Table of contents for issues of Supercomputing Frontiers and Innovations

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Volume 1, Number 1, 2014
Volume 1, Number 2, 2014
Volume 1, Number 3, 2014
Volume 2, Number 1, 2015
Volume 2, Number 2, 2015
Volume 2, Number 3, 2015
Volume 2, Number 4, 2015
Volume 3, Number 1, 2016
Volume 3, Number 2, 2016
Volume 3, Number 3, 2016
Volume 3, Number 4, 2016
Volume 4, Number 1, 2017
Volume 4, Number 2, 2017
Volume 4, Number 3, 2017


Supercomputing Frontiers and Innovations
Volume 1, Number 1, 2014

            Franck Cappello and   
                   Al Geist and   
              William Gropp and   
                Sanjay Kale and   
                Bill Kramer and   
                      Marc Snir   Toward Exascale Resilience: 2014 update  5--28
               Mateo Valero and   
              Miquel Moreto and   
                 Marc Casas and   
             Eduard Ayguade and   
                  Jesus Labarta   Runtime-Aware Architectures: A First
                                  Approach . . . . . . . . . . . . . . . . 29--44
              Oliver Fuhrer and   
               Carlos Osuna and   
          Xavier Lapillonne and   
                Tobias Gysi and   
                Ben Cumming and   
               Mauro Bianco and   
             Andrea Arteaga and   
    Thomas Christoph Schulthess   Towards a performance portable,
                                  architecture agnostic implementation
                                  strategy for weather and climate models  45--62
                 Rio Yokota and   
           George Turkiyyah and   
                    David Keyes   Communication Complexity of the Fast
                                  Multipole Method and its Algebraic
                                  Variants . . . . . . . . . . . . . . . . 63--84
              Jack Dongarra and   
               Azzam Haidar and   
               Jakub Kurzak and   
             Piotr Luszczek and   
            Stanimire Tomov and   
                   Asim YarKhan   Model-Driven One-Sided Factorizations on
                                  Multicore Accelerated Systems  . . . . . 85--115
       Julian Martin Kunkel and   
               Michael Kuhn and   
                  Thomas Ludwig   Exascale Storage Systems --- An
                                  Analytical Study of Expenses . . . . . . 116--134

Supercomputing Frontiers and Innovations
Volume 1, Number 2, 2014

              Claudia Rosas and   
       Judit Giménez and   
           Jesús Labarta   Scalability prediction for fundamental
                                  performance factors  . . . . . . . . . . 4--19
           Hayk Shoukourian and   
              Torsten Wilde and   
               Axel Auweter and   
                     Arndt Bode   Predicting the Energy and Power
                                  Consumption of Strong and Weak Scaling
                                  HPC Applications . . . . . . . . . . . . 20--41
            Thomas Sterling and   
              Daniel Kogler and   
           Matthew Anderson and   
               Maciej Brodowicz   SLOWER: A performance model for Exascale
                                  computing  . . . . . . . . . . . . . . . 42--57
            Torsten Hoefler and   
                    Dmitry Moor   Energy, Memory, and Runtime Tradeoffs
                                  for Implementing Collective
                                  Communication Operations . . . . . . . . 58--75
              Seung Woo Son and   
            Zhengzhang Chen and   
            William Hendrix and   
              Ankit Agrawal and   
              Wei-keng Liao and   
                 Alok Choudhary   Data Compression for the Exascale
                                  Computing Era --- Survey . . . . . . . . 76--88
           Satoshi Matsuoka and   
               Hitoshi Sato and   
               Osamu Tatebe and   
         Michihiro Koibuchi and   
              Ikki Fujiwara and   
               Shuji Suzuki and   
            Masanori Kakuta and   
             Takashi Ishida and   
             Yutaka Akiyama and   
          Toyotaro Suzumura and   
                  Koji Ueno and   
           Hiroki Kanezashi and   
               Takemasa Miyoshi   Extreme Big Data (EBD): Next Generation
                                  Big Data Infrastructure Technologies
                                  Towards Yottabyte/Year . . . . . . . . . 89--107
                     Bernd Mohr   Scalable parallel performance
                                  measurement and analysis tools ---
                                  state-of-the-art and future challenges   108--123

Supercomputing Frontiers and Innovations
Volume 1, Number 3, 2014

            Antoni Artigues and   
 Fernando Martin Cucchietti and   
     Carlos Tripiana Montes and   
              David Vicente and   
             Hadrien Calmet and   
            Guillermo Marin and   
         Guillaume Houzeaux and   
                Mariano Vazquez   Scientific Big Data Visualization: a
                                  coupled tools approach . . . . . . . . . 4--18
                 Onur Mutlu and   
            Lavanya Subramanian   Research Problems and Opportunities in
                                  Memory Systems . . . . . . . . . . . . . 19--55
        Alexander N. Daryin and   
                 Anton A. Korzh   Early evaluation of direct large-scale
                                  InfiniBand networks with adaptive
                                  routing  . . . . . . . . . . . . . . . . 56--69
             Alexey Lastovetsky   Heterogeneous parallel computing: from
                                  clusters of workstations to hierarchical
                                  hybrid platforms . . . . . . . . . . . . 70--87
          Boris M. Glinskiy and   
            Igor M. Kulikov and   
        Alexey V. Snytnikov and   
        Alexey A. Romanenko and   
           Igor G. Chernykh and   
             Vitaly A. Vshivkov   Co-design of Parallel Numerical Methods
                                  for Plasma Physics and Astrophysics  . . 88--98


Supercomputing Frontiers and Innovations
Volume 2, Number 1, 2015

       Vladimir V. Voevodin and   
       Alexander S. Antonov and   
                  Jack Dongarra   AlgoWiki: an Open Encyclopedia of
                                  Parallel Algorithmic Features  . . . . . 4--18
           Milan Mihajlovic and   
            Lars Ailo Bongo and   
           Raimondas Ciegis and   
              Neki Frasheri and   
             Dragi Kimovski and   
                Peter Kropf and   
          Svetozar Margenov and   
             Maya Neytcheva and   
              Thomas Rauber and   
              Gudula Runger and   
               Roman Trobec and   
                 Roel Wuyts and   
          Roman Wyrzykowski and   
                      Jing Gong   Applications for ultrascale computing    19--48
            Rabab Al-Omairy and   
          Guillermo Miranda and   
               Hatem Ltaief and   
              Rosa M. Badia and   
           Xavier Martorell and   
              Jesus Labarta and   
                    David Keyes   Dense Matrix Computations on NUMA
                                  Architectures with Distance-Aware Work
                                  Stealing . . . . . . . . . . . . . . . . 49--72
               Xiangke Liao and   
             Shaoliang Peng and   
                  Yutong Lu and   
                 Yingbo Cui and   
                Chengkun Wu and   
                  Heng Wang and   
                     Jiajun Wen   Neo-heterogeneous Programming and
                                  Parallelized Optimization of a Human
                                  Genome Re-sequencing Analysis Software
                                  Pipeline on TH-2 Supercomputer . . . . . 73--83

Supercomputing Frontiers and Innovations
Volume 2, Number 2, 2015

           Georges Da Costa and   
           Thomas Fahringer and   
  Juan Antonio Rico Gallego and   
                Ivan Grasso and   
             Atanas Hristov and   
           Helen D. Karatza and   
         Alexey Lastovetsky and   
           Fabrizio Marozzo and   
                 Dana Petcu and   
    Georgios L. Stavrinides and   
             Domenico Talia and   
              Paolo Trunfio and   
             Hrachya Astsatryan   Exascale Machines Require New
                                  Programming Paradigms and Runtimes . . . 6--27
            Jesus Carretero and   
         Javier Garcia-Blas and   
             David E. Singh and   
              Florin Isaila and   
         Alexey Lastovetsky and   
           Thomas Fahringer and   
                Radu Prodan and   
              Peter Zangerl and   
         Christi Symeonidou and   
             Afshin Fassihi and   
Horacio Pérez-Sánchez   Acceleration of MPI mechanisms for
                                  sustainable HPC applications . . . . . . 28--45
              Pascal Bouvry and   
               Rudolf Mayer and   
          Jakub Muszy\'nski and   
                 Dana Petcu and   
             Andreas Rauber and   
          Gianluca Tempesti and   
                 Tuan Trinh and   
      Sébastien Varrette   Resilience within Ultrascale Computing
                                  System: Challenges and Opportunities
                                  from Nesus Project . . . . . . . . . . . 46--63
          Francisco Almeida and   
             Javier Arteaga and   
             Vicente Blanco and   
                Alberto Cabrera   Energy Measurement Tools for Ultrascale
                                  Computing: A Survey  . . . . . . . . . . 64--76
            Jesus Carretero and   
        Salvatore Distefano and   
                 Dana Petcu and   
                 Daniel Pop and   
              Thomas Rauber and   
         Gudula Rünger and   
                 David E. Singh   Energy-efficient Algorithms for
                                  Ultrascale Systems . . . . . . . . . . . 77--104
              Michel Bagein and   
              Jorge Barbosa and   
             Vicente Blanco and   
              Ivona Brandic and   
              Samuel Cremer and   
           Sebastien Fremal and   
              Helen Karatza and   
            Laurent Lefevre and   
              Toni Mastelic and   
             Ariel Oleksiak and   
        Anne-Cecile Orgerie and   
    Georgios L. Stavrinides and   
             Sebastien Varrette   Energy Efficiency for Ultrascale
                                  Systems: Challenges and Trends from
                                  Nesus Project  . . . . . . . . . . . . . 105--131

Supercomputing Frontiers and Innovations
Volume 2, Number 3, 2015

          Marek Michalewicz and   
                    Yuefan Deng   Foreword . . . . . . . . . . . . . . . . 4
                    Hank Childs   Data Exploration at the Exascale . . . . 5--13
        Kenneth Hon Kim Ban and   
          Jakub Chrzeszczyk and   
              Andrew Howard and   
                Dongyang Li and   
                    Tin Wee Tan   InfiniCloud: Leveraging the Global
                                  InfiniCortex Fabric and OpenStack Cloud
                                  for Borderless High Performance
                                  Computing of Genomic Data  . . . . . . . 14--27
               Jonathan Low and   
          Jakub Chrzeszczyk and   
              Andrew Howard and   
            Andrzej Chrzeszczyk   Performance Assessment of InfiniBand HPC
                                  Cloud Instances on Intel Haswell and
                                  Intel Sandy Bridge Architectures . . . . 28--40
                 David Rohr and   
           Gvozden Neskovic and   
            Volker Lindenstruth   The L-CSC cluster: Optimizing power
                                  efficiency to become the greenest
                                  supercomputer in the world in the
                                  Green500 list of November 2014 . . . . . 41--48
              Kevin A. Huck and   
          Allan Porterfield and   
               Nick Chaimov and   
             Hartmut Kaiser and   
            Allen D. Malony and   
            Thomas Sterling and   
                     Rob Fowler   An Autonomic Performance Environment for
                                  Exascale . . . . . . . . . . . . . . . . 49--66
           Kenneth Moreland and   
             Matthew Larsen and   
                    Hank Childs   Visualization for Exascale: Portable
                                  Performance is Critical  . . . . . . . . 67--75
             Nachiket Kapre and   
                Pradeep Moorthy   A Case for Embedded FPGA-based SoCs in
                                  Energy-Efficient Acceleration of Graph
                                  Problems . . . . . . . . . . . . . . . . 76--86

Supercomputing Frontiers and Innovations
Volume 2, Number 4, 2015

                  Ben Swift and   
            Andrew Sorensen and   
              Henry Gardner and   
                Peter Davis and   
                Viktor K. Decyk   Live Programming in Scientific
                                  Simulation . . . . . . . . . . . . . . . 4--15
       Marek T. Michalewicz and   
       \Lukasz P. Or\lowski and   
                    Yuefan Deng   Creating interconnect topologies by
                                  algorithmic edge removal: MOD and SMOD
                                  graphs . . . . . . . . . . . . . . . . . 16--47
      Alexander V. Nemukhin and   
           Igor V. Polyakov and   
         Alexander I. Moskovsky   Multi-Scale Supercomputing of Large
                                  Molecular Aggregates: A Case Study of
                                  the Light-Harvesting Photosynthetic
                                  Center . . . . . . . . . . . . . . . . . 48--54
       Alexander A. Danilov and   
         Kirill M. Terekhov and   
            Igor N. Konshin and   
            Yuri V. Vassilevski   Parallel software platform INMOST: a
                                  framework for numerical modeling . . . . 55--66
              Jack Dongarra and   
              M. Abalenkovs and   
             A. Abdelfattah and   
                   M. Gates and   
                  A. Haidar and   
                  J. Kurzak and   
                P. Luszczek and   
                   S. Tomov and   
                I. Yamazaki and   
                     A. YarKhan   Parallel Programming Models for Dense
                                  Linear Algebra on Heterogeneous Systems  67--86


Supercomputing Frontiers and Innovations
Volume 3, Number 1, 2016

                      Suo Guang   NR-MPI: A Non-stop and Fault Resilient
                                  MPI Supporting Programmer Defined Data
                                  Backup and Restore for E-scale Super
                                  Computing Systems  . . . . . . . . . . . 4--21
              Ilya I. Levin and   
        Alexey I. Dordopulo and   
       Alexander M. Fedorov and   
                Igor A. Kalyaev   Reconfigurable computer systems: from
                                  the first FPGAs towards liquid cooling
                                  systems  . . . . . . . . . . . . . . . . 22--40
    Alexander V. Goncharsky and   
          Sergey Y. Romanov and   
         Sergey Y. Seryozhnikov   Supercomputer technologies in
                                  tomographic imaging applications . . . . 41--66
     Alexander A. Moskovsky and   
          Egor A. Druzhinin and   
          Alexey B. Shmelev and   
        Vladimir V. Mironov and   
                   Andrey Semin   Server Level Liquid Cooling: Do Higher
                                  System Temperatures Improve Energy
                                  Efficiency?  . . . . . . . . . . . . . . 67--74
               Michael Kuhn and   
              Julian Kunkel and   
                  Thomas Ludwig   Data Compression for Climate Data  . . . 75--94

Supercomputing Frontiers and Innovations
Volume 3, Number 2, 2016

             Fabrice Mizero and   
      Malathi Veeraraghavan and   
                   Qian Liu and   
          Robert D. Russell and   
                 John M. Dennis   A Dynamic Congestion Management System
                                  for InfiniBand Networks  . . . . . . . . 5--20
      Michaël Krajecki and   
             Julien Loiseau and   
       François Alin and   
             Christophe Jaillet   Many-Core Approaches to Combinatorial
                                  Problems: case of the Langford Problem   21--37
              John L. Gustafson   A Radical Approach to Computation with
                                  Real Numbers . . . . . . . . . . . . . . 38--53
          Jakub Chrzeszczyk and   
              Andrew Howard and   
        Andrzej Chrzeszczyk and   
                  Ben Swift and   
                Peter Davis and   
               Jonathan Low and   
                Tin Wee Tan and   
                    Kenneth Ban   InfiniCloud 2.0: distributing High
                                  Performance Computing across continents  54--71
        Dmitry A. Nikitenko and   
         Sergey A. Zhumatiy and   
                Pavel A. Shvets   Making Large-Scale Systems Observable
                                  --- Another Inescapable Step Towards
                                  Exascale . . . . . . . . . . . . . . . . 72--79
        Mikhail A. Naumenko and   
          Vyacheslav V. Samarin   Application of CUDA technology to
                                  calculation of ground states of few-body
                                  nuclei by Feynman's continual integrals
                                  method . . . . . . . . . . . . . . . . . 80--95

Supercomputing Frontiers and Innovations
Volume 3, Number 3, 2016

           Iosif B. Meyerov and   
        Sergey I. Bastrakov and   
             Igor A. Surmin and   
         Alexey V. Bashinov and   
         Evgeny S. Efimenko and   
       Artem V. Korzhimanov and   
      Alexander A. Muraviev and   
             Arkady A. Gonoskov   Hybrid CPU + Xeon Phi implementation of
                                  the Particle-in-Cell method for plasma
                                  simulation . . . . . . . . . . . . . . . 5--10
       Matthijs van Waveren and   
     Ahmed Seif El Nawasany and   
             Nasr Hassanein and   
                 David Moon and   
             Niall O'Byrnes and   
                  Alain Clo and   
        Karthikeyan Murugan and   
                  Antonio Arena   Easy Access to HPC Resources through the
                                  Application GUI  . . . . . . . . . . . . 11--18
          Jan Fabian Schmid and   
               Julian M. Kunkel   Predicting I/O Performance in HPC Using
                                  Artificial Neural Networks . . . . . . . 19--33
           Julian Martin Kunkel   Analyzing Data Properties using
                                  Statistical Sampling --- Illustrated on
                                  Scientific File Formats  . . . . . . . . 34--39
                 Jiri Jaros and   
              Filip Vaverka and   
              Bradley E. Treeby   Spectral Domain Decomposition Using
                                  Local Fourier Basis: Application to
                                  Ultrasound Simulation on a Cluster of
                                  GPUs . . . . . . . . . . . . . . . . . . 40--55
             Kedar Kulkarni and   
              Shreeya Badhe and   
               Geetanjali Gadre   HCA aware Parallel Communication
                                  Library: A feasibility study for
                                  offloading MPI requirements  . . . . . . 56--60
       Alexander S. Antonov and   
           Alexey V. Frolov and   
          Hiroaki Kobayashi and   
            Igor N. Konshin and   
           Alexey M. Teplov and   
          Vadim V. Voevodin and   
           Vladimir V. Voevodin   Parallel Processing Model for Cholesky
                                  Decomposition Algorithm in AlgoWiki
                                  Project  . . . . . . . . . . . . . . . . 61--70
            Mariem El Afrit and   
                 Yann Le Du and   
       Rafaël Del Pino and   
                   Guolin Zhang   Data merging for the cultural heritage
                                  imaging based on Chebfun approach  . . . 71--83

Supercomputing Frontiers and Innovations
Volume 3, Number 4, 2016

                 Will Usher and   
                  Ingo Wald and   
                Aaron Knoll and   
              Michael Papka and   
               Valerio Pascucci   In Situ Exploration of Particle
                                  Simulations with CPU Ray Tracing . . . . 4--18
       Brad Joseph Whitlock and   
               Earl P. N. Duque   In Situ Visualization and Production of
                                  Extract Databases  . . . . . . . . . . . 19--29
          Alexander Matthes and   
                 Axel Huebl and   
         René Widera and   
          Sebastian Grottel and   
             Stefan Gumhold and   
               Michael Bussmann   In situ, steerable, hardware-independent
                                  and data-structure agnostic
                                  visualization with ISAAC . . . . . . . . 30--48
                James Kress and   
    Randy Michael Churchill and   
               Scott Klasky and   
                   Mark Kim and   
                Hank Childs and   
                  David Pugmire   Preparing for In Situ Processing on
                                  Upcoming Leading-edge Supercomputers . . 49--65
     Konstantin S. Stefanov and   
             Alexey A. Gradskov   Analysis of CPU Usage Data Properties
                                  and their possible impact on Performance
                                  Monitoring . . . . . . . . . . . . . . . 66--73
      Mikhail S. Malovichko and   
        Nikolay E. Khokhlov and   
          Nikolay B. Yavich and   
             Michael S. Zhdanov   Parallel algorithm for $3$D modeling of
                                  monochromatic acoustic field by the
                                  method of integral equations . . . . . . 74--78


Supercomputing Frontiers and Innovations
Volume 4, Number 1, 2017

               Jakub Kurzak and   
             Piotr Luszczek and   
          Ichitaro Yamazaki and   
                Yves Robert and   
                  Jack Dongarra   Design and Implementation of the PULSAR
                                  Programming System for Large Scale
                                  Computing  . . . . . . . . . . . . . . . 4--26
              Rosa M. Badia and   
             Eduard Ayguade and   
                  Jesus Labarta   Workflows for Science: a Challenge when
                                  Facing the Convergence of HPC and Big
                                  Data . . . . . . . . . . . . . . . . . . 27--47
            Thomas Sterling and   
           Matthew Anderson and   
               Maciej Brodowicz   A Survey: Runtime Software Systems for
                                  High Performance Computing . . . . . . . 48--68
            Roscoe Bartlett and   
             Irina Demeshko and   
               Todd Gamblin and   
              Glenn Hammond and   
       Michael Allen Heroux and   
            Jeffrey Johnson and   
             Alicia Klinvex and   
                  Xiaoye Li and   
       Lois Curfman McInnes and   
           J. David Moulton and   
        Daniel Osei-Kuffuor and   
               Jason Sarich and   
                Barry Smith and   
          James Willenbring and   
              Ulrike Meier Yang   xSDK Foundations: Toward an
                                  Extreme-scale Scientific Software
                                  Development Kit  . . . . . . . . . . . . 69--82
               William Tang and   
                   Bei Wang and   
            Stephane Ethier and   
                    Zhihong Lin   Performance Portability of HPC Discovery
                                  Science Software: Fusion Energy
                                  Turbulence Simulations at Extreme Scale  83--97

Supercomputing Frontiers and Innovations
Volume 4, Number 2, 2017

               Asmi H. Shah and   
         Jonathan D. Picker and   
               Saumya S. Jamuar   Using High Performance Computing to
                                  Create and Freely Distribute the South
                                  Asian Genomic Database, Necessary for
                                  Precision Medicine in this Population    4--12
                   Yang Yao and   
                 Khoon-Seng Yeo   An Application of GPU Acceleration in
                                  CFD Simulation for Insect Flight . . . . 13--26
           Maciej Brodowicz and   
                Thomas Sterling   Simultac Fonton: A Fine-Grain
                                  Architecture for Extreme Performance
                                  beyond Moore's Law . . . . . . . . . . . 27--37
                 Earle Jennings   The Simultaneous Transmit And Receive
                                  (STAR) Message Protocol  . . . . . . . . 38--53
                 Earle Jennings   Core Module Optimizing PDE Sparse Matrix
                                  Models With HPCG Example . . . . . . . . 54--70
          John L. Gustafson and   
              Isaac T. Yonemoto   Beating Floating Point at its Own Game:
                                  Posit Arithmetic . . . . . . . . . . . . 71--86
              Gabriel Noaje and   
                 Alan Davis and   
               Jonathan Low and   
                   Seng Lim and   
              Geok Lian Tan and   
          \Lukasz Or\lowski and   
              Dominic Chien and   
               Sing-Wu Liou and   
                Tin Wee Tan and   
                 Yves Poppe and   
        Kenneth Ban Hon Kim and   
              Andrew Howard and   
            David Southwell and   
            Jason Gunthorpe and   
              Marek Michalewicz   InfiniCortex --- From Proof-of-concept
                                  to Production  . . . . . . . . . . . . . 87--102

Supercomputing Frontiers and Innovations
Volume 4, Number 3, 2017

          Saurabh Hukerikar and   
            Christian Engelmann   Resilience Design Patterns: A Structured
                                  Approach to Resilience at Extreme Scale  4--42
            Takuma Kawamura and   
              Tomoyuki Noda and   
               Yasuhiro Idomura   Performance Evaluation of Runtime Data
                                  Exploration Framework based on In-Situ
                                  Particle Based Volume Rendering  . . . . 43--54
             Michael Vetter and   
                Stephan Olbrich   Development and Integration of an
                                  In-Situ Framework for Flow Visualization
                                  of Large-Scale, Unsteady Phenomena in
                                  ICON . . . . . . . . . . . . . . . . . . 55--67
           Nuttiiya Seekhao and   
                Joseph JaJa and   
                Luc Mongeau and   
         Nicole Y. K. Li-Jessen   In Situ Visualization for $3$D
                                  Agent-Based Vocal Fold Inflammation and
                                  Repair Simulation  . . . . . . . . . . . 68--79
Ekaterina Olegovna Tyutlyaeva and   
           Sergey Konyukhov and   
              Igor Odintsov and   
            Alexander Moskovsky   Seismic Processing Performance Analysis
                                  on Different Hardware Environment  . . . 80--90
     Germán Ceballos and   
                 Andra Hugo and   
             Erik Hagersten and   
           David Black-Schaffer   Exploring Scheduling Effects on Task
                                  Performance with TaskInsight . . . . . . 91--98
               Roman Kaplan and   
              Leonid Yavits and   
                    Ran Ginosar   From Processing-in-Memory to
                                  Processing-in-Storage  . . . . . . . . . 99--116