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Hamburg, Germany

Ziegenhein P.,German Cancer Research Center | Kamerling C.P.,German Cancer Research Center | Bangert M.,German Cancer Research Center | Kunkel J.,Deutsches Klimarechenzentrum | Oelfke U.,German Cancer Research Center
Physics in Medicine and Biology | Year: 2013

Intensity modulated treatment plan optimization is a computationally expensive task. The feasibility of advanced applications in intensity modulated radiation therapy as every day treatment planning, frequent re-planning for adaptive radiation therapy and large-scale planning research severely depends on the runtime of the plan optimization implementation. Modern computational systems are built as parallel architectures to yield high performance. The use of GPUs, as one class of parallel systems, has become very popular in the field of medical physics. In contrast we utilize the multi-core central processing unit (CPU), which is the heart of every modern computer and does not have to be purchased additionally. In this work we present an ultra-fast, high precision implementation of the inverse plan optimization problem using a quasi-Newton method on pre-calculated dose influence data sets. We redefined the classical optimization algorithm to achieve a minimal runtime and high scalability on CPUs. Using the proposed methods in this work, a total plan optimization process can be carried out in only a few seconds on a low-cost CPU-based desktop computer at clinical resolution and quality. We have shown that our implementation uses the CPU hardware resources efficiently with runtimes comparable to GPU implementations, at lower costs. © 2013 Institute of Physics and Engineering in Medicine. Source

Weigel T.,Deutsches Klimarechenzentrum | Weigel T.,University of Hamburg | Kindermann S.,Deutsches Klimarechenzentrum | Lautenschlager M.,Deutsches Klimarechenzentrum | Lautenschlager M.,World Data Center for Climate
Data Science Journal | Year: 2014

Persistent Identifiers (PIDs) have lately received a lot of attention from scientific infrastructure projects and communities that aim to employ them for management of massive amounts of research data and metadata objects. Such usage scenarios, however, require additional facilities to enable automated data management with PIDs. In this article, we present a conceptual framework that is based on the idea of using common abstract data types (ADTs) in combination with PIDs. This provides a well-defined interface layer that abstracts from both underlying PID systems and higher-level applications. Our practical implementation is based on the Handle System, yet the fundamental concept of PID-based ADTs is transferable to other infrastructures, and it is well suited to achieve interoperability between them. Source

Weigel T.,Deutsches Klimarechenzentrum | Weigel T.,University of Hamburg | Lautenschlager M.,Deutsches Klimarechenzentrum | Lautenschlager M.,World Data Center for Climate | And 3 more authors.
Data Science Journal | Year: 2013

Several scientific communities relying on e-science infrastructures are in need of persistent identifiers for data and contextual information. In this article, we present a framework for persistent identification that fundamentally supports context information. It is installed as a number of low-level requirements and abstract data type descriptions, flexible enough to envelope context information while remaining compatible with existing definitions and infrastructures. The abstract data type definitions we draw from the requirements and exemplary use cases can act as an evaluation tool for existing implementations or as a blueprint for future persistent identification infrastructures. A prototypic implementation based on the Handle System is briefly introduced. We also lay the groundwork for establishing a graph of persistent entities that can act as a base layer for more sophisticated information schemas to preserve context information. Source

Eyring V.,German Aerospace Center | Righi M.,German Aerospace Center | Lauer A.,German Aerospace Center | Evaldsson M.,Swedish Meteorological and Hydrological Institute | And 34 more authors.
Geoscientific Model Development | Year: 2016

A community diagnostics and performance metrics tool for the evaluation of Earth system models (ESMs) has been developed that allows for routine comparison of single or multiple models, either against predecessor versions or against observations. The priority of the effort so far has been to target specific scientific themes focusing on selected essential climate variables (ECVs), a range of known systematic biases common to ESMs, such as coupled tropical climate variability, monsoons, Southern Ocean processes, continental dry biases, and soil hydrology-climate interactions, as well as atmospheric CO2 budgets, tropospheric and stratospheric ozone, and tropospheric aerosols. The tool is being developed in such a way that additional analyses can easily be added. A set of standard namelists for each scientific topic reproduces specific sets of diagnostics or performance metrics that have demonstrated their importance in ESM evaluation in the peer-reviewed literature. The Earth System Model Evaluation Tool (ESMValTool) is a community effort open to both users and developers encouraging open exchange of diagnostic source code and evaluation results from the Coupled Model Intercomparison Project (CMIP) ensemble. This will facilitate and improve ESM evaluation beyond the state-of-the-art and aims at supporting such activities within CMIP and at individual modelling centres. Ultimately, we envisage running the ESMValTool alongside the Earth System Grid Federation (ESGF) as part of a more routine evaluation of CMIP model simulations while utilizing observations available in standard formats (obs4MIPs) or provided by the user. © 2016 Author(s). Source

Riedel M.,Juelich Supercomputing Center | Wittenburg P.,Max Planck Institute For Meteorologie | van de Sanden M.,Stichting Academisch Rekencentrum Amsterdam | Rybicki J.,Juelich Supercomputing Center | And 22 more authors.
Journal of Internet Services and Applications | Year: 2013

The wide variety of scientific user communities work with data since many years and thus have already a wide variety of data infrastructures in production today. The aim of this paper is thus not to create one new general data architecture that would fail to be adopted by each and any individual user community. Instead this contribution aims to design a reference model with abstract entities that is able to federate existing concrete infrastructures under one umbrella. A reference model is an abstract framework for understanding significant entities and relationships between them and thus helps to understand existing data infrastructures when comparing them in terms of functionality, services, and boundary conditions. A derived architecture from such a reference model then can be used to create a federated architecture that builds on the existing infrastructures that could align to a major common vision. This common vision is named as 'ScienceTube' as part of this contribution that determines the high-level goal that the reference model aims to support. This paper will describe how a well-focused use case around data replication and its related activities in the EUDAT project aim to provide a first step towards this vision. Concrete stakeholder requirements arising from scientific end users such as those of the European Strategy Forum on Research Infrastructure (ESFRI) projects underpin this contribution with clear evidence that the EUDAT activities are bottom-up thus providing real solutions towards the so often only described 'high-level big data challenges'. The followed federated approach taking advantage of community and data centers (with large computational resources) further describes how data replication services enable data-intensive computing of terabytes or even petabytes of data emerging from ESFRI projects. © 2013 Riedel et al.; licensee Springer. Source

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