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  • 1.
    Aguilar, Xavier
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Towards Scalable Performance Analysis of MPI Parallel Applications2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

      A considerably fraction of science discovery is nowadays relying on computer simulations. High Performance Computing  (HPC) provides scientists with the means to simulate processes ranging from climate modeling to protein folding. However, achieving good application performance and making an optimal use of HPC resources is a heroic task due to the complexity of parallel software. Therefore, performance tools  and runtime systems that help users to execute  applications in the most optimal way are of utmost importance in the landscape of HPC.  In this thesis, we explore different techniques to tackle the challenges of collecting, storing, and using  fine-grained performance data. First, we investigate the automatic use of real-time performance data in order to run applications in an optimal way. To that end, we present a prototype of an adaptive task-based runtime system that uses real-time performance data for task scheduling. This runtime system has a performance monitoring component that provides real-time access to the performance behavior of anapplication while it runs. The implementation of this monitoring component is presented and evaluated within this thesis. Secondly, we explore lossless compression approaches  for MPI monitoring. One of the main problems that  performance tools face is the huge amount of fine-grained data that can be generated from an instrumented application. Collecting fine-grained data from a program is the best method to uncover the root causes of performance bottlenecks, however, it is unfeasible with extremely parallel applications  or applications with long execution times. On the other hand, collecting coarse-grained data is scalable but  sometimes not enough to discern the root cause of a performance problem. Thus, we propose a new method for performance monitoring of MPI programs using event flow graphs. Event flow graphs  provide very low overhead in terms of execution time and  storage size, and can be used to reconstruct fine-grained trace files of application events ordered in time.

  • 2.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fuerlinger, Karl
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Automatic On-Line Detection of MPI Application Structure with Event Flow Graphs2015In: EURO-PAR 2015: PARALLEL PROCESSING, Springer Berlin/Heidelberg, 2015, p. 70-81Conference paper (Refereed)
    Abstract [en]

    The deployment of larger and larger HPC systems challenges the scalability of both applications and analysis tools. Performance analysis toolsets provide users with means to spot bottlenecks in their applications by either collecting aggregated statistics or generating loss-less time-stamped traces. While obtaining detailed trace information is the best method to examine the behavior of an application in detail, it is infeasible at extreme scales due to the huge volume of data generated. In this context, knowing the application structure, and particularly the nesting of loops in iterative applications is of great importance as it allows, among other things, to reduce the amount of data collected by focusing on important sections of the code. In this paper we demonstrate how the loop nesting structure of an MPI application can be extracted on-line from its event flow graph without the need of any explicit source code instrumentation. We show how this knowledge on the application structure can be used to compute postmortem statistics as well as to reduce the amount of redundant data collected. To that end, we present a usage scenario where this structure information is utilized on-line (while the application runs) to intelligently collect fine-grained data for only a few iterations of an application, considerably reducing the amount of data gathered.

  • 3.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fürlinger, Karl
    Ludwig-Maximilians-Universitat (LMU).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    MPI Trace Compression Using Event Flow Graphs2014Conference paper (Refereed)
    Abstract [en]

    Understanding how parallel applications behave is crucial for using high-performance computing (HPC) resources efficiently. However, the task of performance analysis is becoming increasingly difficult due to the growing complexity of scientific codes and the size of machines. Even though many tools have been developed over the past years to help in this task, current approaches either only offer an overview of the application discarding temporal information, or they generate huge trace files that are often difficult to handle.

    In this paper we propose the use of event flow graphs for monitoring MPI applications, a new and different approach that balances the low overhead of profiling tools with the abundance of information available from tracers. Event flow graphs are captured with very low overhead, require orders of magnitude less storage than standard trace files, and can still recover the full sequence of events in the application. We test this new approach with the NERSC-8/Trinity Benchmark suite and achieve compression ratios up to 119x.

  • 4.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fürlinger, Karl
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Visual MPI Performance Analysis using Event Flow Graphs2015In: Procedia Computer Science, ISSN 1877-0509, E-ISSN 1877-0509, Vol. 51, p. 1353-1362Article in journal (Refereed)
    Abstract [en]

    Event flow graphs used in the context of performance monitoring combine the scalability and low overhead of profiling methods with lossless information recording of tracing tools. In other words, they capture statistics on the performance behavior of parallel applications while pre- serving the temporal ordering of events. Event flow graphs require significantly less storage than regular event traces and can still be used to recover the full ordered sequence of events performed by the application.  In this paper we explore the usage of event flow graphs in the context of visual performance analysis. We show that graphs can be used to quickly spot performance problems, helping to better understand the behavior of an application. We demonstrate our performance analysis approach with MiniFE, a mini-application that mimics the key performance aspects of finite- element applications in High Performance Computing (HPC).

  • 5.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fürlinger, Karl
    Ludwig-Maximilians-Universität München.
    Online Performance Data Introspection with IPM2014In: Proceedings of the 15th IEEE International Conference on High Performance Computing and Communications (HPCC 2013), IEEE Computer Society, 2014, p. 728-734Conference paper (Refereed)
    Abstract [en]

    Exascale systems will be heterogeneous architectures with multiple levels of concurrency and energy constraints. In such a complex scenario, performance monitoring and runtime systems play a major role to obtain good application performance and scalability. Furthermore, online access to performance data becomes a necessity to decide how to schedule resources and orchestrate computational elements: processes, threads, tasks, etc. We present the Performance Introspection API, an extension of the IPM tool that provides online runtime access to performance data from an application while it runs. We describe its design and implementation and show its overhead on several test benchmarks. We also present a real test case using the Performance Introspection API in conjunction with processor frequency scaling to reduce power consumption.

  • 6.
    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.

  • 7.
    Ahmed, Laeeq
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Edlund, Åke
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spjuth, O.
    Using iterative MapReduce for parallel virtual screening2013In: 2013 IEEE 5th International Conference on Cloud Computing Technology and Science (CloudCom), IEEE Computer Society, 2013, p. 27-32Conference paper (Refereed)
    Abstract [en]

    Virtual Screening is a technique in chemo informatics used for Drug discovery by searching large libraries of molecule structures. Virtual Screening often uses SVM, a supervised machine learning technique used for regression and classification analysis. Virtual screening using SVM not only involves huge datasets, but it is also compute expensive with a complexity that can grow at least up to O(n2). SVM based applications most commonly use MPI, which becomes complex and impractical with large datasets. As an alternative to MPI, MapReduce, and its different implementations, have been successfully used on commodity clusters for analysis of data for problems with very large datasets. Due to the large libraries of molecule structures in virtual screening, it becomes a good candidate for MapReduce. In this paper we present a MapReduce implementation of SVM based virtual screening, using Spark, an iterative MapReduce programming model. We show that our implementation has a good scaling behaviour and opens up the possibility of using huge public cloud infrastructures efficiently for virtual screening.

  • 8.
    Artman, Henrik
    et al.
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Brynielsson, Joel
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Edlund, Lena
    Fallgren, Per
    Forsberg, Lars
    Ghilagaber, Gebrenegus
    Gustavii, Jonathan
    Herzing, Mathias
    Häckner, Jonas
    Jacobsson, Adam
    Jacobsson, Eva-Maria
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Källmén, Håkan
    Lindquist, Sinna
    Lundström, Anders
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Muren, Astri
    Sjöberg, Eric
    Thuresson, Björn
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Tjörnhammar, Edward
    Wickström, Hans
    Effektiv miljötillsyn: Slutrapport2013Report (Other academic)
    Abstract [sv]

    Målsättningen har varit att ta fram ny kunskap inom miljötillsynen och därigenom uppnå en effektivare miljötillsyn samt att få in nya vetenskapliga perspektiv på miljötillsyn.

    I rapporten studeras metoder för inspektioner och det kommunikativa samspelet mellan inspektören och företrädare för den verksamhet som inspekteras, hur den institutionella ramen för inspektionsprocessen fungerar samt visar på möjligheter att mäta effekterna av inspektioner och tillsyn.

    Naturvårdsverket kommer att ha resultatet som ett kunskapsunderlag i fortsatt arbete med tillsynsvägledning och utveckling av hur tillsyn och tillsynsvägledning kan följas upp och utvärderas.

  • 9. Beck, A.
    et al.
    Innocenti, M. E.
    Lapenta, G.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Multi-level multi-domain algorithm implementation for two-dimensional multiscale particle in cell simulations2014In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 271, p. 430-443Article in journal (Refereed)
    Abstract [en]

    There are a number of modeling challenges posed by space weather simulations. Most of them arise from the multiscale and multiphysics aspects of the problem. The multiple scales dramatically increase the requirements, in terms of computational resources, because of the need of performing large scale simulations with the proper small-scales resolution. Lately, several suggestions have been made to overcome this difficulty by using various refinement methods which consist in splitting the domain into regions of different resolutions separated by well defined interfaces. The multiphysics issues are generally treated in a similar way: interfaces separate the regions where different equations are solved. This paper presents an innovative approach based on the coexistence of several levels of description, which differ by their resolutions or, potentially, by their physics. Instead of interacting through interfaces, these levels are entirely simulated and are interlocked over the complete extension of the overlap area. This scheme has been applied to a parallelized, two-dimensional, Implicit Moment Method Particle in Cell code in order to investigate its multiscale description capabilities. Simulations of magnetic reconnection and plasma expansion in vacuum are presented and possible implementation options for this scheme on very large systems are also discussed.

  • 10.
    Berglund, Daniel
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Gene-EnvironmentInteraction Analysis UsingGraphic Cards2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Genome-wide association studies(GWAS) are used to find associations betweengenetic markers and diseases. One part of GWAS is to study interactions be-tween markers which can play an important role in the risk for the disease. Thesearch for interactions can be computationally intensive. The aim of this thesiswas to improve the performance of software used for gene-environment interac-tion by using parallel programming techniques on graphical processors. A studyof the new programs performance, speedup and efficiency was made using mul-tiple simulated datasets. The program shows significantly better performancecompared with the older program.

  • 11. 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.

  • 12. 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.

  • 13. Castellano, G.
    et al.
    Karpouzis, K.
    Martin, J. -C
    Morency, L. -P
    Peters, Christopher
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Riek, L. D.
    5th international workshop on affective interaction in natural environments (AFFINE): Interacting with affective artefacts in the wild2013In: Proceedings - 2013 Humaine Association Conference on Affective Computing and Intelligent Interaction, ACII 2013, 2013, p. 727-Conference paper (Refereed)
    Abstract [en]

    This workshop covers real-time computational techniques for the recognition and interpretation of human affective and social behaviour, and techniques for synthesis of believable social behaviour supporting real-time adaptive human-agent and human-robot interaction in real-world environments.

  • 14. 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.

  • 15. Corrigan, L. J.
    et al.
    Basedow, C.
    Küster, D.
    Kappas, A.
    Peters, Christopher
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Castellano, G.
    Mixing implicit and explicit probes: Finding a ground truth for engagement in social human-robot interactions2014In: HRI '14 Proceedings of the 2014 ACM/IEEE international conference on Human-robot interaction, IEEE Computer Society, 2014, p. 140-141Conference paper (Refereed)
    Abstract [en]

    In our work we explore the development of a computational model capable of automatically detecting engagement in social human-robot interactions from real-time sensory and contextual input. However, to train the model we need to establish ground truths of engagement from a large corpus of data collected from a study involving task and social-task engagement. Here, we intend to advance the current state-of-the-art by reducing the need for unreliable post-experiment questionnaires and costly time-consuming annotation with the novel introduction of implicit probes. A non-intrusive, pervasive and embedded method of collecting informative data at different stages of an interaction.

  • 16. Corrigan, L. J.
    et al.
    Peters, Christopher
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Castellano, G.
    Identifying task engagement: Towards personalised interactions with educational robots2013In: Proceedings - 2013 Humaine Association Conference on Affective Computing and Intelligent Interaction, ACII 2013, 2013, p. 655-658Conference paper (Refereed)
    Abstract [en]

    The focus of this project is to design, develop and evaluate a new computational model for automatically detecting change in task engagement. This work will be applied to robotic tutors to enhance and support the learning experience, enabling timely pedagogical and empathic intervention. This work is intended to forward the current state of the art by 1) exploring how to automatically detect engagement with a learning task, 2) designing and developing new approaches to machine learning for adaptive platform-independent modelling and 3) evaluation of its effectiveness for building and maintaining learner engagement across different tutor embodiments, for example a physical and virtual embodiment.

  • 17. Corrigan, Lee J.
    et al.
    Basedow, Christina
    Küster, Dennis
    Kappas, Arvid
    Peters, Christopher
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Castellano, Ginevra
    Uppsala University.
    Perception matters! Engagement in task orientated social robotics2015In: Proceedings of the 24th IEEE International Symposium on Robot and Human Interactive Communication, 2015, p. 375-380Conference paper (Refereed)
    Abstract [en]

    Engagement in task orientated social robotics is a complex phenomenon, consisting of both task and social elements. Previous work in this area tends to focus on these aspects in isolation without consideration for the positive or negative effects one might cause the other. We explore both, in an attempt to understand how engagement with the task might effect the social relationship with the robot, and vice versa. In this paper, we describe the analysis of participant self-report data collected during an exploratory pilot study used to evaluate users’ “perception of engagement”. We discuss how the results of our analysis suggest that ultimately, it was the users’ own perception of the robots’ characteristics such as friendliness, helpfulness and attentiveness which led to sustained engagement with both the task and robot

     

  • 18. Daldorff, Lars K. S.
    et al.
    Toth, Gabor
    Gombosi, Tamas I.
    Lapenta, Giovanni
    Amaya, Jorge
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Brackbill, Jeremiah U.
    Two-way coupling of a global Hall magnetohydrodynamics model with a local implicit particle-in-cell model2014In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 268, p. 236-254Article in journal (Refereed)
    Abstract [en]

    Computational models based on a fluid description of the plasma, such as magnetohydrodynamic (MHD) and extended magnetohydrodynamic (XMHD) codes are highly efficient, but they miss the kinetic effects due to the assumptions of small gyro radius, charge neutrality, and Maxwellian thermal velocity distribution. Kinetic codes can properly take into account the kinetic effects, but they are orders of magnitude more expensive than the fluid codes due to the increased degrees of freedom. If the fluid description is acceptable in a large fraction of the computational domain, it makes sense to confine the kinetic model to the regions where kinetic effects are important. This coupled approach can be much more efficient than a pure kinetic model. The speed up is approximately the volume ratio of the full domain relative to the kinetic regions assuming that the kinetic code uses a uniform grid. This idea has been advocated by [1] but their coupling was limited to one dimension and they employed drastically different grid resolutions in the fluid and kinetic models. We describe a fully two-dimensional two-way coupling of a Hall MHD model BATS-R-US with an implicit Particle-in-Cell (PIC) model iPIC3D. The coupling can be performed with identical grid resolutions and time steps. We call this coupled computational plasma model MHD-EPIC (MHD with Embedded PIC regions). Our verification tests show that MHD-EPIC works accurately and robustly. We show a two-dimensional magnetosphere simulation as an illustration of the potential future applications of MHD-EPIC.

  • 19. Deca, J.
    et al.
    Divin, A.
    Lapenta, G.
    Lembège, B.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Horányi, M.
    Electromagnetic Particle-in-Cell Simulations of the Solar Wind Interaction with Lunar Magnetic Anomalies2014In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 112, no 15, p. 151102-Article in journal (Refereed)
    Abstract [en]

    We present the first three-dimensional fully kinetic and electromagnetic simulations of the solar wind interaction with lunar crustal magnetic anomalies (LMAs). Using the implicit particle-in-cell code IPIC3D, we confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface forming a mini-magnetosphere, as suggested by spacecraft observations and theory. In contrast to earlier magnetohydrodynamics and hybrid simulations, the fully kinetic nature of IPIC3D allows us to investigate the space charge effects and in particular the electron dynamics dominating the near-surface lunar plasma environment. We describe for the first time the interaction of a dipole model centered just below the lunar surface under plasma conditions such that only the electron population is magnetized. The fully kinetic treatment identifies electromagnetic modes that alter the magnetic field at scales determined by the electron physics. Driven by strong pressure anisotropies, the mini-magnetosphere is unstable over time, leading to only temporal shielding of the surface underneath. Future human exploration as well as lunar science in general therefore hinges on a better understanding of LMAs.

  • 20. Deca, J.
    et al.
    Lapenta, G.
    Marchand, R.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spacecraft charging analysis with the implicit particle-in-cell code iPic3D2013In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 20, no 10, p. 102902-Article in journal (Refereed)
    Abstract [en]

    We present the first results on the analysis of spacecraft charging with the implicit particle-in-cell code iPic3D, designed for running on massively parallel supercomputers. The numerical algorithm is presented, highlighting the implementation of the electrostatic solver and the immersed boundary algorithm; the latter which creates the possibility to handle complex spacecraft geometries. As a first step in the verification process, a comparison is made between the floating potential obtained with iPic3D and with Orbital Motion Limited theory for a spherical particle in a uniform stationary plasma. Second, the numerical model is verified for a CubeSat benchmark by comparing simulation results with those of PTetra for space environment conditions with increasing levels of complexity. In particular, we consider spacecraft charging from plasma particle collection, photoelectron and secondary electron emission. The influence of a background magnetic field on the floating potential profile near the spacecraft is also considered. Although the numerical approaches in iPic3D and PTetra are rather different, good agreement is found between the two models, raising the level of confidence in both codes to predict and evaluate the complex plasma environment around spacecraft.

  • 21. Deca, Jan
    et al.
    Divin, Andrey
    Lembege, Bertrand
    Horanyi, Mihaly
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, Giovanni
    General mechanism and dynamics of the solar wind interaction with lunar magnetic anomalies from 3-D particle-in-cell simulations2015In: Journal of Geophysical Research - Space Physics, ISSN 2169-9380, E-ISSN 2169-9402, Vol. 120, no 8, p. 6443-6463Article in journal (Refereed)
    Abstract [en]

    We present a general model of the solar wind interaction with a dipolar lunar crustal magnetic anomaly (LMA) using three-dimensional full-kinetic and electromagnetic simulations. We confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface, forming a so-called minimagnetosphere, as suggested by spacecraft observations and theory. We show that the LMA configuration is driven by electron motion because its scale size is small with respect to the gyroradius of the solar wind ions. We identify a population of back-streaming ions, the deflection of magnetized electrons via the E x B drift motion, and the subsequent formation of a halo region of elevated density around the dipole source. Finally, it is shown that the presence and efficiency of the processes are heavily impacted by the upstream plasma conditions and, on their turn, influence the overall structure and evolution of the LMA system. Understanding the detailed physics of the solar wind interaction with LMAs, including magnetic shielding, particle dynamics and surface charging is vital to evaluate its implications for lunar exploration.

  • 22. Deca, Jan
    et al.
    Divin, Andrey
    Wang, Xu
    Lembege, Bertrand
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Horanyi, Mihaly
    Lapenta, Giovanni
    Three-dimensional full-kinetic simulation of the solar wind interaction with a vertical dipolar lunarmagnetic anomaly2016In: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 43, no 9, p. 4136-4144Article in journal (Refereed)
    Abstract [en]

    A detailed understanding of the solar wind interaction with lunar magnetic anomalies (LMAs) is essential to identify its implications for lunar exploration and to enhance our physical understanding of the particle dynamics in a magnetized plasma. We present the first three-dimensional full-kinetic electromagnetic simulation case study of the solar wind interaction with a vertical dipole, resembling a medium-size LMA. In contrast to a horizontal dipole, we show that a vertical dipole twists its field lines and cannot form a minimagnetosphere. Instead, it creates a ring-shaped weathering pattern and reflects up to 21% (four times more as compared to the horizontal case) of the incoming solar wind ions electrostatically through the normal electric field formed above the electron shielding region surrounding the cusp. This work delivers a vital piece to fully comprehend and interpret lunar observations, as we find the amount of reflected ions to be a tracer for the underlying field structure.

  • 23. Divin, A.
    et al.
    Khotyaintsev, Yu. V.
    Vaivads, A.
    Andre, M.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, G.
    Evolution of the lower hybrid drift instability at reconnection jet front2015In: Journal of Geophysical Research - Space Physics, ISSN 2169-9380, E-ISSN 2169-9402, Vol. 120, no 4, p. 2675-2690Article in journal (Refereed)
    Abstract [en]

    We investigate current-driven modes developing at jet fronts during collisionless reconnection. Initial evolution of the reconnection is simulated using conventional 2-D setup starting from the Harris equilibrium. Three-dimensional PIC calculations are implemented at later stages, when fronts are fully formed. Intense currents and enhanced wave activity are generated at the fronts because of the interaction of the fast flow plasma and denser ambient current sheet plasma. The study reveals that the lower hybrid drift instability develops quickly in the 3-D simulation. The instability produces strong localized perpendicular electric fields, which are several times larger than the convective electric field at the front, in agreement with Time History of Events and Macroscale Interactions during Substorms observations. The instability generates waves, which escape the front edge and propagate into the undisturbed plasma ahead of the front. The parallel electron pressure is substantially larger in the 3-D simulation compared to that of the 2-D. In a time similar to Omega(-1)(ci), the instability forms a layer, which contains a mixture of the jet plasma and current sheet plasma. The results confirm that the lower hybrid drift instability is important for the front evolution and electron energization.

  • 24. 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.

  • 25. Eriksson, S.
    et al.
    Lapenta, G.
    Newman, D. L.
    Phan, T. D.
    Gosling, J. T.
    Lavraud, B.
    Khotyaintsev, Y. V.
    Carr, C. M.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Goldman, M. V.
    On Multiple Reconnection X-Lines and Tripolar Perturbations of Strong Guide Magnetic Fields2015In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 805, no 1, article id 43Article in journal (Refereed)
    Abstract [en]

    We report new multi-spacecraft Cluster observations of tripolar guide magnetic field perturbations at a solar wind reconnection exhaust in the presence of a guide field B-M. which is almost four times as strong as the reversing field B-L. The novel tripolar field consists of two narrow regions of depressed B-M, with an observed 7%-14% Delta B-M magnitude relative to the external field, which are found adjacent to a wide region of enhanced BM within the exhaust. A stronger reversing field is associated with each B-M depression. A kinetic reconnection simulation for realistic solar wind conditions and the observed strong guide field reveals that tripolar magnetic fields preferentially form across current sheets in the presence of multiple X-lines as magnetic islands approach one another and merge into fewer and larger islands. The simulated Delta B-M/Delta X-N over the normal width Delta X-N between a B-M minimum and the edge of the external region agree with the normalized values observed by Cluster. We propose that a tripolar guide field perturbation may be used to identify candidate regions containing multiple X-lines and interacting magnetic islands at individual solar wind current sheets with a strong guide field.

  • 26.
    Gholami, Ali
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Lind, Anna-Sara
    Reichel, Jane
    Litton, Jan-Eric
    Edlund, Åke
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Privacy Threat Modeling for Emerging BiobankClouds2014In: Procedia Computer Science: The 5th International Conference on Emerging Ubiquitous Systems and Pervasive Networks (EUSPN-2014)/ The 4th International Conference on Current and Future Trends of Information and Communication Technologies in Healthcare (ICTH 2014)/ Affiliated Workshops, Elsevier, 2014, Vol. 37, p. 489-496Conference paper (Refereed)
    Abstract [en]

    There is an increased amount of data produced by next generation sequencing (NGS) machines which demand scalable storage and analysis of genomic data. In order to cope with this huge amount of information, many biobanks are interested in cloud computing capabilities such as on-demand elasticity of computing power and storage capacity. There are several security and privacy requirements mandated by personal data protection legislation which hinder biobanks from migrating big data generated by the NGS machines. This paper describes the privacy requirements of platform-as-service BiobankClouds according to the European Data Protection Directive (DPD). It identifies several key privacy threats which leave BiobankClouds vulnerable to an attack. This study benefits health-care application designers in the requirement elicitation cycle when building privacy-preserving BiobankCloud platforms.

  • 27.
    Gholami, Ali
    et al.
    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.
    Svensson, Gert
    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.
    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.
    Eickhoff, M.
    Brasche, G.
    ScaBIA: Scalable brain image analysis in the cloud2013In: CLOSER 2013 - Proceedings of the 3rd International Conference on Cloud Computing and Services Science, 2013, p. 329-336Conference paper (Refereed)
    Abstract [en]

    The use of cloud computing as a new paradigm has become a reality. Cloud computing leverages the use of on-demand CPU power and storage resources while eliminating the cost of commodity hardware ownership. Cloud computing is now gaining popularity among many different organizations and commercial sectors. In this paper, we present the scalable brain image analysis (ScaBIA) architecture, a new model to run statistical parametric analysis (SPM) jobs using cloud computing. SPM is one of the most popular toolkits in neuroscience for running compute-intensive brain image analysis tasks. However, issues such as sharing raw data and results, as well as scalability and performance are major bottlenecks in the "single PC"-execution model. In this work, we describe a prototype using the generic worker (GW), an e-Science as a service middleware, on top of Microsoft Azure to run and manage the SPM tasks. The functional prototype shows that ScaBIA provides a scalable framework for multi-job submission and enables users to share data securely using storage access keys across different organizations.

  • 28. Goldman, M. V.
    et al.
    Newman, D. L.
    Lapenta, G.
    Andersson, L.
    Gosling, J. T.
    Eriksson, S.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Eastwood, J. P.
    Ergun, R.
    Cerenkov Emission of Quasiparallel Whistlers by Fast Electron Phase-Space Holes during Magnetic Reconnection2014In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 112, no 14, p. 145002-Article in journal (Refereed)
    Abstract [en]

    Kinetic simulations of magnetotail reconnection have revealed electromagnetic whistlers originating near the exhaust boundary and propagating into the inflow region. The whistler production mechanism is not a linear instability, but rather is Cerenkov emission of almost parallel whistlers from localized moving clumps of charge (finite-size quasiparticles) associated with nonlinear coherent electron phase space holes. Whistlers are strongly excited by holes without ever growing exponentially. In the simulation the whistlers are emitted in the source region from holes that accelerate down the magnetic separatrix towards the x line. The phase velocity of the whistlers upsilon(phi) in the source region is everywhere well matched to the hole velocity upsilon(H) as required by the Cerenkov condition. The simulation shows emission is most efficient near the theoretical maximum upsilon(phi) = half the electron Alfven speed, consistent with the new theoretical prediction that faster holes radiate more efficiently. While transferring energy to whistlers the holes lose coherence and dissipate over a few local ion inertial lengths. The whistlers, however, propagate to the x line and out over many 10's of ion inertial lengths into the inflow region of reconnection. As the whistlers pass near the x line they modulate the rate at which magnetic field lines reconnect.

  • 29.
    Gong, Jing
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Cray Inc..
    Henty, David
    University of Edinburgh.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fischer, Paul
    Argonne National Laboratory.
    Heisey, Katherine
    Argonne National Laboratory.
    OpenACC Acceleration of Nek5000: a Spectral Element Code2013Conference paper (Other academic)
  • 30.
    Gong, Jing
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    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, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Cebamanos, Luis
    Hart, Alistair
    Min, Misun
    Fischer, Paul
    NekBone with Optimizaed OpenACC directives2015Conference paper (Refereed)
    Abstract [en]

    Accelerators and, in particular, Graphics Processing Units (GPUs) have emerged as promising computing technologies which may be suitable for the future Exascale systems. Here, we present performance results of NekBone, a benchmark of the Nek5000 code, implemented with optimized OpenACC directives and GPUDirect communications. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. Results of an optimized NekBone version lead to 78 Gflops performance on a single node. In addition, a performance result of 609 Tflops has been reached on 16, 384 GPUs of the Titan supercomputer at Oak Ridge National Laboratory.

     

  • 31.
    Gong, Jing
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    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, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Peplinski, Adam
    Hart, Alistair
    Doleschal, Jens
    Henty, David
    Fischer, Paul
    Nek5000 with OpenACC2015In: Solving software challenges for exascale, 2015, p. 57-68Conference paper (Refereed)
    Abstract [en]

    Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flows. We follow up on an earlier study which ported the simplified version of Nek5000 to a GPU-accelerated system by presenting the hybrid CPU/GPU implementation of the full Nek5000 code using OpenACC. The matrix-matrix multiplication, the Nek5000 gather-scatter operator and a preconditioned Conjugate Gradient solver have implemented using OpenACC for multi-GPU systems. We report an speed-up of 1.3 on single node of a Cray XK6 when using OpenACC directives in Nek5000. On 512 nodes of the Titan supercomputer, the speed-up can be approached to 1.4. A performance analysis of the Nek5000 code using Score-P and Vampir performance monitoring tools shows that overlapping of GPU kernels with host-accelerator memory transfers would considerably increase the performance of the OpenACC version of Nek5000 code.

  • 32.
    Griggio, Carla F.
    et al.
    KTH. Université Paris -Sud XI Orsay, France; EIT ICT Labs, France.
    Romero, Mario
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Georgia Institute of Technology.
    Canvas Dance: An Interactive Dance Visualization for Large-Group Interaction2015In: Proceedings of the 33rd Annual ACM Conference Extended Abstracts on Human Factors in Computing Systems, ACM Digital Library, 2015, p. 379-382Conference paper (Refereed)
    Abstract [en]

    We present Canvas Dance, a prototype of an interactive dance visualization for large-group interaction that targets non-professional dancers in informal environments such as parties or nightclubs, and uses the smartphones of the dancers as the input device for the motion signal. The visualization is composed of individual representations for each dancer, and the visual mappings designed for their dance moves have three main goals: to help the users identify their own representation, to uncover and inspire imitation among dancers, and to support unpredictable dance moves.

  • 33.
    Griggio, Carla
    et al.
    KTH. EIT ICT Labs Master School, Sweden.
    Romero, Mario
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Leiva, Germán
    KTH. EIT ICT Labs Master School, Sweden.
    Towards an Interactive Dance Visualization for Inspiring Coordination Between Dancers2015Conference paper (Refereed)
    Abstract [en]

    In this work in progress we present early results in the process of understanding how interactive dance visualizations can inspire coordinated dance moves between dancers in informal contexts. Inspired by observations at nightclubs and parties with DJs, we designed an interactive dance visualization prototype called "Canvas Dance" and evaluated it in a user study with 3 small groups of people. We conclude by offering a set of design considerations for future work on interactive dance visualizations for non-professional dancers in informal contexts.

  • 34.
    Hasselqvist, Hanna
    et al.
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Bogdan, Cristian
    KTH, School of Computer Science and Communication (CSC), Media Technology and Interaction Design, MID.
    Romero, Mario
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Shafqat, Omar
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Applied Thermodynamics and Refrigeration.
    Supporting Energy Management as a Cooperative Amateur Activity2015In: Proceedings of the 33rd Annual ACM Conference Extended Abstracts on Human Factors in Computing Systems, ACM Digital Library, 2015, p. 1483-1488Conference paper (Refereed)
    Abstract [en]

    There is increasing concern regarding current energy feedback approaches as they focus on the individual level, and mostly on household electricity, while the bulk of energy use often lies in heating and cooling. The aim is typically to change user routines, which does not bring a long-lasting impact. In our case study, we address these concerns for apartment buildings by looking at housing cooperatives, the dominant form of apartment ownership in the Nordic countries. These cooperatives manage the heating costs in common and therefore have a large potential for energy saving through long-lasting improvements and investments. We also emphasise the amateur nature of energy work within such cooperatives and consider the implications of our field study findings, interpreted through these amateur and cooperative perspectives, for the design of interactive artefacts.

  • 35. Henri, P.
    et al.
    Cerri, S. S.
    Califano, F.
    Pegoraro, F.
    Rossi, C.
    Faganello, M.
    Sebek, O.
    Travnicek, P. M.
    Hellinger, P.
    Frederiksen, J. T.
    Nordlund, A.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Keppens, R.
    Lapenta, G.
    Nonlinear evolution of the magnetized Kelvin-Helmholtz instability: From fluid to kinetic modeling2013In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 20, no 10, p. 102118-Article in journal (Refereed)
    Abstract [en]

    The nonlinear evolution of collisionless plasmas is typically a multi-scale process, where the energy is injected at large, fluid scales and dissipated at small, kinetic scales. Accurately modelling the global evolution requires to take into account the main micro-scale physical processes of interest. This is why comparison of different plasma models is today an imperative task aiming at understanding cross-scale processes in plasmas. We report here the first comparative study of the evolution of a magnetized shear flow, through a variety of different plasma models by using magnetohydrodynamic (MHD), Hall-MHD, two-fluid, hybrid kinetic, and full kinetic codes. Kinetic relaxation effects are discussed to emphasize the need for kinetic equilibriums to study the dynamics of collisionless plasmas in non trivial configurations. Discrepancies between models are studied both in the linear and in the nonlinear regime of the magnetized Kelvin-Helmholtz instability, to highlight the effects of small scale processes on the nonlinear evolution of collisionless plasmas. We illustrate how the evolution of a magnetized shear flow depends on the relative orientation of the fluid vorticity with respect to the magnetic field direction during the linear evolution when kinetic effects are taken into account. Even if we found that small scale processes differ between the different models, we show that the feedback from small, kinetic scales to large, fluid scales is negligible in the nonlinear regime. This study shows that the kinetic modeling validates the use of a fluid approach at large scales, which encourages the development and use of fluid codes to study the nonlinear evolution of magnetized fluid flows, even in the collisionless regime.

  • 36.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    de Abreu, Rodrigo Vilela
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Müller, Kaspar
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Nazarov, Murtazo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spühler, Jeannette Hiromi
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Unicorn: Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry2013In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 80, no SI, p. 310-319Article in journal (Refereed)
    Abstract [en]

    We present a framework for adaptive finite element computation of turbulent flow and fluid structure interaction, with focus on general algorithms that allow for complex geometry and deforming domains. We give basic models and finite element discretization methods, adaptive algorithms and strategies for efficient parallel implementation. To illustrate the capabilities of the computational framework, we show a number of application examples from aerodynamics, aero-acoustics, biomedicine and geophysics. The computational tools are free to download open source as Unicorn, and as a high performance branch of the finite element problem solving environment DOLFIN, both part of the FEniCS project.

  • 37.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    FEniCS-HPC: Automated predictive high-performance finite element computing with applications in aerodynamics2016In: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015, Springer-Verlag New York, 2016, Vol. 9573, p. 356-365Conference paper (Refereed)
    Abstract [en]

    Developing multiphysics nite element methods (FEM) andscalable HPC implementations can be very challenging in terms of soft-ware complexity and performance, even more so with the addition ofgoal-oriented adaptive mesh renement. To manage the complexity we inthis work presentgeneraladaptive stabilized methods withautomatedimplementation in the FEniCS-HPCautomatedopen source softwareframework. This allows taking the weak form of a partial dierentialequation (PDE) as input in near-mathematical notation and automati-cally generating the low-level implementation source code and auxiliaryequations and quantities necessary for the adaptivity. We demonstratenew optimal strong scaling results for the whole adaptive frameworkapplied to turbulent ow on massively parallel architectures down to25000 vertices per core with ca. 5000 cores with the MPI-based PETScbackend and for assembly down to 500 vertices per core with ca. 20000cores with the PGAS-based JANPACK backend. As a demonstration ofthe high impact of the combination of the scalability together with theadaptive methodology allowing prediction of gross quantities in turbulent ow we present an application in aerodynamics of a full DLR-F11 aircraftin connection with the HiLift-PW2 benchmarking workshop with goodmatch to experiments.

  • 38.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Ctr Appl Math, Spain.
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Ctr Appl Math, Spain.
    Jansson, Niclas
    RIKEN Advanced Institute for Computational Science, Kobe, Japan.
    De Abreu, Rodrigo Vilela
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Towards a parameter-free method for high Reynolds number turbulent flow simulation based on adaptive finite element approximation2015In: Computer Methods in Applied Mechanics and Engineering, ISSN 0045-7825, E-ISSN 1879-2138, Vol. 288, p. 60-74Article in journal (Refereed)
    Abstract [en]

    We present work towards a parameter-free method for turbulent flow simulation based on adaptive finite element approximation of the Navier-Stokes equations at high Reynolds numbers. In this model, viscous dissipation is assumed to be dominated by turbulent dissipation proportional to the residual of the equations, and skin friction at solid walls is assumed to be negligible compared to inertial effects. The result is a computational model without empirical data, where the only parameter is the local size of the finite element mesh. Under adaptive refinement of the mesh based on a posteriori error estimation, output quantities of interest in the form of functionals of the finite element solution converge to become independent of the mesh resolution, and thus the resulting method has no adjustable parameters. No ad hoc design of the mesh is needed, instead the mesh is optimised based on solution features, in particular no bounder layer mesh is needed. We connect the computational method to the mathematical concept of a dissipative weak solution of the Euler equations, as a model of high Reynolds number turbulent flow, and we highlight a number of benchmark problems for which the method is validated. 

  • 39.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics, Spain .
    Jansson, Niclas
    RIKEN Advanced Institute for Computational Science, Japan .
    Vilela De Abrea, Rodrigo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Time-resolved adaptive FEM simulation of the DLR-F11 aircraft model at high Reynolds number2014In: 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014, 2014Conference paper (Other academic)
    Abstract [en]

    We present a time-resolved, adaptive finite element method for aerodynamics, together with the results from the HiLiftPW-2 workshop, where this method is used to compute the flow past a DLR-F11 aircraft model at realistic Reynolds number. The mesh is automatically constructed by the method as part of the computation, and no explicit turbulence model is needed. The effect of unresolved turbulent boundary layers is modeled by a simple parametrization of the wall shear stress in terms of the skin friction. In the extreme case of very high Reynolds numbers we approximate the small skin friction by zero skin friction, corresponding to a free slip boundary condition, which results in a computational model without any model parameter that needs tuning. Thus, the simulation methodology by- passes the main challenges posed by high Reynolds number CFD: the design of an optimal computational mesh, turbulence (or subgrid) modeling, and the cost of boundary layer res- olution. The results from HiLiftPW-2 presented in this report show good agreement with experimental data for a range of different angles of attack, while using orders of magnitude fewer degrees of freedom than what is needed in state of the art methods such as RANS. 

  • 40.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Vilela de Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Johnson, Claes
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Computability and Adaptivity in CFD2016In: Encyclopedia of Computational Mechanics, John Wiley & Sons, 2016Chapter in book (Refereed)
  • 41.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Johnson, Claes
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    New Theory of Flight2015In: Journal of Mathematical Fluid Mechanics, ISSN 1422-6928, E-ISSN 1422-6952, Vol. 18, no 2, p. 219-241Article in journal (Other academic)
    Abstract [en]

    We present a new mathematical theory explaining the fluid mechanics of sub-sonic flight, which is fundamentally different from the existing boundary layer-circulation theory by Prandtl-Kutta-Zhukovsky formed 100 year ago. The new the-ory is based on our new resolution of d’Alembert’s paradox showing that slightlyviscous bluff body flow can be viewed as zero-drag/lift potential flow modified by3d rotational slip separation arising from a specific separation instability of po-tential flow, into turbulent flow with nonzero drag/lift. For a wing this separationmechanism maintains the large lift of potential flow generated at the leading edgeat the price of small drag, resulting in a lift to drag quotient of size15

  • 42.
    Hoffman, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Vilela De Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Computation of slat noise sources using adaptive FEM and lighthill's analogy2013In: 19th AIAA/CEAS Aeroacoustics Conference, 2013Conference paper (Refereed)
    Abstract [en]

    This is a summary of preliminary results from simulations with the 30P30N high-lift device. We used the General Galerkin finite element method (G2), where no explicit subgrid model is used, and where the computational mesh is adaptively refined with respect to a posteriori error estimates for a quantity of interest. The mesh is fully unstructured and the solutions are time-resolved, which are key ingredients for solving challenging industrial applications in the field of aeroacoustics. We present preliminary results containing time-averaged quantities and snapshots of unsteady quantities, all reasonably agreeing with previous computational efforts. One important finding is that the use of adaptively generated meshes seems to be a more effcient way of computing aeroacoustic sources than by using "handmade" meshes.

  • 43. Innocenti, M. E.
    et al.
    Beck, A.
    Ponweiser, T.
    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.
    Lapenta, G.
    Introduction of temporal sub-stepping in the Multi-Level Multi-Domain semi-implicit Particle-In-Cell code Parsek2D-MLMD2015In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 189, p. 47-59Article in journal (Refereed)
    Abstract [en]

    In this paper, the introduction of temporal sub-stepping in Multi-Level Multi-Domain (MLMD) simulations of plasmas is discussed. The MLMD method addresses the multi-scale nature of space plasmas by simulating a problem at different levels of resolution. A large-domain "coarse grid" is simulated with low resolution to capture large-scale, slow processes. Smaller scale, local processes are obtained through a "refined grid" which uses higher resolution. Very high jumps in the resolution used at the different levels can be achieved thanks to the Implicit Moment Method and appropriate grid interlocking operations. Up to now, the same time step was used at all the levels. Now, with temporal sub-stepping, the different levels can also benefit from the use of different temporal resolutions. This saves further resources with respect to "traditional" simulations done using the same spatial and temporal stepping on the entire domain. It also prevents the levels from working at the limits of the stability condition of the Implicit Moment Method. The temporal sub-stepping is tested with simulations of magnetic reconnection in space. It is shown that, thanks to the reduced costs of MLMD simulations with respect to single-level simulations, it becomes possible to verify with realistic mass ratios scaling laws previously verified only for reduced mass ratios. Performance considerations are also provided.

  • 44. Innocenti, M.E.
    et al.
    Goldman, M.
    Newman, D.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, G.
    Evidence of magnetic field switch-off in collisionless magnetic reconnection2015In: Astrophysical Journal Letters, ISSN 2041-8205, E-ISSN 2041-8213, Vol. 810, no 2Article in journal (Refereed)
    Abstract [en]

    The long-term evolution of large domain particle-in-cell simulations of collisionless magnetic reconnection is investigated following observations that show two possible outcomes for collisionless reconnection: toward a Petschek-like configuration or toward multiple X points. In the present simulation, a mixed scenario develops. At earlier time, plasmoids are emitted, disrupting the formation of Petschek-like structures. Later, an almost stationary monster plasmoid forms, preventing the emission of other plasmoids. A situation reminiscent of Petschek’s switch-off then ensues. Switch-off is obtained through a slow shock/rotational discontinuity compound structure. Two external slow shocks (SS) located at the separatrices reduce the in-plane tangential component of the magnetic field, but not to zero. Two transitions reminiscent of rotational discontinuities (RD) in the internal part of the exhaust then perform the final switch-off. Both the SS and the RD are characterized through analysis of their Rankine-Hugoniot jump conditions. A moderate guide field is used to suppress the development of the firehose instability in the exhaust.

  • 45.
    Ivanov, Ilya
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    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.
    Akhmetova, Dana
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Peng, Ivy Bo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Machado, Rui
    Rahn, Mirko
    Bartsch, Valeria
    Hart, Alistair
    Fischer, Paul
    Evaluation of Parallel Communication Models in Nekbone, a Nek5000 mini-application2015In: 2015 IEEE International Conference on Cluster Computing, IEEE , 2015, p. 760-767Conference paper (Refereed)
    Abstract [en]

    Nekbone is a proxy application of Nek5000, a scalable Computational Fluid Dynamics (CFD) code used for modelling incompressible flows. The Nekbone mini-application is used by several international co-design centers to explore new concepts in computer science and to evaluate their performance. We present the design and implementation of a new communication kernel in the Nekbone mini-application with the goal of studying the performance of different parallel communication models. First, a new MPI blocking communication kernel has been developed to solve Nekbone problems in a three-dimensional Cartesian mesh and process topology. The new MPI implementation delivers a 13% performance improvement compared to the original implementation. The new MPI communication kernel consists of approximately 500 lines of code against the original 7,000 lines of code, allowing experimentation with new approaches in Nekbone parallel communication. Second, the MPI blocking communication in the new kernel was changed to the MPI non-blocking communication. Third, we developed a new Partitioned Global Address Space (PGAS) communication kernel, based on the GPI-2 library. This approach reduces the synchronization among neighbor processes and is on average 3% faster than the new MPI-based, non-blocking, approach. In our tests on 8,192 processes, the GPI-2 communication kernel is 3% faster than the new MPI non-blocking communication kernel. In addition, we have used the OpenMP in all the versions of the new communication kernel. Finally, we highlight the future steps for using the new communication kernel in the parent application Nek5000.

  • 46.
    Ivanov, Ilya
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Machado, Rui
    Rahn, Mirko
    Akhmetova, Dana
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fischer, Paul
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Evaluating New Communication Models in the Nek5000 Code for Exascale2015Conference paper (Other academic)
  • 47.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics (BCAM), Bizkaia Basque-Country, Spain .
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Framework for adaptive fluid-structure interaction with industrial applications2013In: International Journal of Materials Engineering Innovation, ISSN 1757-2754, Vol. 4, no 2, p. 166-186Article in journal (Refereed)
    Abstract [en]

    We present developments in the Unicorn-HPC framework for unified continuum mechanics, enabling adaptive finite element computation of fluid-structure interaction, and an overview of the larger FEniCS-HPC framework for automated solution of partial diffential equations of which Unicorn-HPC is a part. We formulate the basic model and finite element discretisation method and adaptive algorithms. We test the framework on a 2D model problem consisting of a flexible beam in channel flow, and to illustrate the capabilities of the computational framework, we show two application examples from industry and medicine. We simulate a flexible mixer plate in turbulent flow in an exhaust system where the target output is aeroacoustic quantities. The second example is a self-oscillating vocal fold configuration, where the ultimate goal is to predict how the voice is affected by physiological changes from aerodynamics. Here we give the displacement signal of a point on the folds.

  • 48.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Adaptive error control in finite element methods using the error representation as error indicator2013Report (Other academic)
    Abstract [en]

    In this paper we present a new a posteriori adaptive finite elementmethod (FEM) directly using the error representation as a local errorindicator, and representing the primal and dual solutions in the samefinite element space (here piecewise continuous linear functions onthe same mesh). Since this approach gives a global a posteriori errorestimate that is zero (due to the Galerkin orthogonality), the errorrepresentation has historically been thought to contain no informationabout the error. However, we show the opposite, that locally, theorthogonal error representation behaves very similar to thenon-orthogonal error representation using a quadratic approximation ofthe dual. We present evidence of this both in the form of an a prioriestimate for the local error indicator and a detailed computationalinvestigation showing that the two methods exhibit very similarbehavior and performance, and thus confirming the theoreticalprediction. We also present a stabilized version of the method fornon-elliptic partial differential equations (PDE) where the errorrepresentation is no longer orthogonal, and where both the local errorindicator and global error estimate behave similar to the errorrepresentation using a quadratic approximation of the dual.

  • 49.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Spühler, Jeannette
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Automated adaptive error control in finite element methods using the error representation as error indicator2014Report (Other academic)
    Abstract [en]

    In this paper we present a new adaptive finite element method directly using the a posteriori error representation as a local error  indicator, and representing the primal and dual solutions in the same finite element space (here piecewise continuous linear functions on the same mesh). Since this approach gives a global a posteriori error estimate that is zero (due to Galerkin orthogonality), the error representation has traditionally been thought to contain no information about the error. However, we show the opposite, that locally, the orthogonal error representation behaves very similar to the non-orthogonal error representation using a higher order approximation of the dual,  which is a standard approach to overcome the problem of a zero error estimate. We present evidence of this both in the  form of an a priori estimate for the local error indicator for an elliptic model problem  and a detailed computational investigation showing that the two methods exhibit very similar behavior and performance, and thus confirming the theoretical prediction. We also present computational results using a stabilized version of the method for non-elliptic partial differential equations where the error representation is no longer orthogonal, and where both the local error indicator and global error estimate behave similar to the error representation using a higher order approximation of the dual. The benefits of this adaptive method are generality and simplicity in formulation, sharpness, and efficiency since high order approximation of the dual and computation of additional constructs such as jump terms over interior facets or local problems are avoided.

  • 50.
    Jansson, Johan
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Holmberg, Andreas
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering, MWL Flow acoustics.
    Vilela De Abreu, Rodrigo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Niyazi Cem
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Karlsson, Mikael
    Åbom, Mats
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering, MWL Flow acoustics.
    Adaptive stabilized finite element framework for simulation of vocal fold turbulent fluid-structure interaction2013In: Proceedings of Meetings on Acoustics: Volume 19, 2013, Acoustical Society of America (ASA), 2013, p. 1-9Conference paper (Refereed)
    Abstract [en]

    As a step toward building a more complete model of voice production mechanics, we assess the feasibility of a fluid-structure simulation of the vocal fold mechanics in the Unicorn incompressible Unified Continuum framework. The Unicorn framework consists of conservation equations for mass and momentum, a phase function selecting solid or fluid constitutive laws, a convection equation for the phase function and moving mesh methods for tracking the interface, and discretization through an adaptive stabilized finite element method. The framework has been validated for turbulent flow for both low and high Reynolds numbers and has the following features: implicit turbulence modeling (turbulent dissipation only occurs through numerical stabilization), goal-oriented mesh adaptivity, strong, implicit fluid-structure coupling and good scaling on massively parallel computers. We have applied the framework for turbulent fluid-structure interaction simulation of vocal folds, and present initial results. Acoustic quantities have been extracted from the framework in the setting of an investigation of a configuration approximating an exhaust system with turbulent flow around a flexible triangular steel plate in a circular duct. We present some results of the investigation as well as results of the framework applied to other problems.

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