KM3NeT is a future European deep-sea research infrastructure hosting a new generation neutrino detectors that – located at the bottom of the Mediterranean Sea – will open a new window on the universe ...and answer fundamental questions both in particle physics and astrophysics. International collaborative scientific experiments, like KM3NeT, are generating datasets which are increasing exponentially in both complexity and volume, making their analysis, archival, and sharing one of the grand challenges of the 21st century. These experiments, in their majority, adopt computing models consisting of different Tiers with several computing centres and providing a specific set of services for the different steps of data processing such as detector calibration, simulation and data filtering, reconstruction and analysis. The computing requirements are extremely demanding and, usually, span from serial to multi-parallel or GPU-optimized jobs. The collaborative nature of these experiments demands very frequent WAN data transfers and data sharing among individuals and groups. In order to support the aforementioned demanding computing requirements we enabled Grid Computing resources, operated by EGI, within the KM3NeT computing model. In this study we describe our first advances in this field and the method for the KM3NeT users to utilize the EGI computing resources in a simulation-driven use-case.
Sometimes, the maelstrom of a crisis can be captured in a single image. The image of the mundane, barely noticeable movement of an urban dweller as they go about their everyday life. Athens and the ...War on Public Space commences from images just like this one, collected over a two-year period of research (2012–2014) in Athens during a time of severe financial and political crisis. For the author-curators of this volume, public space became a light-sensitive surface upon which they could begin to map the material imprints of the most structural and violent characteristics of the crisis, and their research spread in different directions, tracking the role of infrastructure and the shifts the financial crisis brought about upon built environments, the violent manifestations of the official anti-migrant policy, the rise of racism, the imposition of the emergency upon public space, and the phenomenology of mass transit.
Today, urbanization is described as one of the major global challenges. The rapid demographic transformations taking place in certain regions of the Global South — especially in countries of Africa ...and Southeast Asia — bring a sense of urgency to the discussion on cities. Rapid and uncontrolled urbanization in Global South, combined with social inequalities, poverty and environmental degradation, renders many urban populations vulnerable and precarious. With an emphasis on the urban expansion of the Global South, an international agenda is formed nowadays, focusing on the structural functions of the cities and their shielding against the negative effects of the current global crisis; a crisis taking today the form of an economic, environmental, and migration crisis. Thus, sustainability and resilience of the cities, and especially of those in the Global South, are turned into the key questions of urban planning and urban governance policies. Yet, they are also gradually turned into an object of military problematizations, as Western armed forces are strongly interested today in the urban phenomena and the functions of the cities, perceiving urban environment not only as a potential field of military operations but as a source of irregular threats; describing, in other words, the cities of the Global South not only as sites that host potential enemies but as enemies per se. More specifically, from the end of the 20th century U.S. military focuses on urban informality and its security implications, imposing a new understanding of the urban world. This is today more evident, as rapid demographic changes render urban systems and informal urban settlements in particular more vulnerable, and this vulnerability is directly problematized in public security terms. Through the relevant anti-urban theoretical frameworks, the cities of the Global South are conceived as feral systems that have to be tamed; and this taming calls for direct intervention. Military imposes, in this way, its presence in the field of urban problematizations, and building on the deception of contemporary neoliberal narratives calls today for urban resilience. As the world urbanizes rapidly and the notions of crisis and emergency are shaping the dominant social imaginary and the modern governmental agenda, urban sustainability, adaptability, and resilience are turned into an overall public security issue and eventually into an object of military interest. Hence, when the military theorists wonder how to make contemporary “fragile” urban systems more “resilient”, they actually wonder how to build forcibly resilient subjectivities and impose, after all, resilience and patience against an inescapable oppression.
MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web ...server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.
The primary objective of SIRENE is to simulate the response to neutrino events of any type of high energy neutrino telescope. Additionally, it implements different geometries for a neutrino detector ...and different configurations and characteristics of photo-multiplier tubes (PMTs) inside the optical modules of the detector through a library of C+ + classes. This could be considered a massive statistical analysis of photo-electrons. Aim of this work is the development of a multithreaded version of the SIRENE detector simulation software for high energy neutrinos. This approach allows utilization of multiple CPU cores leading to a potentially significant decrease in the required execution time compared to the sequential code. We are making use of the OpenMP framework for the production of multithreaded code running on the CPU. Finally, we analyze the feasibility of a GPU-accelerated implementation.
We present a design of a Mobile Grid Resource Management System aimed at integrating mobile resources to an existing Grid infrastructure, while creating a platform for interoperability with ...telecommunications providers. In order to reduce the load on an existing infrastructure, we separate responsibilities and run additional features on mobile resources. Finally we present the Ikaros-EG implementation, IkarosM android application and the mobile-Grid concept.The system used for our implementation was the NCSR “Demokritos” ZEUS computer Cluster, where the Ikaros-EG framework consisting of a meta-data collector and the Ikaros-EG plug-in has been installed. The ZEUS cluster has local and Grid access to data and meta-data from numerous scientific experiments. Our objective was to incorporate the mobile resources using the NCSR Demokritos campus wireless infrastructure in order to run applications concerning accounting, statistics, or further data/meta-data formatting.
•Proposes a dynamically coordinated I/O architecture based on input parameters.•Creates, on the fly, dedicated or semi-dedicated clusters of HDDs per job.•Provides coordinated parallel data transfers ...on the overall data flow.•Minimizes disk and network contention.•Improves performance by 33% with the 1/3 of the available hard disks.
High performance computing (HPC) has crossed the Petaflop mark and is reaching the Exaflop range quickly. The exascale system is projected to have millions of nodes, with thousands of cores for each node. At such an extreme scale, the substantial amount of concurrency can cause a critical contention issue for I/O system. This study proposes a dynamically coordinated I/O architecture for addressing some of the limitations that current parallel file systems and storage architectures are facing with very large-scale systems. The fundamental idea is to coordinate I/O accesses according to the topology/profile of the infrastructure, the load metrics, and the I/O demands of each application. The measurements have shown that by using IKAROS approach we can fully utilize the provided I/O and network resources, minimize disk and network contention, and achieve better performance.
We present the design of IKAROS: an HTTP-based distributed file system, which provides file access scalability and targets a large variety of operating systems and storage systems. IKAROS bypasses ...the server bottleneck enabling clients to access storage directly, while supporting the usage of multiple types of meta-data. It enables low-consumption, low-specification and low-cost devices to achieve a high throughput data transfer, responding to highly demanding applications. We present data transfer results comparing IKAROS, NFS, PVFS2 and HDFS on a Small Office/Home Office Network Attached Storage infrastructure. We show that IKAROS architecture satisfies and outperforms the data rate demands of high performance applications. We also present experimental results which compare IKAROS and GridFTP using the European Grid Infrastructure. IKAROS performs better in most cases while being competitive at the rest.
We present an ad-hoc "nearby" storage, based on IKAROS and social networking services, such as Facebook. By design, IKAROS is capable to increase or decrease the number of nodes of the I/O system ...instance on the fly, without bringing everything down or losing data. IKAROS is capable to decide the file partition distribution schema, by taking on account requests from the user or an application, as well as a domain or a Virtual Organization policy. In this way, it is possible to form multiple instances of smaller capacity higher bandwidth storage utilities capable to respond in an ad-hoc manner. This approach, focusing on flexibility, can scale both up and down and so can provide more cost effective infrastructures for both large scale and smaller size systems. A set of experiments is performed comparing IKAROS with PVFS2 by using multiple clients requests under HPC IOR benchmark and MPICH2.
pWebDAV: A Multi-Tier Storage System Filippidis, Christos; Cotronis, Yiannis
2018 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP)
Conference Proceeding
Experiments using the Large Hadron Collider (LHC) currently generate tens of petabytes of reduced data per year, observational and simulation data in the climate domain is expected to reach eXabytes ...by 2021, and light source experiments are expected to generate hundreds of terabytes per day. At such extreme scale, the substantial amount of concurrency can cause critical contention issue of the I/O system. This study introduces pWebDAV as a heterogeneous, multi-tier storage system. pWebDAV proposes a dynamically coordinated I/O architecture offering overall data flow solutions (remote-local access). The fundamental idea is to implement, for each data transfer, I/O policies on the fly. pWebDAV controls all I/O nodes, participating in the data transfer, directly regardless of the tier. pWebDAV approach can fully utilize the provided I/O & network resources and is able to minimize disk and network contention. The focus in this study is the Metadata node scalability performance.
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