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  • 1. Abdullah, Matin
    et al.
    Feig, Michael
    Pettitt, Montgomery
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    SimDB: A Problem Solving Environment for Molecular Dynamics Simulation and Analysis2000Conference paper (Refereed)
    Abstract [en]

    The design of a software environment, SimDB, for molecular dynamics simulation and analysis is presented as an example of virtual laboratories enabled by high-speed networks connecting substantial computing and storage resources with more modest local compuation and visualization resources available to research groups. SimDB includes large-scale, dynamic, distributed data repositories. The simulated data sets, trajectories, are usually interpreted through reduced data sets, processed data sets, calculated by analysis functions. Both trajectory data and processed data are saved, but in differnt data bases, with processed data bases having several smaller objects for each trajectory. A browser based user interface with a well defined API allows for a wide array of analysis functions. Analysis functions are executed only if the requested analysis result is not available. The ability to incorporate user defined functions is a critical feature of SimDB.

  • 2.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gimenez, Judit
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Scalability analysis of Dalton, a molecular structure program2013In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, no 8, p. 2197-2204Article in journal (Refereed)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.

  • 3.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Gimenez, Judit
    Barcelona Supercomputing Center, Universitat Politecnica de Catalunya, Barcelona, Spain.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Scaling Dalton, a molecular electronic structure program2011In: Seventh International Conference on e-Science, e-Science 2011, 5-8 December 2011, Stockholm, Sweden, IEEE conference proceedings, 2011, p. 256-262Conference paper (Refereed)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a characterization and performance optimization of Dalton that increases the scalability and parallel efficiency of the application. We also propose asolution that helps to avoid the master/worker design of Daltonto become a performance bottleneck for larger process numbers and increase the parallel efficiency.

  • 4.
    Ahsant, Mehran
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    On-demand Restricted Delegation: A Framework for Dynamic, Context-Aware, Least-Privilege Delegation in Grids2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In grids, delegation is a key facility that can be used to authenticate and authorize requests on behalf of disconnected users. In current grid systems,delegation is either performed dynamically, in an unrestricted manner, or by a secure but static method. Unfortunately, the former compromises security and the latter cannot satisfy the requirements of dynamic grid application execution. Therefore, development of a delegation framework that enables a restricted and flexible delegation mechanism becomes increasingly urgent as grids are adopted by new communities and grow in size. The main barriers in development of such a mechanism are the requirements for dynamic execution of grid applications, which make it difficult to anticipate required access rights for completing tasks in advance.

    Another significant architectural requirement in grids is federated security and trust. A considerable barrier to achieving this is cross-organizational authentication and identification. Organizations participating in Virtual Organizations (VOs) may use different security infrastructures that implement different protocols for authentication and identification; thus, there exists a need to provide an architectural mechanism for lightweight, rapid and interoperable translation of security credentials from an original format to a format understandable by recipients.

    This thesis contributes the development of a delegation framework that utilizes a mechanism for determining and acquiring only required rights and credentials for completing a task, when they are needed. This is what we call an on-demand delegation framework that realizes a bottom-up delegation model and provides a just-in-time acquisition of rights for restricted and dynamic delegation.

    In this thesis, we further contribute the development of a credential mapping mechanism using off-the-shelf standards and technologies. This mechanism provides support for an on-the-fly exchange of different types of security credentials used by the security mechanisms of existing grids.

  • 5.
    Ahsant, Mehran
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Basney, Jim
    Workflows in Dynamic and Restricted Delegation2009In: 2009 INTERNATIONAL CONFERENCE ON AVAILABILITY, RELIABILITY, AND SECURITY (ARES), New York: IEEE , 2009, p. 17-24Conference paper (Refereed)
    Abstract [en]

    Delegation is a key facility in dynamic, distributed and collaborative environments like e rids and enables an effective use of a wide range of dynamic applications. Traditional delegation frameworks approach a top-down model of delegation for delegating rights from a superior to a subordinate in advance before a delegate starts off a delegated task. However, a top-down model of delegation cannot meet all the requirements of dynamic execution of distributed applications, as in such environments. required access rights for completing a task cannot easily be anticipated in advance. Delegating fewer rights than required for completing a task may cause the task execution to fail while delegating more rights than needed may threaten abuse by malicious parties. It is therefore reasonable and more robust to utilize a mechanism that allows determining and acquiring only required rights and credentials for completing a task, when they are needed. This is what we call an on-demand delegation framework, which realizes a bottom-up delegation model and provides a just-in-time acquisition of rights for a restricted and dynamic delegation. In this paper we elaborate the concept of bottom-up delegation and describe how an on-demand delegation framework can leverage workflows to meet the requirements of the least privileges principle. We also discuss the vital need for dynamic and adaptive scientific workflows to support an on-demand delegation framework. We present three different models or bottom-up delegation, which cover a wide range or usage scenarios in Grids and dynamic collaborative environments. Using a standard RBAC authorization model and a graph-based workflow model (DAG), we define and analyze a formal model of our proposed bottom-up delegation approach.

  • 6.
    Ahsant, Mehran
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Basney, Jim
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Dynamic, Context-Aware, Least-Privilege Grid Delegation2007In: 8th IEEE/ACM International Conference on Grid Computing, New York: IEEE , 2007, p. 209-216Conference paper (Refereed)
    Abstract [en]

    Performing delegation in large scale, dynamic and distributed environments with large numbers of shared resources is more challenging than inside local administrative domains. In dynamic environments like Grids, on one hand, delegating a restricted set of rights reduces exposure to attack but also limits the flexibility and dynamism of the application; on the other hand, delegating all rights provides maximum flexibility but increases exposure. This issue has not yet been adequately addressed by current Grid security mechanisms and is becoming a very challenging and crucial issue for future Grid development. Therefore, providing an effective delegation mechanism which meets the requirements of the least privilege principle is becoming an essential need. Furthermore, we are witnessing a phenomenal increase in the automation of organizational tasks and decision making, as well as the computerization of information related services, requiring automated delegation mechanisms. In order to meet these requirements we introduce an Active Delegation Framework which extends our previous work on on-demand delegation, making it context-aware. The framework provides a just-in-time, restricted and dynamic delegation mechanism for Grids. In this paper we describe the development of this framework and its implementation and integration with the Globus Toolkit.

  • 7.
    Ahsant, Mehran
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Mulmo, Olle
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Basney, Jim
    Lee, Adam J.
    Toward An On-demand Restricted Delegation Mechanism for Grids2006In: 2006 7TH IEEE/ACM INTERNATIONAL CONFERENCE ON GRID COMPUTING, New York: IEEE , 2006, p. 152-159Conference paper (Refereed)
    Abstract [en]

    Grids are intended to enable cross-organizationalinteractions which makes Grid security a challenging and nontrivialissue. In Grids, delegation is a key facility that canbe used to authenticate and authorize requests on behalf ofdisconnected users. In current Grid systems there is a tradeoffbetween flexibility and security in the context of delegation.Applications must choose between limited or full delegation: onone hand, delegating a restricted set of rights reduces exposure toattack but also limits the flexibility/dynamism of the application;on the other hand, delegating all rights provides maximumflexibility but increases exposure. In this paper, we propose anon-demand restricted delegation mechanism, aimed at addressingthe shortcomings of current delegation mechanisms by providingrestricted delegation in a flexible fashion as needed for Grid applications.This mechanism provides an ontology-based solutionfor tackling one the most challenging issues in security systems,which is the principle of least privileges. It utilizes a callbackmechanism, which allows on-demand provisioning of delegatedcredentials in addition to observing, screening, and auditingdelegated rights at runtime. This mechanism provides supportfor generating delegation credentials with a very limited andwell-defined range of capabilities or policies, where a delegatoris able to grant a delegatee a set of restricted and limited rights,implicitly or explicitly.

  • 8.
    Ahsant, Mehran
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Mulmo, Olle
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Nefedova, V.
    Ananthakrishnan, R.
    Liming, L.
    Madduri, R.
    Pearlman, L.
    Siebenlist, F.
    Streamlining Grid Operations: Definition and Deployment of a Portal-based User Registration Service2006In: Journal of Grid Computing, ISSN 1572-9814, Vol. 4, no 2, p. 135-144Article in journal (Refereed)
    Abstract [en]

    Manual management of public key credentials can be a significant and often off-putting obstacle to Grid use, particularly for casual users. We describe the Portal-based User Registration Service (PURSE), a set of tools for automating user registration, credential creation, and credential management tasks. PURSE provides the system developer with a set of customizable components, suitable for integration with portals, that can be used to address the full lifecycle of Grid credential management. We describe the PURSE design and its use in portals for two systems, the Earth System Grid data access system and the Swegrid computational Grid. In both cases, the user is entirely freed from the need to create or manage public key credentials, thus simplifying the Grid experience and reducing opportunities for error. We argue that this capturing of common use cases in a reusable ‘solution’ can be a model for how Grid ease-of-use can be addressed in other domains as well.

  • 9.
    Ahsant, Mehran
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Surridge, Mike
    Leonard, Thomas
    Krishna, Ananth
    Mulmo, Olle
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Dynamic Trust Federation in Grids2006In: Trust Management, Proceedings / [ed] Stolen, K; Winsborough, WH; Martinelli, F; Massacci, F, 2006, Vol. 3986, p. 3-18Conference paper (Refereed)
    Abstract [en]

    Grids are becoming economically viable and productive tools. They provide a way of utilizing a vast array of linked resources such as computing systems, databases and services online within Virtual Organizations (VO). However, today's Grid architectures are not capable of supporting dynamic, agile federation across multiple administrative domains and the main barrier, which hinders dynamic federation over short time scales is security. Federating security and trust is one of the most significant architectural issues in Grids. Existing relevant standards and specifications can be used to federate security services, but do not directly address the dynamic extension of business trust relationships into the digital domain. In this paper we describe an experiment which highlights those challenging architectural issues and forms the basis of an approach that combines a dynamic trust federation and a dynamic authorization mechanism for addressing dynamic security trust federation in Grids. The experiment made with the prototype described in this paper is used in the NextGRID(1) project to define the requirements of next generation Grid architectures adapted to business application needs.

  • 10.
    Ahsant, Mehran
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Talavera González, Esteban
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Basney, Jim
    Security Credential Mapping in Grids2009In: 2009 INTERNATIONAL CONFERENCE ON AVAILABILITY, RELIABILITY, AND SECURITY (ARES), New York: IEEE , 2009, p. 481-486Conference paper (Refereed)
    Abstract [en]

    Federating security and trust is one of the most significant architectural requirements in grids. In this regard, one challenging issue is the cross-organizational authentication and identification. Organizations participated in Virtual Organizations (VOs) may use different security infrastructures that implement different authentication and identification protocols. Thus, arises an architectural need to provide a mechanism for a lightweight, rapid and interoperable translation of security credentials from an original format to a format understandable by recipients. In this paper, we describe the development and the implementation of an architecture for credential mapping in grids using off-the-shelf technologies and standard specifications. Our open-source implementation of this architecture provides support for an on-the-fly exchange for different types of security credentials used by diverse grid security infrastructures'.

  • 11.
    Alassi, Sepideh
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Kowarschik, M.
    Pohl, T.
    Köstler, H.
    Rude, U.
    Estimating blood flow based on 2D angiographic image sequences2012In: Bildverarbeitung für die Medizin 2012 : Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 18. bis 20. März 2012 in Berlin, Springer-Verlag New York, 2012, p. 380-385Conference paper (Refereed)
    Abstract [en]

    The assessment of hemodynamics based on medical image data represents an attractive means in order to enhance diagnostic imaging capabilities, to evaluate clinical outcomes of therapies focusing on the patient's vascular system, as well as to guide minimally invasive interventional procedures in the catheter lab. We present a first evaluation along with comparisons of algorithmic approaches towards the quantitative determination of blood flow based on 2D angiography image data.

  • 12.
    Alexius, Per
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Elahi, B. Maryam
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Hedman, Fredrik
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Mucci, Phillip
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Netzer, Gilbert
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Shah, Zeeshan Ali
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    A black-box approach to performance analysis of grid middleware2008In: Euro-Par 2007 Workshops: Parallel Processing / [ed] Bouge, L; Forsell, M; Traff, JL; Streit, A; Ziegler, W; Alexander, M; Childs, S, 2008, Vol. 4854, p. 62-71Conference paper (Refereed)
    Abstract [en]

    We propose a black-box approach to performance analysis of grid middleware and present the architecture of a non-invasive platform-independent evaluation tool that quantifies the effects of the overhead imposed by grid middleware on both the throughput of the system and on the turnaround times of grid applications. This approach is a step towards producing a middleware independent, comparable, reproducible and fair performance! analysis of grid middlewares. The result of such performance analysis can be used by system administrators to tune the system configuration and by developers to find the bottlenecks and problems in their design and implementation of the system. It can also be used to devise more optimized usage patterns. As a proof of concept, we describe the implementation details of the evaluation tool for UNICORE 5 and demonstrate the result of initial experiments.

  • 13.
    Andersson, Ulf
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, School of Computer Science and Communication (CSC).
    Qiu, Min
    KTH, School of Information and Communication Technology (ICT), Microelectronics and Information Technology, IMIT.
    Zhang, Ziyang
    KTH, School of Information and Communication Technology (ICT), Microelectronics and Information Technology, IMIT.
    Parallel Power Computation for Photonic Crystal Devices2006In: Methods and Applications of Analysis, ISSN 1073-2772, E-ISSN 1945-0001, Vol. 13, no 2, p. 149-156Article in journal (Refereed)
    Abstract [en]

    Three-dimensional finite-different time-domain (3D FDTD) simulation of photonic crystal devices often demands large amount of computational resources. In many cases it is unlikely to carry out the task on a serial computer. We have therefore parallelized a 3D FDTD code using MPI. Initially we used a one-dimensional topology so that the computational domain was divided into slices perpendicular to the direction of the power flow. Even though the speed-up of this implementation left considerable room for improvement, we were nevertheless able to solve largescale and long-running problems. Two such cases were studied: the power transmission in a two-dimensional photonic crystal waveguide in a multilayered structure, and the power coupling from a wire waveguide to a photonic crystal slab. In the first case, a power dip due to TE/TM modes conversion is observed and in the second case, the structure is optimized to improve the coupling. We have also recently completed a full three-dimensional topology parallelization of the FDTD code.

  • 14.
    Andersson, Ulf
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Wylie, B. J. N.
    Performance engineering of GemsFDTD computational electromagnetics solver2012In: Applied Parallel and Scientific Computing, Springer Berlin/Heidelberg, 2012, Vol. 7133 LNCS, no PART 1, p. 314-324Conference paper (Refereed)
    Abstract [en]

    Since modern high-performance computer systems consist of many hardware components and software layers, they present severe challenges for application developers who are primarily domain scientists and not experts with continually evolving hardware and system software. Effective tools for performance analysis are therefore decisive when developing performant scalable parallel applications. Such tools must be convenient to employ in the application development process and analysis must be both clear to interpret and yet comprehensive in the level of detail provided. We describe how the Scalasca toolset was applied in engineering the GemsFDTD computational electromagnetics solver, and the dramatic performance and scalability gains thereby achieved.

  • 15.
    Apostolov, Rossen
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Axner, Lilit
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Agren, Hans
    Ayugade, Eduard
    Duta, Mihai
    Gelpi, Jose Luis
    Gimenez, Judit
    Goni, Ramon
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Jamitzky, Ferdinand
    Kranzmuller, Dieter
    Labarta, Jesus
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Orozco, Modesto
    Peterson, Magnus
    Satzger, Helmut
    Trefethen, Anne
    Scalable Software Services for Life Science2011In: Proceedings of 9th HealthGrid conference, 2011Conference paper (Refereed)
    Abstract [en]

    Life Science is developing into one of the largest e- Infrastructure users in Europe, in part due to the ever-growing amount of biological data. Modern drug design typically includes both sequence bioinformatics, in silico virtual screening, and free energy calculations, e.g. of drug binding. This development will accelerate tremendously, and puts high demands on simulation software and support services. e-Infrastructure projects such as PRACE/DEISA have made important advances on hardware and scalability, but have largely been focused on theoretical scalability for large systems, while typical life science applications rather concern small-to-medium size molecules. Here, we propose to address this with by implementing new techniques for efficient small-system parallelization combined with throughput and ensemble computing to enable the life science community to exploit the largest next-generation e-Infrastructures. We will also build a new cross-disciplinary Competence Network for all of life science, to position Europe as the world-leading community for development and maintenance of this software e-Infrastructure. Specifically, we will (1) develop new hierarchical parallelization approaches explicitly based on ensemble and high-throughput computing for new multi-core and streaming/GPU architectures, and establish open software standards for data storage and exchange, (2) implement, document, and maintain such techniques in pilot European open-source codes such as the widely used GROMACS & DALTON, a new application for ensemble simulation (DISCRETE), and large-scale bioinformatics protein annotation, (3) create a Competence Centre for scalable life science software to strengthen Europe as a major software provider and to enable the community to exploit e-Infrastructures to their full extent. This Competence Network will provide training and support infrastructure, and establish a long-term framework for maintenance and optimization of life science codes.

  • 16.
    Apostolov, Rossen
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Yonezawa, Yasushige
    Standley, Daron M
    Kikugawa, Gota
    Takano, Yu
    Nakamura, Haruki
    Membrane attachment facilitates ligand access to the active site in monoamine oxidase A2009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 25, p. 5864-5873Article in journal (Refereed)
    Abstract [en]

    Monoamine oxidase membrane enzymes are responsible for the catalytic breakdown of extra- and intracellular neurotransmitters and are targets for the development of central nervous system drugs. We analyzed the dynamics of rat MAOA by performing multiple independent molecular dynamics simulations of membrane-bound and membrane-free forms to clarify the relationship between the mechanics of the enzyme and its function, with particular emphasis on the significance of membrane attachment. Principal component analysis of the simulation trajectories as well as correlations in the fluctuations of the residues pointed to the existence of three domains that define the global dynamics of the protein. Interdomain anticorrelated movements in the membrane-bound system facilitated the relaxation of interactions between residues surrounding the substrate cavity and induced conformational changes which expanded the active site cavity and opened putative pathways for substrate uptake and product release. Such events were less pronounced in the membrane-free system due to differences in the nature of the dominant modes of motion. The presence of the lipid environment is suggested to assist in decoupling the interdomain motions, consistent with the observed reduction in enzyme activity under membrane-free conditions. Our results are also in accordance with mutational analysis which shows that modifications of interdomain hinge residues decrease the activity of rat MAOA in solution.

  • 17. Appleton, O
    et al.
    Jones, B
    Kranzlmüller, D
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    The EGEE-II Project: Evolution Towards a Permanent European Grid Initiative2008In: Advances in Parallel Computing: High Performance Computing and Grids in Action / [ed] Lucio Grandinetti, IOS Press, 2008, 16, p. 424-435Chapter in book (Refereed)
    Abstract [en]

    Enabling Grids for E-sciencE represents the worlds' largest multidisciplinary grid infrastructure today. Co-funded by the European Commission, it brings together more than 90 partners in 32 countries to produce a reliable and scalable computing resource available to the European and global research community. At present, it consists of more than 200 sites in over 40 countries and makes more than 35,000 CPUs available to users 24 hours a day, 7 days a week. This article provides an overview of EGEE, its infrastructure, middleware, applications and support structures. From this experience, the current state of future plans will be explained, which is summarized under the term European Grid Initiative (EGI), and represents an emerging federated model for sustainable future grid infrastructures.

  • 18.
    Ardestani, Shahrzad
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Håkansson, Carl Johan
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Livenson, I.
    Stranak, P.
    Dima, E.
    Blommesteijn, D.
    Van De Sanden, M.
    B2SHARE: An open eScience data sharing platform2015In: Proceedings - 11th IEEE International Conference on eScience, IEEE , 2015, p. 448-453Conference paper (Refereed)
    Abstract [en]

    Scientific data sharing is becoming an essential service for data driven science and can significantly improve the scientific process by making reliable, and trustworthy data available. Thereby reducing redundant work, and providing insights on related research and recent advancements. For data sharing services to be useful in the scientific process, they need to fulfill a number of requirements that cover not only discovery, and access to data. But to ensure the integrity, and reliability of published data as well. B2SHARE, developed by the EUDAT project, provides such a data sharing service to scientific communities. For communities that wish to download, install and maintain their own service, it is also available as software. B2SHARE is developed with a focus on user-friendliness, reliability, and trustworthiness, and can be customized for different organizations and use-cases. In this paper we discuss the design, architecture, and implementation of B2SHARE. We show its usefulness in the scientific process with some case studies in the biodiversity field.

  • 19. Austad, H.
    et al.
    Zangerl, Thomas
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Confusa: A cross federated personal certificate portal2010In: TERENA Networking Conference 2010: A cross federated personal certificate portal, 2010Conference paper (Refereed)
    Abstract [en]

    We are steadily progressing towards a world where a digital identity is required to gain entrance to a wide variety of services. From access to supercomputers and computational grids to web-services or asserting the authorship of an email, the need for secure digital identities is only growing. The process for obtaining these digital tokens must be simple yet secure for all parties involved, and it must extend to virtually all types of applications. One well tested technology, X.509 certificates, can work with most of these platforms, and the existing Identity Federations can be used to initially assert a user's identity. By using these two together, we have been built a service where a user can use the local authentication credentials combination to gain world-wide recognized X.509 credentials in a matter of minutes.

  • 20. Austin, S
    et al.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Lefer, B
    Morris, G
    Morris, P.A.
    Walter, D.K.
    Atmospheric Balloon Studies: A Collaboration Between Minority and Traditional Undergraduate and Graduate Institutions2008Conference paper (Refereed)
    Abstract [en]

    The Minority University Consortium for Earth and Space Sciences (MUCESS), a collaboration among diverse minority institutions dedicated to increasing the number of underrepresented students pursuing professional and research careers in Earth and Atmospheric Science and Space Science, were informed that they had been funded by NSF for a faculty and student research opportunity in atmospheric science. Among the institutions only Medgar Evers College, City University of New York had a prior program in ozone monitoring and a bachelor's degree in environmental science. The funding provided an opportunity to strengthen the initial team with the addition of G. Morris, Valparaiso University and B. Lefer, University of Houston as both had an ongoing ozone research program. The grant enabled MEC to continue their activities and the University of Houston-Downtown to increase the number of launches per year. South Carolina State University is able to strengthen their support system and incorporate the activities into both their academic and outreach programs. The opportunity to partner with G. Morris and B. Lefer will enable the institutions to expand their ozonesonde launches to include both tropospheric and stratospheric ozone distribution and transport. Faculty student workshops will be an integral part of the program as the activity will increase the scientific knowledge of the participants.

    The program provides an opportunity for minority students to pursue studies in the geosciences and develop the skills and knowledge to pursue graduate degrees in the discipline.

  • 21.
    Axner, Lilit
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Bernsdorf, Joerg M.
    Zeiser, Thomas
    Lammers, Peter
    Linxweiler, Jan
    Hoekstra, Alfonsb G.
    Performance evaluation of a Parallel Sparse Lattice Boltzmann Solver2008In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 227, no 10, p. 4895-4911Article in journal (Refereed)
    Abstract [en]

    We develop a performance prediction model for a parallelized sparse lattice Boltzmann solver and present performance results for simulations of flow in a variety of complex geometries. A special focus is on partitioning and memory/load balancing strategy for geometries with a high solid fraction and/or complex topology such as porous media, fissured rocks and geometries from medical applications. The topology of the lattice nodes representing the fluid fraction of the computational domain is mapped on a graph. Graph decomposition is performed with both multilevel recursive-bisection and multilevel k-way schemes based on modified Kernighan–Lin and Fiduccia–Mattheyses partitioning algorithms. Performance results and optimization strategies are presented for a variety of platforms, showing a parallel efficiency of almost 80% for the largest problem size. A good agreement between the performance model and experimental results is demonstrated.

  • 22.
    Axner, Lilit
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Jeays, Adam
    Hoekstra, Alfons G
    Lawford, Pat
    Hose, Rod
    Sloot, Peter M.A
    Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods2009In: Biomedical engineering online, ISSN 1475-925X, E-ISSN 1475-925X, Vol. 8, no 23, p. 28-Article in journal (Refereed)
    Abstract [en]

    Background: Systolic blood flow has been simulated in the abdominal aorta and the superior mesenteric artery. The simulations were carried out using two different computational hemodynamic methods: the finite element method to solve the Navier Stokes equations and the lattice Boltzmann method. Results: We have validated the lattice Boltzmann method for systolic flows by comparing the velocity and pressure profiles of simulated blood flow between methods. We have also analyzed flow-specific characteristics such as the formation of a vortex at curvatures and traces of flow. Conclusion: The lattice Boltzmann Method is as accurate as a Navier Stokes solver for computing complex blood flows. As such it is a good alternative for computational hemodynamics, certainly in situation where coupling to other models is required.

  • 23. Babar, M. A.
    et al.
    Mohagheghi, P.
    Edlund, Åke
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Mosser, S.
    Mikkonen, T.
    Küngas, P.
    Nordic Symposium on cloud computing and internet technologies (NordiCloud)2012In: WICSA/ECSA '12 Proceedings of the WICSA/ECSA 2012 Companion Volume, ACM , 2012, p. 1-4Conference paper (Refereed)
    Abstract [en]

    This is an introduction to the NordiCloud Symposium collocated with WICSA/ECSA 2012.

  • 24. Baillie, Clive
    et al.
    Brickner, Ralph
    Gupta, Rajan
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    QCD with Dynamical Fermions on the Connection Machine1989Conference paper (Refereed)
    Abstract [en]

    We have implemented Quantum Chromo-Dynamics (QCD) on the massively parallel Connection Machine in *Lisp. The code uses dynamical Wilson fermions and the Hybrid Monte Carlo Algorithm (HMCA) to update the lattice. We describe our program and give performance measurements for it. With no tuning or optimization, the code runs at approximately 500 to 1000 MFLOPS on a 64-K Connection Machine, model CM-2, depending on the VP ratio.

  • 25. Berman, F.
    et al.
    Casanova, H.
    Chien, A.
    Cooper, K.
    Dail, H.
    Dasgupta, A.
    Deng, W.
    Dongarra, J.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Kennedy, K.
    Koelbel, C.
    Liu, B.
    Liu, X.
    Mandal, A.
    Marin, G.
    Mazina, M.
    Mellor-Crummey, J.
    Mendes, C.
    Olugbile, A.
    Patel, M.
    Reed, D.
    Shi, Z.
    Sievert, O.
    Xia, H.
    YarKhan, A.
    New grid scheduling and rescheduling methods in the GrADS Project2005In: International journal of parallel programming, ISSN 0885-7458, E-ISSN 1573-7640, Vol. 33, no 3-Feb, p. 209-229Article in journal (Refereed)
    Abstract [en]

    The goal of the Grid Application Development Software (GrADS) Project is to provide programming tools and an execution environment to ease program development for the Grid. This paper presents recent extensions to the GrADS software framework: a new approach to scheduling workflow computations, applied to a 3-D image reconstruction application; a simple stop/migrate/restart approach to rescheduling Grid applications, applied to a QR factorization benchmark; and a process-swapping approach to rescheduling, applied to an N-body simulation. Experiments validating these methods were carried out on both the GrADS MacroGrid (a small but functional Grid) and the MicroGrid (a controlled emulation of the Grid).

  • 26. Bessani, A.
    et al.
    Brandt, J.
    Bux, M.
    Cogo, V.
    Dimitrova, L.
    Dowling, Jim
    KTH, School of Information and Communication Technology (ICT), Software and Computer systems, SCS.
    Gholami, Ali
    KTH.
    Hakimzadeh, Kamal
    KTH, School of Information and Communication Technology (ICT), Software and Computer systems, SCS.
    Hummel, M.
    Ismail, Mahmoud
    KTH, School of Information and Communication Technology (ICT), Software and Computer systems, SCS.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Leser, U.
    Litton, J. -E
    Martinez, R.
    Niazi, Salman
    KTH, School of Information and Communication Technology (ICT), Software and Computer systems, SCS.
    Reichel, J.
    Zimmermann, K.
    BiobankCloud: A platform for the secure storage, sharing, and processing of large biomedical data sets2016In: 1st International Workshop on Data Management and Analytics for Medicine and Healthcare, DMAH 2015 and Workshop on Big-Graphs Online Querying, Big-O(Q) 2015 held in conjunction with 41st International Conference on Very Large Data Bases, VLDB 2015, Springer, 2016, p. 89-105Conference paper (Refereed)
    Abstract [en]

    Biobanks store and catalog human biological material that is increasingly being digitized using next-generation sequencing (NGS). There is, however, a computational bottleneck, as existing software systems are not scalable and secure enough to store and process the incoming wave of genomic data from NGS machines. In the BiobankCloud project, we are building a Hadoop-based platform for the secure storage, sharing, and parallel processing of genomic data. We extended Hadoop to include support for multi-tenant studies, reduced storage requirements with erasure coding, and added support for extensible and consistent metadata. On top of Hadoop, we built a scalable scientific workflow engine featuring a proper workflow definition language focusing on simple integration and chaining of existing tools, adaptive scheduling on Apache Yarn, and support for iterative dataflows. Our platform also supports the secure sharing of data across different, distributed Hadoop clusters. The software is easily installed and comes with a user-friendly web interface for running, managing, and accessing data sets behind a secure 2-factor authentication. Initial tests have shown that the engine scales well to dozens of nodes. The entire system is open-source and includes pre-defined workflows for popular tasks in biomedical data analysis, such as variant identification, differential transcriptome analysis using RNA-Seq, and analysis of miRNA-Seq and ChIP-Seq data.

  • 27. Bongo, Lars Ailo
    et al.
    Ciegis, Raimondas
    Frasheri, Neki
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Kimovski, Dragi
    Kropf, Peter
    Margenov, Svetozar
    Mihajlovic, Milan
    Neytcheva, Maya
    Rauber, Thomas
    Rünger, Gudula
    Trobec, Roman
    Wuyts, Roel
    Wyrzykowski, Roman
    Applications for Ultrascale Computing2015In: Supercomputing Frontiers and Innovations, ISSN 2409-6008, Vol. 2, no 1, p. 19-48Article in journal (Refereed)
    Abstract [en]

    Studies of complex physical and engineering systems, represented by multi-scale and multi-physics computer simulations have an increasing demand for computing power, especially when the simulations of realistic problems are considered. This demand is driven by the increasing size and complexity of the studied systems or the time constraints. Ultrascale computing systems offer a possible solution to this problem. Future ultrascale systems will be large-scale complex computing systems combining technologies from high performance computing, distributed systems, big data, and cloud computing. Thus, the challenge of developing and programming complex algorithms on these systems is twofold. Firstly, the complex algorithms have to be either developed from scratch, or redesigned in order to yield high performance, while retaining correct functional behaviour. Secondly, ultrascale computing systems impose a number of non-functional cross-cutting concerns, such as fault tolerance or energy consumption, which can significantly impact the deployment of applications on large complex systems. This article discusses the state-of-the-art of programming for current and future large scale systems with an emphasis on complex applications. We derive a number of programming and execution support requirements by studying several computing applications that the authors are currently developing and discuss their potential and necessary upgrades for ultrascale execution.

  • 28.
    Brandi, Maya
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Brocke, E
    Talukdar, Husain Ahammad
    KTH, School of Computer Science and Communication (CSC).
    Hanke, Michael
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Bhalla, US
    Djurfeldt, Mikael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Hellgren Kotaleski, Jeanette
    INCF.
    Multiscale modeling through MUSIC multi-simulation: Modeling a dendritic spine using MOOSE and NeuroRD2011In: Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics, 2011Conference paper (Refereed)
    Abstract [en]

    The nervous system encompasses structure and phenomena at different spatial and temporal scales from molecule to behavior. In addition, different scales are described by different physical and mathematical formalisms. The dynamics of second messenger pathways can be formulated as stochastic reaction-diffusion systems [1] while the electrical dynamics of the neuronal membrane is often described by compartment models and the Hodgkin-Huxley formalism. In neuroscience, there is an increasing need and interest to study multi-scale phenomena where multiple scales and physical formalisms are covered by a single model. While there exists simulators/frameworks, such as GENESIS and MOOSE [3], which span such scales (kinetikit/HH-models), most software applications are specialized for a given domain. Here, we report about initial steps towards a framework for multi-scale modeling which builds on the concept of multi-simulations [2]. We aim to provide a standard API and communication framework allowing parallel simulators targeted at different scales and/or different physics to communicate on-line in a cluster environment. Specifically, we show prototype work on simulating the effect on receptor induced cascades on membrane excitability. Electrical properties of a compartment model is simulated in MOOSE, while receptor induced cascades are simulated in NeuroRD  [4,7] . In a prototype system, the two simulators are connected using PyMOOSE [5] and JPype [6]. The two models with their different physical properties (membrane currents in MOOSE, molecular biophysics in NeuroRD), are joined into a single model system.  We demonstrate the interaction of the numerical solvers of two simulators (MOOSE, NeuroRD) targeted at different spatiotemporal scales and different physics while solving a multi-scale problem. We analyze some of the problems that may arise in multi-scale multi-simulations and present requirements for a generic API for parallel solvers. This work represents initial steps towards a flexible modular framework for simulation of large-scale multi-scale multi-physics problems in neuroscience. References 1. Blackwell KT: An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines. J Neurosci Meth 2006, 157: 142-153. 2. Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Hellgren Kotaleski J, Ekeberg Ö: Run-Time Interoperability Between Neural Network Simulators Based on the MUSIC Framework. Neurinform 2010, 8: 43-60. 3. Dudani N, Ray S, George S, Bhalla US: Multiscale modeling and interoperability in MOOSE. Neuroscience 2009, 10(Suppl 1): 54. 4. Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blacwell KT: The Role of Type 4 Phosphdiesterases in Generating Microdomains of cAMP: Large Scale Stochastic Simulations.

  • 29.
    Brandi, Maya
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Brocke, Ekaterina
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Talukdar, Husain A.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Hanke, Michael
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA.
    Bhalla, Upinder S.
    National Centre for Biological Sciences, Bangalore, India.
    Hällgren-Kotaleski, Jeanette
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Djurfeldt, Mikael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Connecting MOOSE and NeuroRD through MUSIC: towards a communication framework for multi-scale modeling2011In: Twentieth Annual Computational Neuroscience Meeting: CNS*2011, Springer Science+Business Media B.V., 2011Conference paper (Refereed)
  • 30. Brickner, R.G
    et al.
    Baillie, C.F
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    QCD on the Connection Machine: Beyond-Lisp1991In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 65, p. 39-51Article in journal (Refereed)
    Abstract [en]

     We report on the status of code development for a simulation of quantum chromodynamics (QCD) with dynamical Wilson fermions on the Connection Machine model CM-2. Our original code, written in * Lisp, gave performance in the near-GFLOPS range. We have rewritten the most time-consuming parts of the code in the low-level programming system CMIS, including the matrix multiply and the communication. Current versions of the code run at approximately 3.6 GFLOPS for the fermion matrix inversion, and we expect the next version to reach or exceed 5 GFLOPS.

  • 31.
    Brocke, Ekaterina
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Djurfeldt, Mikael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Efficient spike communication in the MUSIC multi-simulation framework2011In: Twentieth Annual Computational Neuroscience Meeting: CNS*2011, Springer Science+Business Media B.V., 2011Conference paper (Refereed)
  • 32. Brunet, Jean-Philippe
    et al.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    All–to–All Broadcast with Applications on the Connection Machine1992In: International Journal of Supercomputer Applications, Vol. 6, no 3, p. 241-256Article in journal (Refereed)
    Abstract [en]

    An all-to-all broadcast algorithm that exploits concur rent communication on all channels of the Connection Machine system CM-200 binary cube network is de scribed. Issues in integrating a physical all-to-all broad cast between processing nodes into a language envi ronment using a global address space are discussed. Timings for the physical broadcast between nodes and for the virtual broadcast are given. The peak data transfer rate for the physical broadcast on a CM-200 is 5.9 gigabytes/sec, and the peak rate for the virtual broadcast is 31 gigabytes/sec. Array reshaping is an effective performance optimization technique. An ex ample is given where reshaping improved perfor mance by a factor of 7 by reducing the amount of local data motion. We also show how to exploit symmetry for computation of an interaction matrix using the all- to-all broadcast function. Further optimizations are suggested for N-body-type calculations. Using the all- to-all broadcast function, a peak rate of 9.3 GFLOPS/ sec has been achieved for the N-body computations in 32-bit precision on a 2,048 node Connection Machine system CM-200.

  • 33.
    Cameron, David
    et al.
    University of Oslo, Nordic Data Grid Facility, Kastrup, Danmark.
    Gholami, Ali
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Karpenko, Dmytro
    University of Oslo.
    Konstantinov, Aleksandr
    University of Oslo, Vilnius University Institute of Applied Research.
    Adaptive data management in the ARC Grid middleware2011In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 331, no 062006Article in journal (Refereed)
    Abstract [en]

    The Advanced Resource Connector (ARC) Grid middleware was designed almost 10 years ago, and has proven to be an attractive distributed computing solution and successful in adapting to new data management and storage technologies. However, with an ever-increasing user base and scale of resources to manage, along with the introduction of more advanced data transfer protocols, some limitations in the current architecture have become apparent. The simple first-in first-out approach to data transfer leads to bottlenecks in the system, as does the built-in assumption that all data is immediately available from remote data storage. We present an entirely new data management architecture for ARC which aims to alleviate these problems, by introducing a three-layer structure. The top layer accepts incoming requests for data transfer and directs them to the middle layer, which schedules individual transfers and negotiates with various intermediate catalog and storage systems until the physical file is ready to be transferred. The lower layer performs all operations which use large amounts of bandwidth, i.e. the physical data transfer. Using such a layered structure allows more efficient use of the available bandwidth as well as enabling late-binding of jobs to data transfer slots based on a priority system. Here we describe in full detail the design and implementation of the new system.

  • 34. Capuccini, Marco
    et al.
    Ahmed, Laeeq
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schaal, Wesley
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Spjuth, Ola
    Large-scale virtual screening on public cloud resources with Apache Spark2017In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 9, article id 15Article in journal (Refereed)
    Abstract [en]

    Background: Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level. Open source implementations of MapReduce include Apache Hadoop and the more recent Apache Spark. Results: We developed a method to run existing docking-based screening software on distributed cloud resources, utilizing the MapReduce approach. We benchmarked our method, which is implemented in Apache Spark, docking a publicly available target receptor against similar to 2.2 M compounds. The performance experiments show a good parallel efficiency (87%) when running in a public cloud environment. Conclusion: Our method enables parallel Structure-based virtual screening on public cloud resources or commodity computer clusters. The degree of scalability that we achieve allows for trying out our method on relatively small libraries first and then to scale to larger libraries.

  • 35. Cazzola, E.
    et al.
    Curreli, D.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Lapenta, G.
    On the ions acceleration via collisionless magnetic reconnection in laboratory plasmas2016In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 23, no 11, article id 112108Article in journal (Refereed)
    Abstract [en]

    This work presents an analysis of the ion outflow from magnetic reconnection throughout fully kinetic simulations with typical laboratory plasma values. A symmetric initial configuration for the density and magnetic field is considered across the current sheet. After analyzing the behavior of a set of nine simulations with a reduced mass ratio and with a permuted value of three initial electron temperatures and magnetic field intensity, the best ion acceleration scenario is further studied with a realistic mass ratio in terms of the ion dynamics and energy budget. Interestingly, a series of shock wave structures are observed in the outflow, resembling the shock discontinuities found in recent magnetohydrodynamic simulations. An analysis of the ion outflow at several distances from the reconnection point is presented, in light of possible laboratory applications. The analysis suggests that magnetic reconnection could be used as a tool for plasma acceleration, with applications ranging from electric propulsion to production of ion thermal beams. © 2016 Author(s).

  • 36. Cazzola, E.
    et al.
    Innocenti, M. E.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Goldman, M. V.
    Newman, D. L.
    Lapenta, G.
    On the electron dynamics during island coalescence in asymmetric magnetic reconnection2015In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 22, no 9, article id 092901Article in journal (Refereed)
    Abstract [en]

    We present an analysis of the electron dynamics during rapid island merging in asymmetric magnetic reconnection. We consider a doubly periodic system with two asymmetric transitions. The upper layer is an asymmetric Harris sheet of finite width perturbed initially to promote a single reconnection site. The lower layer is a tangential discontinuity that promotes the formation of many X-points, separated by rapidly merging islands. Across both layers, the magnetic field and the density have a strong jump, but the pressure is held constant. Our analysis focuses on the consequences of electron energization during island coalescence. We focus first on the parallel and perpendicular components of the electron temperature to establish the presence of possible anisotropies and non-gyrotropies. Thanks to the direct comparison between the two different layers simulated, we can distinguish three main types of behavior characteristic of three different regions of interest. The first type represents the regions where traditional asymmetric reconnections take place without involving island merging. The second type of regions instead shows reconnection events between two merging islands. Finally, the third regions identify the regions between two diverging island and where typical signature of reconnection is not observed. Electrons in these latter regions additionally show a flat-top distribution resulting from the saturation of a two-stream instability generated by the two interacting electron beams from the two nearest reconnection points. Finally, the analysis of agyrotropy shows the presence of a distinct double structure laying all over the lower side facing the higher magnetic field region. This structure becomes quadrupolar in the proximity of the regions of the third type. The distinguishing features found for the three types of regions investigated provide clear indicators to the recently launched Magnetospheric Multiscale NASA mission for investigating magnetopause reconnection involving multiple islands.

  • 37.
    Chen, Yawen
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Shen, Hong
    Zhang, Haibo
    KTH, School of Electrical Engineering (EES), Automatic Control.
    A Novel P-shape Tessellation Approach on Double-Loop Networks2009In: 2009 IEEE INTERNATIONAL SYMPOSIUM ON IT IN MEDICINE & EDUCATION, VOLS 1 AND 2, PROCEEDINGS, NEW YORK: IEEE , 2009, p. 507-511Conference paper (Refereed)
    Abstract [en]

    Double loop computer networks are widely used in the design and implementation of local area networks and parallel processing architectures. However the embedding problems on double-loop networks have not been well studied due to the complexity of double-loop networks. Since the traditional L-shape, designed to compute the diameter of double-loop networks, is not efficient to solve embedding problems, we propose a novel tessellation approach to partition the geometric plane of double-loop networks into a set of parallelogram shaped tiles, called P-shape. Our proposed tessellation technique, P-shape, is a useful theoretical tool for embedding meshes on double-loop networks, and can be extended to analyze other problems as a bridge between regular graphs and double-loop networks.

  • 38. Chiang, Chao-Lin
    et al.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Residue Arithmetic and VLSI1983Conference paper (Refereed)
    Abstract [en]

    In the residue number system arithmetic is carried out on each digit individually. There is no carry chain. This locality is of particular interest in VLSI. An evaluation of different implementations of residue arithmetic is carried out, and the effects of reduced feature sizes estimated. At the current state of technology the traditional table lookup method is preferable for a range that requires a maximum modulus that is represented by up to 4 bits, while an array of adders offers the best performance fur 7 or more bits. A combination of adders and tables covers 5 and 6 bits the best. At 0.5 mu m feature size table lookup is competitive only up to 3 bits, These conclusions are based on sample designs in nMOS.

  • 39. Cohen, D
    et al.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Mathematical Approach to Computational Networks1983Conference paper (Refereed)
    Abstract [en]

    This report deals with design principles for iterative computational networks. Such computational networks are used for performing repetitive computations which typically are not data-dependent. Most of the signal processing algorithms, like FFT and filtering, belong to this class. The main idea in this report is the development of mathematical notation for expressing such designs. This notation captures the important features and properties of these computational networks, and can be used for analyzing, designing, and objectively evaluating computational networks.

  • 40. Cohen, Danny
    et al.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    An Algebraic Description of Array Implementations of FFT Algorithms1982Conference paper (Refereed)
  • 41. Crook, S. M.
    et al.
    Bednar, J. A.
    Berger, S.
    Cannon, R.
    Davison, A. P.
    Djurfeldt, Mikael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Eppler, J.
    Kriener, B.
    Furber, S.
    Graham, B.
    Plesser, H. E.
    Schwabe, L.
    Smith, L.
    Steuber, V.
    Van Albada, S.
    Creating, documenting and sharing network models2012In: Network, ISSN 0954-898X, E-ISSN 1361-6536, Vol. 23, no 4, p. 131-149Article, review/survey (Refereed)
    Abstract [en]

    As computational neuroscience matures, many simulation environments are available that are useful for neuronal network modeling. However, methods for successfully documenting models for publication and for exchanging models and model components among these projects are still under development. Here we briefly review existing software and applications for network model creation, documentation and exchange. Then we discuss a few of the larger issues facing the field of computational neuroscience regarding network modeling and suggest solutions to some of these problems, concentrating in particular on standardized network model terminology, notation, and descriptions and explicit documentation of model scaling. We hope this will enable and encourage computational neuroscientists to share their models more systematically in the future.

  • 42. Demchenko, Y.
    et al.
    Gommans, L.
    De Laat, C.
    Taal, A.
    Wan, A.
    Mulmo, Olle
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Using workflow for dynamic security context management in Grid-based applications2006In: Proc. IEEE ACM Int. Workshop Grid Comput., 2006, p. 72-79Conference paper (Refereed)
    Abstract [en]

    This paper presents ongoing research and current results on the development of flexible access control infrastructures for complex resource provisioning in Grid-based collaborative applications and on-demand network services provisioning. We investigate the use of workflow concepts for the required orchestration of multiple Grid resources and/or services across multiple administrative and security domains. In particular, workflow execution and management tools can be used to track security context changes that are dependent on the application domain, execution stage defined policies, or user and/or service attributes. The paper discusses what specific functionality should be added to Grid-oriented authorization frameworks to handle such dynamic service-related security contexts. As an example, the paper explains how such functionality can be achieved in the GAAA Authorization framework and GAAA toolkit. Suggestions are given about integration with the Globus Toolkit's Authorization Framework. Additionally, the paper analyses what possibilities of expressing and handling dynamic security contexts are available in XACML and SAML, and how the VO concept can be used for managing dynamic security associations of users and resources. The paper is based on experiences gained from major Grid based and Grid oriented projects such as EGEE, NextGrid, Collaboratory.nl and GigaPort Research on Network.

  • 43. Demchenko, Yuri
    et al.
    Mulmo, Olle
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Gornmans, Leon
    de Laat, Cees
    Wan, Alfred
    Dynamic security context management in Grid-based applications2008In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 24, no 5, p. 434-441Article in journal (Refereed)
    Abstract [en]

    This paper summarises ongoing research and recent results on the development of flexible access control infrastructure for complex resource provisioning in Grid-based collaborative applications and on-demand network services provisioning. The paper analyses the general access control model for Grid-based applications and discusses what mechanisms can be used for expressing and handling dynamic domain or process/workflowrelated security context. Suggestions are given on what specific functionality should be added to the Grid-oriented authorization frameworks to handle such dynamic security context. As an example, the paper explains how such functionality can be achieved in the GAAA Authorization framework (GAAA-AuthZ) and GAAA toolkit. Additionally, the paper describes AuthZ ticket format for extended AuthZ session management. The paper is based on experiences gained from major Grid-based and Grid-oriented projects such as EGEE, Phosphorus, NextGRID, and GigaPort Research on Network.

  • 44. Di Remigio, Roberto
    et al.
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. Université de Toulouse III (Paul Sabatier), France.
    Frediani, Luca
    Saue, Trond
    Four-Component Relativistic Calculations in Solution with the Polarizable Continuum Model of Solvation: Theory, Implementation, and Application to the Group 16 Dihydrides H2X (X = O, S, Se, Te, Po)2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5061-5077Article in journal (Refereed)
    Abstract [en]

    We present a formulation of four-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a four-component PCM-SCF state is also derived, as well as the explicit form of the additional contributions to the first-order response equations. The implementation of such a four-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach, we present and analyze calculations of solvation effects on the geometries, electric dipole moments, and static electric dipole polarizabilities for the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

  • 45. Divin, A.
    et al.
    Lapenta, G.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Newman, D. L.
    Goldman, M. V.
    Numerical simulations of separatrix instabilities in collisionless magnetic reconnection2012In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 19, no 4, p. 042110-Article in journal (Refereed)
    Abstract [en]

    Electron scale dynamics of magnetic reconnection separatrix jets is studied in this paper. Instabilities developing in directions both parallel and perpendicular to the magnetic field are investigated. Implicit particle-in-cell simulations with realistic electron-to-ion mass ratio are complemented by a set of small scale high resolution runs having the separatrix force balance as the initial condition. A special numerical procedure is developed to introduce the force balance into the small scale runs. Simulations show the development of streaming instabilities and consequent formation of electron holes in the parallel direction. A new electron jet instability develops in the perpendicular direction. The instability is closely related to the electron MHD Kelvin-Helmholtz mode and is destabilized by a flow, perpendicular to magnetic field at the separatrix. Tearing instability of the separatrix electron jet is modulated strongly by the electron MHD Kelvin-Helmholtz mode.

  • 46. Divin, A.
    et al.
    Lapenta, Giovanni
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Semenov, V. S.
    Erkaev, N. V.
    Korovinskiy, D. B.
    Biernat, H. K.
    Scaling of the inner electron diffusion region in collisionless magnetic reconnection2012In: Journal of Geophysical Research, ISSN 0148-0227, E-ISSN 2156-2202, Vol. 117, p. A06217-Article in journal (Refereed)
    Abstract [en]

    The Sweet-Parker analysis of the inner electron diffusion region of collisionless magnetic reconnection is presented. The study includes charged particles motion near the X-line and an appropriate approximation of the off-diagonal term for the electron pressure tensor. The obtained scaling shows that the width of the inner electron diffusion region is equal to the electron inertial length, and that electrons are accelerated up to the electron Alfven velocity in X-line direction. The estimated effective plasma conductivity is based on the electron gyrofrequency rather than the binary collision frequency, and gives the extreme (minimal) value of the plasma conductivity similar to Bohm diffusion. The scaling properties are verified by means of Particle-in-Cell simulations. An ad hoc parameter needs to be introduced to the scaling relations in order to better match the theory and simulations.

  • 47. Divin, A.
    et al.
    Semenov, V.
    Korovinskiy, D.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Deca, J.
    Olshevsky, V.
    Lapenta, G.
    A new model for the electron pressure nongyrotropy in the outer electron diffusion region2016In: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 43, no 20, p. 10565-10573Article in journal (Refereed)
    Abstract [en]

    We present a new model to describe the electron pressure nongyrotropy inside the electron diffusion region (EDR) in an antiparallel magnetic reconnection scenario. A combination of particle-in-cell simulations and analytical estimates is used to identify such a component of the electron pressure tensor in the rotated coordinates, which is nearly invariant along the outflow direction between the X line and the electron remagnetization points in the outer EDR. It is shown that the EDR two-scale structure (inner and outer parts) is formed due to superposition of the nongyrotropic meandering electron population and gyrotropic electron population with large anisotropy parallel to the magnetic field upstream of the EDR. Inside the inner EDR the influence of the pressure anisotropy can largely be ignored. In the outer EDR, a thin electron layer with electron flow speed exceeding the E x B drift velocity is supported by large-momentum flux produced by the electron pressure anisotropy upstream of the EDR. We find that this fast electron exhaust flow with |V(e)xB|>|E| is in fact a constituent part of the EDR, a finding which will steer the interpretation of the Magnetospheric Multiscale Mission (MMS) data.

  • 48.
    Djurfeldt, Mikael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    The Connection-set Algebra: a formalism for therepresentation of connectivity structure inneuronal network models, implementations in Python and C++, and their use in simulators2011In: Twentieth Annual Computational Neuroscience Meeting:: CNS*2011, 2011Conference paper (Refereed)
  • 49.
    Djurfeldt, Mikael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    The Connection-set Algebra-A Novel Formalism for the Representation of Connectivity Structure in Neuronal Network Models2012In: Neuroinformatics, ISSN 1539-2791, E-ISSN 1559-0089, Vol. 10, no 3, p. 287-304Article in journal (Refereed)
    Abstract [en]

    The connection-set algebra (CSA) is a novel and general formalism for the description of connectivity in neuronal network models, from small-scale to large-scale structure. The algebra provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. CSA is expressive enough to describe a wide range of connection patterns, including multiple types of random and/or geometrically dependent connectivity, and can serve as a concise notation for network structure in scientific writing. CSA implementations allow for scalable and efficient representation of connectivity in parallel neuronal network simulators and could even allow for avoiding explicit representation of connections in computer memory. The expressiveness of CSA makes prototyping of network structure easy. A C+ + version of the algebra has been implemented and used in a large-scale neuronal network simulation (Djurfeldt et al., IBM J Res Dev 52(1/2):31-42, 2008b) and an implementation in Python has been publicly released.

  • 50.
    Djurfeldt, Mikael
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. nternational Neuroinformatics Coordinating Facility, Stockholm, Sweden .
    Davison, Andrew P.
    Eppler, Jochen M.
    Efficient generation of connectivity in neuronal networks from simulator-independent descriptions2014In: Frontiers in Neuroinformatics, ISSN 1662-5196, E-ISSN 1662-5196, Vol. 8, p. 43-Article in journal (Refereed)
    Abstract [en]

    Simulator-independent descriptions of connectivity in neuronal networks promise greater ease of model sharing, improved reproducibility of simulation results, and reduced programming effort for computational neuroscientists. However, until now, enabling the use of such descriptions in a given simulator in a computationally efficient way has entailed considerable work for simulator developers, which must be repeated for each new connectivity-generating library that is developed. We have developed a generic connection generator interface that provides a standard way to connect a connectivity-generating library to a simulator, such that one library can easily be replaced by another, according to the modeler's needs. We have used the connection generator interface to connect C++ and Python implementations of the previously described connection-set algebra to the NEST simulator. We also demonstrate how the simulator-independent modeling framework PyNN can transparently take advantage of this, passing a connection description through to the simulator layer for rapid processing in C++ where a simulator supports the connection generator interface and falling-back to slower iteration in Python otherwise. A set of benchmarks demonstrates the good performance of the interface.

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