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DEEP - Extreme Scale Technologies

Deliverables

Repository for training material

Design, access information and initial contents for the training repository.

Prototype software implementation

Initial software implementation of all software components. Report on status of their integration, functionality and capabilities.

Complete system-SW implementation

Full software implementation with the full required functionality, ready for deployment on the DEEP EST prototype.

Prototype programming environment implementation

Initial programming environment setup ready to be tested, including all involved components and interfaces.

Complete programming environment implementation

Fully functional and optimised programming environment available and ready to be deployed on the prototype.

Application use cases and traces

Use cases integrated in JUBE and Extrae trace files provided to WP2

Final DEEP-EST prototype report

Description of the final DEEP-EST prototype, including all its modules and components: CM, ESB, DAM, FN, fabri3, NAM and GCE, and a description of the infrastructure preparation and the prototype’s installation process.

Quality control plan

Definition of the quality control processes and templates for internal verification and document review for all project results and deliverables.

Policy briefing

Briefing for political deciders and lobbying groups detailing conclusions from project results and impact on HPC development in Europe.

Modular Supercomputer architecture assessment and outlook

Summary of architecture experience, outlook, and recommendations for future improvements.

Prototype assessment

Results of verification tests.

Final report on applications experience

Report performance improvements over the project, compare with other platforms, and detail porting efforts and ease-of-use.

Programming environment support report

Report on final optimisations and summary of the maintenance experience (e.g. installation on the system, bug correction, user feedback).

Tests for prototype assessment

Tests to be run on the prototype constructed in WP4 to make sure that it fulfils the specifications and criteria specified in D3.2.

Communication plan, toolkit and owned channels

Details of the communication and brand strategy including a toolkit with materials like logos and collateral templates and DEEP EST communication channels.

Design and specification of programming environment

Detailed specification of the overall programming model.

Initial application analysis and models

Initial results of the application analysis, modelling approach and first set of models created.

Software specification

High level specifications of the complete system software stack, including description of interfaces and interdependencies between the packages.

DEEP-EST benchmark suites

Describe the selected application and low-level benchmarks, and the workloads to be used by Tk2.1 and Tk2.2.

Application distribution strategy

Details the use of modules by the applications, including partitioning and mapping of the different parts to modules.

Software support report

Report on final software optimisations and summary of the maintenance experience (e.g. installation on the system, bug correction, user feedback).

Collection of software requirements

List of requirements that the WP5 and WP6 software must fulfil, and preliminary specification of the overall software architecture.

Final report

Description of the technical and scientific results of the project.

Application co-design input

Documents requirements of all applications for co-design; includes all data analytics SW requirements, compute, memory & communication performance, footprints, communication patterns, etc.

Benchmarking, evaluation and prediction report

Report detailing the benchmarking results in Tk2.1 and Tk2.2, as well as the final application models and Exascale predictions of Tk2.3 and Tk2.4.

Case study booklet

Success stories and best practices gained from the early access program.

Final outreach activity

Final brochure or project video, or an event or a combination of these. It will be decided during the project which will be deemed most appropriate.

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Publications

DCDB Wintermute: Enabling Online and Holistic Operational Data Analytics on HPC Systems

Author(s): Alessio Netti, Micha Müller, Carla Guillen, Michael Ott, Daniele Tafani, Gence Ozer, Martin Schulz
Published in: Proceedings of the 29th International Symposium on High-Performance Parallel and Distributed Computing, 2020, Page(s) 101-112, ISBN 9781450370523
Publisher: ACM
DOI: 10.1145/3369583.3392674

A Linux Kernel Scheduler Extension for Multi-core Systems

Author(s): Aleix Roca, Samuel Rodriguez, Albert Segura, Kevin Marquet, Vicenc Beltran
Published in: 2019 IEEE 26th International Conference on High Performance Computing, Data, and Analytics (HiPC), 2019, Page(s) 353-362, ISBN 978-1-7281-4535-8
Publisher: IEEE
DOI: 10.1109/hipc.2019.00050

Towards Data-Flow Parallelization for Adaptive Mesh Refinement Applications

Author(s): Kevin Sala, Alejandro Rico, Vicenc Beltran
Published in: 2020 IEEE International Conference on Cluster Computing (CLUSTER), 2020, Page(s) 314-325, ISBN 978-1-7281-6677-3
Publisher: IEEE
DOI: 10.1109/cluster49012.2020.00042

From facility to application sensor data - modular, continuous and holistic monitoring with DCDB

Author(s): Alessio Netti, Micha Müller, Axel Auweter, Carla Guillen, Michael Ott, Daniele Tafani, Martin Schulz
Published in: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2019, Page(s) 1-27, ISBN 9781450362290
Publisher: ACM
DOI: 10.1145/3295500.3356191

Application-Level Differential Checkpointing for HPC Applications with Dynamic Datasets

Author(s): Kai Keller, Leonardo Bautista-Gomez
Published in: 2019 19th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), Larnaca, Cyprus, 2019, Page(s) 52-61, ISBN 978-1-7281-0912-1
Publisher: IEEE
DOI: 10.1109/ccgrid.2019.00015

Supercomputer Evolution at JSC

Author(s): Estela Suarez; Eicker, Norbert; Lippert, Thomas
Published in: Jülich : John von Neumann Institute for Computing, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 49, 1 - 12 (2018)., 20, 2018, Page(s) 1-12, ISBN 978-3-95806-285-6
Publisher: John von Neumann Institute

Radio-Astronomical Imaging with WSClean and Image-Domain Gridding

Author(s): B. Veenboer, S. Van der Tol, A.R. Offringa, J.W. Romein, T.J. Dijkema
Published in: 2020 XXXIIIrd General Assembly and Scientific Symposium of the International Union of Radio Science, 2020
Publisher: IEEE
DOI: 10.23919/ursigass49373.2020.9232218

Visualizing and Interpreting Unsupervised Solar Wind Classifications

Author(s): Amaya, Jorge; Dupuis, Romain; Innocenti, Maria Elena; Lapenta, Giovanni
Published in: Front. Astron. Space Sci., 1, 2020
Publisher: Frontiers Media S.A.
DOI: 10.3389/fspas.2020.553207

Scalable Workflows for Remote Sensing Data Processing with the Deep-Est Modular Supercomputing Architecture

Author(s): Ernir Erlingsson, Gabriele Cavallaro, Helmut Neukirchen, Morris Riedel
Published in: IGARSS 2019 - 2019 IEEE International Geoscience and Remote Sensing Symposium, 2019, Page(s) 5905-5908, ISBN 978-1-5386-9154-0
Publisher: IEEE
DOI: 10.1109/igarss.2019.8898487

On the Applicability of PEBS based Online Memory Access Tracking for Heterogeneous Memory Management at Scale

Author(s): Aleix Roca Nonell, Balazs Gerofi, Leonardo Bautista-Gomez, Dominique Martinet, Vicenç Beltran Querol, and Yutaka Ishikawa
Published in: MCHPC'18: Workshop on Memory Centric High Performance Computing, 2018, 2018, Page(s) 50-57
Publisher: ACM
DOI: 10.1145/3286475.3286477

Facilitating collaboration in high-performance computing projects with an interaction room

Author(s): Matthias Book, Morris Riedel, Helmut Neukirchen, Markus Götz
Published in: Proceedings of the 4th ACM SIGPLAN International Workshop on Software Engineering for Parallel Systems - SEPS 2017, 2017, Page(s) 46-47, ISBN 9781-450355179
Publisher: ACM Press
DOI: 10.1145/3141865.3142467

Supporting Software Engineering Practices in the Development of Data-Intensive HPC Applications with the JuML Framework

Author(s): Markus Götz, Matthias Book, Christian Bodenstein, Morris Riedel
Published in: Proceedings of the 1st International Workshop on Software Engineering for High Performance Computing in Computational and Data-enabled Science & Engineering - SE-CoDeSE'17, 2017, Page(s) 1-8, ISBN 9781-450351355
Publisher: ACM Press
DOI: 10.1145/3144763.3144765

Supercomputing Evolution at JSC

Author(s): Suarez, Estela; Eicker, Norbert; Lippert, Thomas
Published in: Jülich : John von Neumann Institute for Computing, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series, 49, 1 - 12 (2018)., 1, 2018
Publisher: John von Neumann Institute for Computing

Scaling DBSCAN towards exascale computing for clustering of big data sets

Author(s): E. Erlingsson, G. Cavallaro, M. Riedel, H. Neukirchen
Published in: Abstract at European Geosciences Union (EGU) General Assembly 2018. Geophysical Research Abstracts Vol. 20, 2018
Publisher: Copernicus Publications

PowerSensor 2: A Fast Power Measurement Tool

Author(s): John W. Romein, Bram Veenboer
Published in: 2018 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), 2018, Page(s) 111-113, ISBN 978-1-5386-5010-3
Publisher: IEEE
DOI: 10.1109/ISPASS.2018.00020

The Influence of Sampling Methods on Pixel-Wise Hyperspectral Image Classification with 3D Convolutional Neural Networks

Author(s): Julius Lange, Gabriele Cavallaro, Markus Gotz, Ernir Erlingsson, Morris Riedel
Published in: IGARSS 2018 - 2018 IEEE International Geoscience and Remote Sensing Symposium, 2018, Page(s) 2087-2090, ISBN 978-1-5386-7150-4
Publisher: IEEE
DOI: 10.1109/igarss.2018.8518671

Modular supercomputing design supporting machine learning applications

Author(s): E. Erlingsson, G. Cavallaro, A. Galonska, M. Riedel, H. Neukirchen
Published in: 2018 41st International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2018, Page(s) 0159-0163, ISBN 978-953-233-095-3
Publisher: IEEE
DOI: 10.23919/MIPRO.2018.8400031

Application Performance on a Cluster-Booster System

Author(s): Anke Kreuzer, Norbert Eicker, Jorge Amaya, Estela Suarez
Published in: 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2018, Page(s) 69-78, ISBN 978-1-5386-5555-9
Publisher: 2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)
DOI: 10.1109/IPDPSW.2018.00019

Scaling Support Vector Machines Towards Exascale Computing for Classification of Large-Scale High-Resolution Remote Sensing Images

Author(s): Ernir Erlingsson, Gabriele Cavallaro, Morris Riedel, Helmut Neukirchen
Published in: IGARSS 2018 - 2018 IEEE International Geoscience and Remote Sensing Symposium, 2018, Page(s) 1792-1795, ISBN 978-1-5386-7150-4
Publisher: IEEE
DOI: 10.1109/IGARSS.2018.8517378

Evaluating SLURM Simulator with Real-Machine SLURM and Vice Versa

Author(s): Ana Jokanovic, Marco D'Amico, Julita Corbalan
Published in: 2018 IEEE/ACM Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), 2018, Page(s) 72-82, ISBN 978-1-7281-0182-8
Publisher: IEEE
DOI: 10.1109/pmbs.2018.8641556

Enhancing Remote Sensing Applications towards Exascalewith the DEEP-EST Modular Supercomputer Architecture

Author(s): Cavallaro, Gabriele; Erlingsson, Ernir; Riedel, Morris; Neukirchen, Helmut
Published in: Phi-week - ESA, Frascati, Italy, 2018-11-12 - 2018-11-16, 1, 2018
Publisher: EASC 2018

The DEEP-ER Project: I/O and Resiliency Extensions for the Cluster-Booster Architecture

Author(s): Anke Kreuzer, Jorge Amaya, Norbert Eicker, Raphael Leger, Estela Suarez
Published in: 2018 IEEE 20th International Conference on High Performance Computing and Communications; IEEE 16th International Conference on Smart City; IEEE 4th International Conference on Data Science and Systems (HPCC/SmartCity/DSS), 2018, Page(s) 109-116, ISBN 978-1-5386-6614-2
Publisher: IEEE
DOI: 10.1109/HPCC/SmartCity/DSS.2018.00046

Evaluating Worksharing Tasks on Distributed Environments

Author(s): Marcos Maronas, Xavier Teruel, J. Mark Bull, Eduard Ayguade, Vicenc Beltran
Published in: 2020 IEEE International Conference on Cluster Computing (CLUSTER), 2020, Page(s) 69-80, ISBN 978-1-7281-6677-3
Publisher: IEEE
DOI: 10.1109/cluster49012.2020.00017

Remote Sensing Data Analytics with the Udocker Container Tool using Multi-GPU Deep Learning Systems

Author(s): Gabriele Cavallaro , Valentin Kozlov , Markus Götz , Morris Riedel
Published in: Proc. of the 2019 conference on Big Data from Space (BiDS’2019), 2019
Publisher: Publications Office of the European Union
DOI: 10.2760/848593

Multi-Scale Convolutional SVM Networks for Multi-Class Classification Problems of Remote Sensing Images

Author(s): Gabriele Cavallaro, Yakoub Bazi, Farid Melgani, Morris Riedel
Published in: IGARSS 2019 - 2019 IEEE International Geoscience and Remote Sensing Symposium, 2019, Page(s) 875-878, ISBN 978-1-5386-9154-0
Publisher: IEEE
DOI: 10.1109/IGARSS.2019.8899831

Worksharing Tasks: An Efficient Way to Exploit Irregular and Fine-Grained Loop Parallelism

Author(s): Marcos Maronas, Kevin Sala, Sergi Mateo, Eduard Ayguade, Vicenc Beltran
Published in: 2019 IEEE 26th International Conference on High Performance Computing, Data, and Analytics (HiPC), 2019, Page(s) 383-394, ISBN 978-1-7281-4535-8
Publisher: IEEE
DOI: 10.1109/HiPC.2019.00053

Enabling exible job scheduling for heterogeneous modular supercomputers

Author(s): Ana Jokanovic, Julita Corbalan
Published in: Advances in Computational Biology Conference (AdvCompBio) 2019, 2019
Publisher: Barcelona Supercomputing Center
DOI: 10.7490/f1000research.1117727.1

Correlation-wise Smoothing: Lightweight Knowledge Extraction for HPC Monitoring Data

Author(s): Netti, Alessio; Tafani, Daniele; Ott, Michael; Schulz, Martin
Published in: 35th IEEE International Parallel & Distributed Processing Symposium, accepted for publication, to be published, 2021
Publisher: IEEE

Modular Supercomputing Architecture: From Idea to Production

Author(s): Estela Suarez, Norbert Eicker, Thomas Lippert
Published in: Contemporary High Performance Computing - From Petascale toward Exascale, 3, 2019, Page(s) 223-255, ISBN 9781351036863
Publisher: CRC Press
DOI: 10.1201/9781351036863-9

Performance Study of Non-volatile Memories on a High-End Supercomputer

Author(s): Leonardo Bautista Gomez, Kai Keller, Osman Unsal
Published in: High Performance Computing - ISC High Performance 2018 International Workshops, Frankfurt/Main, Germany, June 28, 2018, Revised Selected Papers, 11203, 2018, Page(s) 145-156, ISBN 978-3-030-02464-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-02465-9_10

Introducing the Task-Aware Storage I/O (TASIO) Library

Author(s): Aleix Roca Nonell, Vicenç Beltran Querol, Sergi Mateo Bellido
Published in: OpenMP: Conquering the Full Hardware Spectrum - 15th International Workshop on OpenMP, IWOMP 2019, Auckland, New Zealand, September 11–13, 2019, Proceedings, 11718, 2019, Page(s) 274-288, ISBN 978-3-030-28595-1
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-28596-8_19

Enhancing Resource Management Through Prediction-Based Policies

Author(s): Antoni Navarro, Arthur F. Lorenzon, Eduard Ayguadé, Vicenç Beltran
Published in: Euro-Par 2020: Parallel Processing - 26th International Conference on Parallel and Distributed Computing, Warsaw, Poland, August 24–28, 2020, Proceedings, 12247, 2020, Page(s) 493-509, ISBN 978-3-030-57674-5
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-57675-2_31

Radio-Astronomical Imaging: FPGAs vs GPUs

Author(s): Bram Veenboer, John W. Romein
Published in: Euro-Par 2019: Parallel Processing - 25th International Conference on Parallel and Distributed Computing, Göttingen, Germany, August 26–30, 2019, Proceedings, 11725, 2019, Page(s) 509-521, ISBN 978-3-030-29399-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-29400-7_36

Editorial: Reproducibility and Rigour in Computational Neuroscience

Author(s): Sharon M. Crook, Andrew P. Davison, Robert A. McDougal, Hans Ekkehard Plesser
Published in: Frontiers in Neuroinformatics, 14, 2020, ISSN 1662-5196
Publisher: Frontiers Research Foundation
DOI: 10.3389/fninf.2020.00023

Embedding particle-in-cell simulations in global magnetohydrodynamic simulations of the magnetosphere

Author(s): Raymond J. Walker, Giovanni Lapenta, Jean Berchem, Mostafa El-Alaoui, David Schriver
Published in: Journal of Plasma Physics, 85/1, 2019, ISSN 0022-3778
Publisher: Cambridge University Press
DOI: 10.1017/s0022377819000072

ECsim-CYL: Energy Conserving Semi-Implicit particle in cell simulation in axially symmetric cylindrical coordinates

Author(s): Diego Gonzalez-Herrero, Alfredo Micera, Elisabetta Boella, Jaeyoung Park, Giovanni Lapenta
Published in: Computer Physics Communications, 236, 2019, Page(s) 153-163, ISSN 0010-4655
Publisher: Elsevier BV
DOI: 10.1016/j.cpc.2018.10.026

Efficient Communication in Distributed Simulations of Spiking Neuronal Networks With Gap Junctions

Author(s): Jakob Jordan, Moritz Helias, Markus Diesmann, Susanne Kunkel
Published in: Frontiers in Neuroinformatics, 14, 2020, Page(s) 12, ISSN 1662-5196
Publisher: Frontiers Research Foundation
DOI: 10.3389/fninf.2020.00012

Extending the OpenCHK Model with advanced checkpoint features

Author(s): Marcos Maroñas, Sergi Mateo, Kai Keller, Leonardo Bautista-Gomez, Eduard Ayguadé, Vicenç Beltran
Published in: Future Generation Computer Systems, 112, 2020, Page(s) 738-750, ISSN 0167-739X
Publisher: Elsevier BV
DOI: 10.1016/j.future.2020.06.003

The Scientific Case for Brain Simulations

Author(s): Gaute T. Einevoll, Alain Destexhe, Markus Diesmann, Sonja Grün, Viktor Jirsa, Marc de Kamps, Michele Migliore, Torbjørn V. Ness, Hans E. Plesser, Felix Schürmann
Published in: Neuron, 102/4, 2019, Page(s) 735-744, ISSN 0896-6273
Publisher: Cell Press
DOI: 10.1016/j.neuron.2019.03.027

Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models

Author(s): Robin Pauli, Philipp Weidel, Susanne Kunkel, Abigail Morrison
Published in: Frontiers in Neuroinformatics, 12, 2018, ISSN 1662-5196
Publisher: Frontiers Research Foundation
DOI: 10.3389/fninf.2018.00046

Accelerating Hybrid Monte Carlo simulations of the Hubbard model on the hexagonal lattice

Author(s): Stefan Krieg, Thomas Luu, Johann Ostmeyer, Philippos Papaphilippou, Carsten Urbach
Published in: Computer Physics Communications, 236, 2019, Page(s) 15-25, ISSN 0010-4655
Publisher: Elsevier BV
DOI: 10.1016/j.cpc.2018.10.008

Performance analysis and implementation details of the Energy Conserving Semi-Implicit Method code (ECsim)

Author(s): Diego Gonzalez-Herrero, Elisabetta Boella, Giovanni Lapenta
Published in: Computer Physics Communications, 229, 2018, Page(s) 162-169, ISSN 0010-4655
Publisher: Elsevier BV
DOI: 10.1016/j.cpc.2018.03.020