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SHAPE White Papers

Overview of the White Papers produced by the SHAPE Projects.


Authors: B. Ciroua*, D. Fernandezb, G. Hautreuxb, D. Woutersb
a Centre Informatique National de l’Enseignament Supérieur (CINES), 950 rue Stt Priest, 34097 Montpellier, France
b Cybeletech, 2 rue de la Piquetterie, 91680 Bruyères le Châtel, France

Abstract: Breeding a new variety is a long process that requires a decade and thousands of experimental trials in fields so as to select the most robust and efficient traits. Some steps in the process of plant selection could be conducted in-silico to reduce the duration and development cost of a new variety.
The plant growth model used in numerical simulations must be calibrated with plant phenotypes data. To define
the optimal experimental protocol to be followed for calibrating the model, the model is run with a genetic
algorithm.
Optimisation of the plant growth model enabled to reduce its computing time by a factor five. Performances of
the whole application were highly improved by implementing a master-slave approach to the optimisation of the
evolutionary algorithm. These performances are function of the number of protocols and realisations considered.

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Authors: Ubaldo Cellaa*, Francesco Salvadoreb, Raffaele Ponzinib
a Design Methods(www.designmethods.aero)
b CINECA

Abstract: An optimisation procedure for catamarans sail plan and appendages is descripted. The method integrates a parametric CAD model, an automatic computational domain generator and a Velocity Prediction Program (VPP) based on a combination of sail RANS computations and analytical models. The sailing speed and course angle are obtained, with an iterative process, solving the forces and moment equilibrium system of equations. Hull forces analytical formulations were developed and tuned against a matrix of CFD solutions. The appendages aerodynamic polars are estimated applying preliminary design criteria from aerospace literature. The procedure permits to find the combination of appendages configuration, rudders setting, sail planform, shape and trim that maximise the VMG (Velocity Made Good). Within the SHAPE programme, the possibility to implement the procedure using Open-Source software is investigated.

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Authors: T. Loosea*, M. Bernreutherb, B. Große-Wöhrmannb, J. Hertzerb, U. Göhner c
a aIngenieurbüro Tobias Loose, Herdweg 13, D-75045 Wössingen, www.tl-ing.eu
b Universität Stuttgart, Höchstleistungsrechenzentrum, Nobelstraße 19, D-70569 Stuttgart, www.hlrs.de
c DYNAmore Gesellschaft für FEM Ingenieurdienstleistungen mbh, Industriestraße 2, D-70565 Stuttgart, www.dynamore.de

Abstract: In this paper the results of the PRACE SHAPE project “HPC Welding” are presented. During this project, a welding structure analysis with the parallel solvers of the LS-DYNA code was performed by Ingenieurbüro Tobias Loose on the Cray XC40 “Hazel Hen” at the High Performance Computing Center (HLRS) in Stuttgart. A variety of test cases relevant for industrial applications have been set up with DynaWeld, a welding and heat treatment pre-processor for LS-DYNA, and run on different numbers of compute cores. The results show that the implicit thermal and mechanical solver scales up to 48 cores depending on the particular test case due to unbalanced workload. The explicit mechanical solver was tested up to 4080 cores with significant scaling. As we know, it was the first time that a welding simulation with the LS-DYNA explicit solver was performed on 4080 cores.

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Authors: L. Fallettia*, S. Theronda, Y. Moisanb, Y. Kervellab
a IDRIS – Orsay, France
b Open Ocean, France

Abstract: Open Ocean is a French SME company which develops innovative on-line solutions to help plan and manage offshore developments. They conceived an oceanographic data study tool which computes and formats data (Pre-Processing and Processing) and which provides relevant oceanographic information to industrial marine companies (Post-Processing) through a web interface. But the “time-to-solution” of this post-processing step is too long and hence not compatible with industrial use. Therefore, the goal of this SHAPE project is to improve post-processing by optimising a parallelized Python program of Open Ocean which processes and computes statistics (e.g. wind speed) on big datasets. To carry this out, engineers of Open Ocean and IDRIS worked together to optimise this program by using resources available in a national supercomputing centre: high performance parallel machine and parallel file system (GPFS, 100 GB/S bandwidth). This paper describes the parallelisation process implemented by Open Ocean and its porting on the Ada machine (IBM cluster of Intel E5-4650 processors, 332 compute nodes) at IDRIS. It also covers performance testing and identification of the bottleneck in the execution.

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Authors: Haysam Teliba1, Marco Cisterninoa, Vittorio Ruggierob, Florian Bernardc
a Optimad Engineering srl.,
b Cineca
c Inria

Abstract: KOPPA (Kinetic Octree Parallel PolyAtomic) is a parallel numerical code for the simulation of rarefied gas dynamics. It is based on a library named PABLO (PArallel Balanced Linear Octree) used to manage octree grids in parallel. The main issue with such numerical codes is the very high execution time which can become prohibitive for some industrial applications. Thanks to the SHAPE project, important improvements have been achieved with respect to execution time and scalability. In particular, some parts of the code have been reimplemented to suit better a MIC (Multi Integrated Cores) architecture. So far, the computational time requirements have been decreased by a factor of almost 8 and a good scalability has been obtained up to 64 processors against 16 initially.

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Authors: J.C. Cajasa*, G. Houzeauxa, D.J. Yanezb, M. Mier-Torrecillaa
a Barcelona Supercomputing Center – Centro Nacional de Supercomputacion, Spain,
b Vortex Bladeless S.L., Spain

Abstract: Vortex-Bladeless is a Spanish SME whose objective is to develop a new concept of wind turbine without blades called Vortex or vorticity wind turbine. This design represents a new paradigm in wind energy and aims to eliminate or reduce many of the existing problems in conventional generators. Due to the significant difference in the project concept, its scope is different from conventional wind turbines. It is particularly suitable for offshore configuration and it could be exploited in wind farms and in environments usually closed to existing ones due to the presence of high intensity winds. The device is composed of a single structural component, and given its morphological simplicity, its manufacturing, transport, storage and installation has clear advantages. The new wind turbine design has no bearings, gears, etcetera, so the maintenance requirements could be drastically reduced and their lifespan is expected to be higher than traditional wind turbines. It is clear that the proposed device is of prime interest, and that scientific investigation of the response of this wind energy generator under different operation scenarios is highly desirable. Thus, the objective of this SHAPE project is to develop the needed tools to simulate Fluid-Structure Interaction (FSI) problems and to reproduce the experimental results for scaled models of the Vortex-Bladeless device. In order to do so the Alya code, developed at the Barcelona Supercomputing Center, is adapted to perform the Fluid-Structure Interaction (FSI) problem simulation. The obtained numerical results match satisfactorily with the experimental results reported.

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Authors: S. Dyena*, A. Lukowskia, R. Ponzinib
a aHydros Innovation, Switzerland
b CINECA, Italy

Abstract: Hydros is an Engineering & Research Swiss company founded in 2007 with several patented designs in the field of marine and sailing yachting. In recent years Hydros is exploring new market segments such as yachts and super-yachts hull design. The usage of HPC resources and open-source softwares can be a valuable tool in the massive shape design optimizations usually performed by Hydros. The main scope of the proposed SHAPE pilot was therefore to evaluate the feasibility of automatic optimal hull design on HPC infrastructure and the impact of such a workflow on the day-by-day work of Hydros personnel. To accomplish this task the project was subdivided into a set of steps including a preliminary validation of a 2DoF CFD analysis of an industrial hull design using open-source code, the scalability test of commercial and open-source CFD code for hull 2DoF modelling, the coupling of the CFD result into an existing CAD modification and optimization loop, and finally the running of a complete optimization loop for an industrial hull design using open-source code on the HPC platform and usability evaluation of the solution provided.

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Authors: Isabella Mazzaa, Ahmet Duranb, Yakup Hundurc, Cristiano Persia, Andrea Santoroa, Mehmet Tuncelb
a Ergolines s.r.l., Area Science Park, Padriciano 99, 34016, Trieste, Italy
b Istanbul Technical University (ITU), Mathematical Engineering, 34469 Sariyer, Istanbul, Turkey.
c Istanbul Technical University (ITU), Physical Engineering, 34469 Sariyer, Istanbul,.

Abstract: Ergolines, an Italian SME expert in the design of electromagnetic stirrers for metal casting, and the project partners at ITU collaborated in a European research project under the EU’s Horizon 2020 Research and Innovation Programme, in particular under the SME HPC Adoption Programme in Europe (SHAPE), organized within the PRACE Research Infrastructure. Custom codes were developed for HPC-based magnetohydrodynamics (MHD) simulations, enabling the design of a dedicated electromagnetic stirrer (EMS) for the electric arc furnaces (EAF). We performed parallel simulations using an OpenFOAM solver and other related programs on IBM-FERMI (a PRACE Tier-0 system) at CINECA, Italy. The fluid-dynamics of liquid steel within the EAF under the effect of electromagnetic stirring has been studied under different simulation parameters.

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Authors: M. Rabitob, C. Arlandinia, I. Spissoa, A. Vannia, P. Cavalloa
a CINECA – Centro di Supercalcolo – Consorzio Interuniversitario
b AMET s.r.l.

Abstract:Fuel consumption issues are currently forcing car manufacturers to increase the use of lightweight
materials in the development of new vehicles. Among those materials, composites are the most
interesting solution. Unfortunately, they show a spread in performance characteristics due both to the
manufacturing process and to the material providers, thus limiting the use of this material to niche
productions. This issue could be solved once a more robust design is in place, taking into account the
scattering of material characteristics when evaluating global performances. This document describes
the work done in the framework of the PRACE SHAPE pilot experiments, aiming to develop with the
help of a HPC approach a new robust methodology (where a robust approach means a statistical one,
compared to the old deterministic approach) to assess the behavior of composite materials with respect
to their resistance to impact load cases, which usually drive vehicle design.

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Authors: Daniele Buccia,*, Gianni Tacciolia, Claudio Arlandinib, Alessandro Chiarinic
a Lapcos scrl, via Confine 2310 41058 Vignola (MO)
b Cineca, via Magnanelli 6/3, 40033 Casalecchio di Reno (BO)
c SCS srl, via Parini 1, 40033 Casalecchio di Reno (BO)

Abstract: The goal of this pilot project is the implementation on a HPC platform a software package we developed for the automation of an analysis workflow based on computational fluid dynamics (CFD) simulations of centrifugal water pumps. This software can compute the
performance curve for pump head (meters) versus flow rate (liters/min). The tool features a rapid virtual test bench for the performances of
new pump designs before manufacturing an actual prototype. CFD analysis was carried out using the open source application OpenFOAM.
The exploitation of the HPC platform and the good scalability of the OpenFOAM software are a key factor in reducing the time to market of
new designs.

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Authors:
R. Eisenschmida*, B. Groe-Wohrmannb
aOPTIMA pharma GmbH, Otto-Hahn-Strasse 1, 74523 Schwabisch Hall, Germany
bHigh Performance Computing Center (HLRS), Nobelstr. 19, 70569 Stuttgart, Germany

Abstract:
In this white paper, the main results of the SHAPE pilot project Enhanced airflow simulations around filling machines in clean rooms are presented. During this project on the Tier-0 system Cray XE6 Hermit at HLRS, Germany, the open source CFD software package OpenFOAM v2.2.2 was utilized to run simulations meeting the requirements of industrial production. Besides testing different turbulence models, emphasis was placed on parallel mesh generation with snappyHexMesh and the decomposition and reconstruction of large meshes with more than 10 million cells.
Furthermore, the cooperation between PRACE and the SME OPTIMA pharma GmbH is described, and a report
on the benefits for the SME, the lessons learned and the future activities is added.

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Authors:
Tristan Cabela, Gabriel Hautreuxa, Eric Boyera, Simon Wongb, Nicolas Mignereyc, Xiangwu Lud, Paul Walshd

aCentre Informatique National de l’Enseignement Superieur, 950, rue de Saint Priest, 34097 Montpellier Cedex 5, France.

bIrish Centre for High-End Computing, 7/F Tower Blg., Trinity Technology & Enterprise Campus, Grand Canal Quay, Dublin 2, Ireland.

cGrand Equipement National de Calcul Intensif, 12, rue de l’Eglise, 75015 Paris, France.

dNSilico Lifescience Ltd., Melbourne Building, CIT Campus, Bishopstown, Cork City, Ireland.

Abstract:
NSilico is an Irish based SME that develops software for the life sciences sector, providing bioinformatics and medical informatics systems to a range of clients. One of the major challenges that their users face is the exponential growth of high-throughput genomic sequence data and the associated computational demands to process such data in a fast and efficient manner. Genomic sequences contain gigabytes of nucleotide data that require detailed comparison with similar sequences in order to determine the nature of functional, structural and evolutionary relationships. In this regard NSilico has been working with computational experts from CINES (France) and ICHEC (Ireland) under the PRACE SHAPE programme to address a key problem that is the rapid alignment of short DNA sequences to reference genomes by deploying the Smith-Waterman algorithm on an
emerging many-core technology, the Intel Xeon Phi co-processor. This white paper will discuss some of the parallelisation and optimisation strategies adopted to achieve performance improvements of the algorithm keeping in mind both existing and future versions of the hardware. The outcome has been an extremely successful collaboration between PRACE and NSilico, resulting in an implementation of the algorithm that can be readily deployed to realise significant performance gains from the next generation of many-core hardware.

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Authors:
Lilit Axnera,b, Jing Gonga,b, Alessandro Chiarinic, Luigi Mascellarod

aPDC-HPC, KTH Royal Institute of Technology, Stockholm, SE-10044, Sweden

bThe Swedish e-Science Center (SeRC), KTH Royal Institute of Technology, Stockholm, SE-10044, Sweden

cSuper Computing Solutions, CINECA, Bologna, 40033, Italy

dMonotricat, Via Fosso della Castelluccia 146/22, Roma, 00134, Italy

Abstract:
In the project we conduct a whole hull simulation of a ship, (including mesh generation of complex geometries,
efficient solvers with various turbulent modelling and optimized parameters as well as visualization), along with
a performance analysis for the simulation. This project makes it possible for Monotricat to take advantage of
HPC-enabled simulation tools and potentially replace the traditional methods.

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Authors:
Herbert Owena*, Patricia Izaguirreb, Gonzalo Kouyoumdjianb and Mariano Vazqueza

aBarcelona Supercomputing Center

bJuan Yacht Design

Abstract:
The objective of this project is to implement LES turbulence models outside the academic world to simulate flow
around sailsIto replace RANS modelsIthatIare the standard in the industry. The implementation and testing in the
finite code ALYA is done by the Barcelona Supercomputing Center so that Juan Yatch Design SL (JYD) can
appreciate the advantages of using a LES formulation for their problem. The obtained results show that LES can
provide significant advantages over RANS simulation] at least for the cases we have studied. There is a
significant difference in the predicted forces that can be related to the fact that RANS can not accurately capture
two vortices created at the top and bottom of the Genoa sail.

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Authors:
Jose Maria Tamayoaa, Pascal de Resseguiera

aENTARES Engineering – Nexio Group, 48 rue Rene Sentenac, 31300 TOULOUSE – FRANCE

Abstract:
We have started the extension of the electromagnetic software CAPITOLE developed at ENTARES Engineering to HPC machines. This has been possible with the aid of the SHAPE pilot project, which has provided us with some expertise and computation hours at Marenostrum III. Two numerical methods have been addressed to solve the resulting dense MoM linear system, MSCBD and MLACA. A new implementation based on asynchronous tasks has been performed for the direct method MSCBD. Dependencies between tasks need to be well defined before moving to a runtime scheduling such as STARPU. As for the iterative method MLACA, a hybrid MPI-OpenMP parallelization has been done with excellent results. So far, electromagnetic models up to 6 Million unknowns have been properly solved.

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Authors:
William Edwardsa, David Findlaya, David Scottb, Paul Grahamb

aAlbatern Ltd.

bEPCC

Abstract:
Albatern develop novel interconnected offshore marine renewable energy devices. The goal of this SHAPE
project was to begin the development of a physics code capable of simulating a large scale Wavenet array (100
or more devices) using HPC technology to extensively parallelise the solution. The simulation capability is
intended to build on Albatern’s in house modelling expertise, allowing the prototyping of arrays that are
currently not possible to simulate due to their scale. Computer visualisation and power prediction of large scale
arrays are also vital to the success of Albatern’s efforts to continue investment in the technology. To facilitate
development, the project was split into an algorithm development task and a HPC implementation task. The
completed HPC simulation method will capture fundamental dynamic phenomena associated with arrays of
wave energy devices while providing a time and cost effective development technology.

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Autjors:
Sebastien Eggenspieler, Guillaume Vincke, Pierre Leveau

Audionamix

Abstract:
The source separation technology developed by Audionamix requires a significant amount of computation. To increase the speed of the technology, several High Performance Computing libraries for linear algebra have been benchmarked with two applications: a simple matrix multiplication and a Non-Negative Matrix Factorization.
The benchmarked libraries were Eigen, Armadillo, MKL and the GPU library Magma. The benchmark returned that for both applications the GPU-based solution performed better than the other solutions. But among CPUbased solutions, Eigen performed better on a complex task than MKL. Thus, making the Magma library as an Eigen back-end seems to have a good potential for HPC-based linear algebra, since this solution would benefit at the same time from the GPU-accelerated computation of Magma and from Eigen’s optimized data transfer.

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Authors:
R. Ponzinia, A. Penzaa, R. Vadorib, B. Puddub

aCINECA, SCAI Department – (ITALY)

bThesan srl – (ITALY)

Abstract:
This work conducted in the field of the PRACE’ SHAPE pilots deals with the optimization of a volumetric machine. The machine is under active development, and a prototype is already working and fully monitored in an experimental mock-loop setup. This prototype operates under controlled conditions on a workbench, giving as an output the efficiency of the machine itself. The main goal is to obtain an increased efficiency through the design and realization of the moving chambers in which fluid flows. In order to obtain such a task, an extensive CFD modelling and simulation is required to perform virtual tests on different design solutions to measure the physical quantities assessing the performance of a given geometry. The final goal is to design a better geometry of the different components, mainly the supply and exhaust chambers, cutting down time and resources needed to realize a physical prototype and to limit the physical realization only on a single geometry of choice. The CFD modelling should allow then, through scientific visualization paradigms and quantifications, to perform a detailed characterization of the fluid dynamics patterns present within the prototype and to identify the main geometrical parameters able to drive the optimal configuration. High Performance Computing facilities and Open-Source tools, such as OpenFOAM, are therefore of capital interest to handle the complex physical model under consideration and to perform a sufficient amount of design configuration analysis.

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