. Collectively these studies implicate ZAP as a cellular protein that can recognize CG-high viral RNA and is possibly a cellular mechanism for determining self from non-self RNA based on the CG composition. TRIM25 has previously been identified as a cofactor for two cytosolic RNA binding proteins that have antiviral functions, RIG-I where it is an essential cofactor, and ZAP where it functions as an enhancing cofactor. The mechanism by which TRIM25 enhances the antiviral activity of ZAP currently remains unclear. Through CLIP-Seq experiments in cells knocked out for TRIM25, we determined that ZAP does not require TRIM25 to recognize CG-high RNA. Using full length mutants of TRIM25 that are deficient for either RNA binding, E3 ligase activity, or formation of higher order multimers, our data suggest that the key biological activity required for TRIM25 to enhance ZAP is the formation of higher order multimers. Analyzing the replication of CG-high HIV-1 in different cell lines indicates that ZAP is not equally potent across all cell lines. The degree of potency ZAP possess against CG-high HIV-1 does not correlate with TRIM25 expression, suggesting the possibility of an additional ZAP cofactor that is heterogeneously expressed in varying cell lines. siRNA screens have been used in an attempt to identify a yet undiscovered cofactor, but so far these experiments have not yielded any such factor

CSA06 Computing, Software and Analysis challenge at the Spanish Tier-1 and Tier-2 sites

This note describes the participation of the Spanish centres PIC, CIEMAT and IFCA as Tier-1 and Tier-2 sites in the CMS CSA06 Computing, Software and Analysis challenge. A number of the facilities, services and workflows have been demonstrated at the 2008 25% scale. Very valuable experience has been gained running the complex computing system under realistic conditions at a significant scale. The focus of this note is on presenting achieved results, operational experience and lessons learnt during the challenge

Storage Management and Access in WLHC computing Grid

One of the big challenges in Grid computing is storage management and access. Several solutions exist to store data in a persistent way. In this work we describe our contribution within the Worldwide LHC Computing Grid project. Substantial samples of data produced by the High Energy Physics detectors at CERN are shipped for initial processing to specific large computing centers worldwide. Such centers are normally able to provide persistent storage for tens of Petabytes of data mostly on tapes. Special physics applications are used to refine and filter the data after spooling the required files from tape to disk. At smaller geographically dispersed centers, physicists perform the analysis of such data stored on disk-only caches. In this thesis we analyze the application requirements such as uniform storage management, quality of storage, POSIX-like file access, performance, etc. Furthermore, security, policy enforcement, monitoring, and accounting need to be addressed carefully in a Grid environment. We then make a survey of the multitude of storage products deployed in the WLCG infrastructure, both hardware and software. We outline the specific features, functionalities and diverse interfaces offered to users. We focus in particular on StoRM, a storage resource manager that we have designed and developed to provide an answer to specific user request for a fast and efficient Grid interface to available parallel file systems. We propose a model for the Storage Resource Management protocol for uniform storage management and access in the Grid. The black box testing methodology has been applied in order to verify the completeness of the specifications and validate the existent implementations. an extension for storage on the Grid. We finally describe and report on the results obtained

Replica maintenance strategy for data grid

Data Grid is an infrastructure that manages huge amount of data files, and provides intensive computational resources across geographically distributed collaboration.Increasing the performance of such system can be achieved by improving the overall resource usage, which includes network and storage resources.Improving network resource usage is achieved by good utilization of network bandwidth that is considered as an important factor affecting job execution time.Meanwhile, improving storage resource usage is achieved by good utilization of storage space usage. Data replication is one of the methods used to improve the performance of data access in distributed systems by replicating multiple copies of data files in the distributed sites.Having distributed the replicas to various locations, they need to be monitored.As a result of dynamic changes in the data grid environment, some of the replicas need to be relocated.In this paper we proposed a maintenance replica placement strategy termed as Unwanted Replica Deletion Strategy (URDS) as a part of Replica maintenance service.The main purpose of the proposed strategy is to find the placement of unwanted replicas to be deleted.OptorSim is used to evaluate the performance of the proposed strategy. The simulation results show that URDS requires less execution time and consumes less network usage and has a best utilization of storage space usage compared to existing approaches