International Journal of High Performance Computing Applications, Volume 31

Volume 31, Number 1, January 2017

Special Issue on Clusters, Clouds and Data for Scientific Computing
Preface

• 
  Jack J. Dongarra, Bernard Tourancheau:
  Guest Editor's Note: Special Issue on Clusters, Clouds and Data for Scientific Computing. 3

Special Issue Articles

• 
  Ewa Deelman, Christopher D. Carothers, Anirban Mandal, Brian Tierney, Jeffrey S. Vetter, Ilya Baldin, Claris Castillo, Gideon Juve, Dariusz Król, Vickie E. Lynch, Benjamin Mayer, Jeremy S. Meredith, Thomas Proffen, Paul Ruth, Rafael Ferreira da Silva:
  PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows. 4-18
• 
  Michela Taufer, Arnold L. Rosenberg:
  Scheduling DAG-based workflows on single cloud instances: High-performance and cost effectiveness with a static scheduler. 19-31
• 
  George Teodoro, Tahsin M. Kurç, Guilherme Andrade, Jun Kong, Renato Ferreira, Joel H. Saltz:
  Application performance analysis and efficient execution on systems with multi-core CPUs, GPUs and MICs: a case study with microscopy image analysis. 32-51
• 
  Anne Benoit, Saurabh K. Raina, Yves Robert:
  Efficient checkpoint/verification patterns. 52-65
• 
  Enric Tejedor, Yolanda Becerra, Guillem Alomar, Anna Queralt, Rosa M. Badia, Jordi Torres, Toni Cortes, Jesús Labarta:
  PyCOMPSs: Parallel computational workflows in Python. 66-82
• 
  Marc Buffat, Anne Cadiou, Lionel Le Penven, Christophe Pera:
  In situ analysis and visualization of massively parallel computations. 83-90
• 
  Shad Kirmani, JeongHyung Park, Padma Raghavan:
  An embedded sectioning scheme for multiprocessor topology-aware mapping of irregular applications. 91-103
• 
  Al Geist, Daniel A. Reed:
  A survey of high-performance computing scaling challenges. 104-113

Volume 31, Number 2, March 2017

Special Issue on High performance computing in modelling and simulation
Special Issue Editorial

• 
  William Spataro, Giuseppe A. Trunfio, Georgios Ch. Sirakoulis:
  High performance computing in modelling and simulation. 117-118

Special Issue Articles

• 
  Ana F. P. Camargos, Viviane Cristine Silva, Jean-Michel Guichon, Gérard Meunier:
  GPU-accelerated iterative solution of complex-entry systems issued from 3D edge-FEA of electromagnetics in the frequency domain. 119-133
• 
  Themistoklis Giitsidis, Nikolaos I. Dourvas, Georgios Ch. Sirakoulis:
  Parallel implementation of aircraft disembarking and emergency evacuation based on cellular automata. 134-151
• 
  Muhammad Irfan Uddin:
  One-IPC high-level simulation of microthreaded many-core architectures. 152-162
• 
  Davide Spataro, Donato D'Ambrosio, Giuseppe Filippone, Rocco Rongo, William Spataro, Davide Marocco:
  The new SCIARA-fv3 numerical model and acceleration by GPGPU strategies. 163-176

Volume 31, Number 3, May - June 2017

Special issue: International Conferences on Parallel, Distributed, and Network-Based Processing (PDP) 2014 and 2015
Original Articles

• 
  Ivan Merelli, Paolo Cozzi, Elisabetta Ronchieri, Daniele Cesini, Daniele D'Agostino:
  Porting bioinformatics applications from grid to cloud: A macromolecular surface analysis application case study. 182-195
• 
  Fabio Tordini, Maurizio Drocco, Claudia Misale, Luciano Milanesi, Pietro Liò, Ivan Merelli, Massimo Torquati, Marco Aldinucci:
  NuChart-II: The road to a fast and scalable tool for Hi-C data analysis. 196-211
• 
  Matthias Diener, Eduardo Henrique Molina da Cruz, Philippe Olivier Alexandre Navaux:
  Modeling memory access behavior for data mapping. 212-228
• 
  Jan G. Cornelis, Jan Lemeire, Tim Bruylants, Peter Schelkens:
  Heterogeneous acceleration of volumetric JPEG 2000 using OpenCL. 229-245
• 
  Fredrik Robertsen, Jan Westerholm, Keijo Mattila:
  Designing a graphics processing unit accelerated petaflop capable lattice Boltzmann solver: Read aligned data layouts and asynchronous communication. 246-255

Volume 31, Number 4, July 2017

Research Papers

• 
  Rune Havnung Bakken, Lars Moland Eliassen:
  Real-time three-dimensional skeletonisation using general-purpose computing on graphics processing units applied to computer vision-based human pose estimation. 259-273
• 
  Lena Oden, Holger Fröning:
  InfiniBand Verbs on GPU: a case study of controlling an InfiniBand network device from the GPU. 274-284
• 
  Anish Varghese, Bob Edwards, Gaurav Mitra, Alistair P. Rendell:
  Programming the Adapteva Epiphany 64-core network-on-chip coprocessor. 285-302
• 
  Miaoqing Huang, Chenggang Lai, Xuan Shi, Zhijun Hao, Haihang You:
  Study of parallel programming models on computer clusters with Intel MIC coprocessors. 303-315
• 
  Rosa Filgueira, Amrey Krause, Malcolm P. Atkinson, Iraklis A. Klampanos, Alexander Moreno:
  dispel4py. 316-334
• 
  Anthony Kougkas, Hassan Eslami, Xian-He Sun, Rajeev Thakur, William Gropp:
  Rethinking key-value store for parallel I/O optimization. 335-356

Volume 31, Number 5, September 2017

Special issue on programming models and applications for multicores and manycores
Special Issue Editorial

• 
  Pavan Balaji, Zhiyi Huang:
  Special issue on programming models and applications for multicores and manycores. 359-360

Special Issue Articles

• 
  Yao Wu, Long Zheng, Brian Heilig, Guang R. Gao:
  HAMR: A dataflow-based real-time in-memory cluster computing engine. 361-374
• 
  Hartwig Anzt, Stanimire Tomov, Jack J. Dongarra:
  On the performance and energy efficiency of sparse linear algebra on GPUs. 375-390
• 
  Jonathan C. Beard, Peng Li, Roger D. Chamberlain:
  RaftLib: A C++ template library for high performance stream parallel processing. 391-404
• 
  Nicholas Chaimov, Khaled Z. Ibrahim, Samuel Williams, Costin Iancu:
  Reaching bandwidth saturation using transparent injection parallelization. 405-421
• 
  Ahmad Qawasmeh, Maxime R. Hugues, Henri Calandra, Barbara M. Chapman:
  Performance portability in reverse time migration and seismic modelling via OpenACC. 422-440
• 
  Peng Li, Jonathan C. Beard, Jeremy D. Buhler:
  Deadlock-free buffer configuration for stream computing. 441-450
• 
  Akhil Langer, Ehsan Totoni, Udatta S. Palekar, Laxmikant V. Kalé:
  Energy-optimal configuration selection for manycore chips with variation. 451-466

Volume 31, Number 6, November 2017

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Research Papers

• 
  Gordon Bell, David H. Bailey, Jack J. Dongarra, Alan H. Karp, Kevin Walsh:
  A look back on 30 years of the Gordon Bell Prize. 469-484
• 
  Felix Schmitt, Robert Dietrich, Guido Juckeland:
  Scalable critical-path analysis and optimization guidance for hybrid MPI-CUDA applications. 485-498
• 
  Sebastião Miranda, Jonas Feldt, Frederico Pratas, Ricardo A. Mata, Nuno Roma, Pedro Tomás:
  Efficient parallelization of perturbative Monte Carlo QM/MM simulations in heterogeneous platforms. 499-516
• 
  Chao Jin, Bronis R. de Supinski, David Abramson, Heidi Poxon, Luiz DeRose, Minh Ngoc Dinh, Mark Endrei, Elizabeth R. Jessup:
  A survey on software methods to improve the energy efficiency of parallel computing. 517-549
• 
  Timothy Dykes, Claudio Gheller, Marzia Rivi, Mel Krokos:
  Splotch. 550-563
• 
  Andrew A. Chien, Pavan Balaji, Nan Dun, Aiman Fang, Hajime Fujita, Kamil Iskra, Zachary A. Rubenstein, Ziming Zheng, Jeff R. Hammond, Ignacio Laguna, D. Richards, Anshu Dubey, Brian van Straalen, Mark Hoemmen, Michael A. Heroux, Keita Teranishi, Andrew R. Siegel:
  Exploring versioned distributed arrays for resilience in scientific applications. 564-590