Optimised access to user analysis data using the gLite DPM

The ScotGrid distributed Tier-2 now provides more that 4MSI2K and 500TB for LHC computing, which is spread across three sites at Durham, Edinburgh and Glasgow. Tier-2 sites have a dual role to play in the computing models of the LHC VOs. Firstly, their CPU resources are used for the generation of Monte Carlo event data. Secondly, the end user analysis data is distributed across the grid to the site's storage system and held on disk ready for processing by physicists' analysis jobs. In this paper we show how we have designed the ScotGrid storage and data management resources in order to optimise access by physicists to LHC data. Within ScotGrid, all sites use the gLite DPM storage manager middleware. Using the EGEE grid to submit real ATLAS analysis code to process VO data stored on the ScotGrid sites, we present an analysis of the performance of the architecture at one site, and procedures that may be undertaken to improve such. The results will be presented from the point of view of the end user (in terms of number of events processed/second) and from the point of view of the site, which wishes to minimise load and the impact that analysis activity has on other users of the system

Monitoring in a grid cluster

The monitoring of a grid cluster (or of any piece of reasonably scaled IT infrastructure) is a key element in the robust and consistent running of that site. There are several factors which are important to the selection of a useful monitoring framework, which include ease of use, reliability, data input and output. It is critical that data can be drawn from different instrumentation packages and collected in the framework to allow for a uniform view of the running of a site. It is also very useful to allow different views and transformations of this data to allow its manipulation for different purposes, perhaps unknown at the initial time of installation. In this context, we present the findings of an investigation of the Graphite monitoring framework and its use at the ScotGrid Glasgow site. In particular, we examine the messaging system used by the framework and means to extract data from different tools, including the existing framework Ganglia which is in use at many sites, in addition to adapting and parsing data streams from external monitoring frameworks and websites

Analysis and improvement of data-set level file distribution in Disk Pool Manager

Of the three most widely used implementations of the WLCG Storage Element specification, Disk Pool Manager[1, 2] (DPM) has the simplest implementation of file placement balancing (StoRM doesn't attempt this, leaving it up to the underlying filesystem, which can be very sophisticated in itself). DPM uses a round-robin algorithm (with optional filesystem weighting), for placing files across filesystems and servers. This does a reasonable job of evenly distributing files across the storage array provided to it. However, it does not offer any guarantees of the evenness of distribution of that subset of files associated with a given "dataset" (which often maps onto a "directory" in the DPM namespace (DPNS)). It is useful to consider a concept of "balance", where an optimally balanced set of files indicates that the files are distributed evenly across all of the pool nodes. The best case performance of the round robin algorithm is to maintain balance, it has no mechanism to improve balance.<p></p> In the past year or more, larger DPM sites have noticed load spikes on individual disk servers, and suspected that these were exacerbated by excesses of files from popular datasets on those servers. We present here a software tool which analyses file distribution for all datasets in a DPM SE, providing a measure of the poorness of file location in this context. Further, the tool provides a list of file movement actions which will improve dataset-level file distribution, and can action those file movements itself. We present results of such an analysis on the UKI-SCOTGRID-GLASGOW Production DPM

Magnetic ordering in systems of reduced dimensionality

The magnetic behaviour of thin films of (111) FCC structures and (0001) corundum structured materials were studied by the mean field analysis and some Monte Carlo simulation. These models were conditioned on a mapping from first principles calculations to the Ising model. The effect of the suggested octopolar reconstruction for the polar (111) surfaces of FCC was also examined

A voyage to Arcturus: a model for automated management of a WLCG Tier-2 facility

With the current trend towards "On Demand Computing" in big data environments it is crucial that the deployment of services and resources becomes increasingly automated. Deployment based on cloud platforms is available for large scale data centre environments but these solutions can be too complex and heavyweight for smaller, resource constrained WLCG Tier-2 sites. Along with a greater desire for bespoke monitoring and collection of Grid related metrics, a more lightweight and modular approach is desired. In this paper we present a model for a lightweight automated framework which can be use to build WLCG grid sites, based on "off the shelf" software components. As part of the research into an automation framework the use of both IPMI and SNMP for physical device management will be included, as well as the use of SNMP as a monitoring/data sampling layer such that more comprehensive decision making can take place and potentially be automated. This could lead to reduced down times and better performance as services are recognised to be in a non-functional state by autonomous systems

Pathways to diagnosis of non-small cell lung cancer: a descriptive cohort study

Little has been published on the diagnostic and referral pathway for lung cancer in Australia. This study set out to quantify general practitioner (GP) and lung specialist attendance and diagnostic imaging in the lead-up to a diagnosis of non-small cell lung cancer (NSCLC) and identify common pathways to diagnosis in New South Wales (NSW), Australia. We used linked health data for participants of the 45 and Up Study (a NSW population-based cohort study) diagnosed with NSCLC between 2006 and 2012. Our main outcome measures were GP and specialist attendances, X-rays and computed tomography (CT) scans of the chest and lung cancer-related hospital admissions. Among our study cohort (N = 894), 60% (n = 536) had ≥4 GP attendances in the 3 months prior to diagnosis of NSCLC, 56% (n = 505) had GP-ordered imaging (chest X-ray or CT scan), 39% (N = 349) attended a respiratory physician and 11% (N = 102) attended a cardiothoracic surgeon. The two most common pathways to diagnosis, accounting for one in three people, included GP and lung specialist (respiratory physician or cardiothoracic surgeon) involvement. Overall, 25% of people (n = 223) had an emergency hospital admission. For 14% of people (N = 129), an emergency hospital admission was the only event identified on the pathway to diagnosis. We found little effect of remoteness of residence on access to services. This study identified a substantial proportion of people with NSCLC being diagnosed in an emergency setting. Further research is needed to establish whether there were barriers to the timely diagnosis of these cases

Pathways to diagnosis of non-small cell lung cancer : a descriptive cohort study

Little has been published on the diagnostic and referral pathway for lung cancer in Australia. This study set out to quantify general practitioner (GP) and lung specialist attendance and diagnostic imaging in the lead-up to a diagnosis of non-small cell lung cancer (NSCLC) and identify common pathways to diagnosis in New South Wales (NSW), Australia. We used linked health data for participants of the 45 and Up Study (a NSW population-based cohort study) diagnosed with NSCLC between 2006 and 2012. Our main outcome measures were GP and specialist attendances, X-rays and computed tomography (CT) scans of the chest and lung cancer-related hospital admissions. Among our study cohort (N = 894), 60% (n = 536) had ≥4 GP attendances in the 3 months prior to diagnosis of NSCLC, 56% (n = 505) had GP-ordered imaging (chest X-ray or CT scan), 39% (N = 349) attended a respiratory physician and 11% (N = 102) attended a cardiothoracic surgeon. The two most common pathways to diagnosis, accounting for one in three people, included GP and lung specialist (respiratory physician or cardiothoracic surgeon) involvement. Overall, 25% of people (n = 223) had an emergency hospital admission. For 14% of people (N = 129), an emergency hospital admission was the only event identified on the pathway to diagnosis. We found little effect of remoteness of residence on access to services. This study identified a substantial proportion of people with NSCLC being diagnosed in an emergency setting. Further research is needed to establish whether there were barriers to the timely diagnosis of these cases

‘Re-reading Raphael Samuel: Politics, Personality and Performance’

For British historian Raphael Samuel, history and politics were inextricable. Best known as the founder of the history workshop movement, the controversial historian took his stance on the democratisation of history-making, becoming an outspoken advocate for public history. Despite making a significant contribution to contemporary historiography, he remains a neglected, even disparaged, figure. This paper contends that the most significant aspect of Samuel’s historical work was not one or other theory of history or argument about the past but his entire way of being an historian. Samuel embodied as much as expressed his ideas, consciously using his personality as a powerful political tool. It is further argued that conventional approaches to intellectual history, focusing on textual outputs, do not fully recognise the significance of performative modes of thinking. Theoretical approaches to performance as identity offer important insight here but can be too schematic in their view of applied and enacted thought. A biographical approach, by contrast, provides the intimate perspective necessary to fully appreciate the fluidity and complexity of such a personality. The paper first situates Samuel in the context of his earlier life, focusing on how and why he created such a public persona and how he adapted it in response to changing circumstances. It then considers the implications and effectiveness of this persona by assessing how it was perceived and narrated by others, acknowledging, in the process, why different groups engaged with and interpreted it differently

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer

AD51B in Familial Breast Cancer

Common variation on 14q24.1, close to RAD51B, has been associated with breast cancer: rs999737 and rs2588809 with the risk of female breast cancer and rs1314913 with the risk of male breast cancer. The aim of this study was to investigate the role of RAD51B variants in breast cancer predisposition, particularly in the context of familial breast cancer in Finland. We sequenced the coding region of RAD51B in 168 Finnish breast cancer patients from the Helsinki region for identification of possible recurrent founder mutations. In addition, we studied the known rs999737, rs2588809, and rs1314913 SNPs and RAD51B haplotypes in 44,791 breast cancer cases and 43,583 controls from 40 studies participating in the Breast Cancer Association Consortium (BCAC) that were genotyped on a custom chip (iCOGS). We identified one putatively pathogenic missense mutation c.541C>T among the Finnish cancer patients and subsequently genotyped the mutation in additional breast cancer cases (n = 5259) and population controls (n = 3586) from Finland and Belarus. No significant association with breast cancer risk was seen in the meta-analysis of the Finnish datasets or in the large BCAC dataset. The association with previously identified risk variants rs999737, rs2588809, and rs1314913 was replicated among all breast cancer cases and also among familial cases in the BCAC dataset. The most significant association was observed for the haplotype carrying the risk-alleles of all the three SNPs both among all cases (odds ratio (OR): 1.15, 95% confidence interval (CI): 1.11–1.19, P = 8.88 x 10−16) and among familial cases (OR: 1.24, 95% CI: 1.16–1.32, P = 6.19 x 10−11), compared to the haplotype with the respective protective alleles. Our results suggest that loss-of-function mutations in RAD51B are rare, but common variation at the RAD51B region is significantly associated with familial breast cancer risk