High Performance Computing in Science and Engineering: 4th International Conference, HPCSE 2019, Karolinka, Czech Republic, May 20–23, 2019, Revised ... (Lecture Notes in Computer Science, 12456)

172 Pages·2021·12.966 MB·English

by  Tomáš Kozubek (editor), Peter Arbenz (editor), Jiří Jaroš (editor), Lubomír Říha (editor), Jakub Šístek (editor), Petr Tichý (editor)

Tomáš Kozubek · Peter Arbenz ·
ˇ
Jiˇrí Jaroš · Lubomír Ríha ·
Jakub Šístek · Petr Tichý (Eds.)
6
5
4
2
1 High Performance Computing

S
C
N in Science and Engineering
L
4th International Conference, HPCSE 2019
Karolinka, Czech Republic, May 20–23, 2019
Revised Selected Papers
Lecture Notes in Computer Science 12456
Founding Editors
Gerhard Goos
Karlsruhe Institute of Technology, Karlsruhe, Germany
Juris Hartmanis
Cornell University, Ithaca, NY, USA
Editorial Board Members
Elisa Bertino
Purdue University, West Lafayette, IN, USA
Wen Gao
Peking University, Beijing, China
Bernhard Steffen
TU Dortmund University, Dortmund, Germany
Gerhard Woeginger
RWTH Aachen, Aachen, Germany
Moti Yung
Columbia University, New York, NY, USA
More information about this subseries at http://www.springer.com/series/7407
áš
Tom Kozubek Peter Arbenz
(cid:129) (cid:129)
ří š í Ří
Ji Jaro Lubom r ha
(cid:129) (cid:129)
Ší ý
Jakub stek Petr Tich (Eds.)
(cid:129)
High Performance Computing
in Science and Engineering
4th International Conference, HPCSE 2019
–
Karolinka, Czech Republic, May 20 23, 2019
Revised Selected Papers
123
Editors
TomášKozubek PeterArbenz
VSB- Technical University of Ostrava ETHZurich
Ostrava-Poruba, Czech Republic Zurich, Switzerland
JiříJaroš Lubomír Říha
BrnoUniversity ofTechnology VSB- Technical University of Ostrava
Brno, Czech Republic Ostrava-Poruba, Czech Republic
JakubŠístek Petr Tichý
Institute of Mathematics of the CAS CharlesUniversity
Prague,Czech Republic Prague,Czech Republic
ISSN 0302-9743 ISSN 1611-3349 (electronic)
Lecture Notesin Computer Science
ISBN 978-3-030-67076-4 ISBN978-3-030-67077-1 (eBook)
https://doi.org/10.1007/978-3-030-67077-1
LNCSSublibrary:SL1–TheoreticalComputerScienceandGeneralIssues
©SpringerNatureSwitzerlandAG2021
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe
material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,
broadcasting, reproduction on microfilms or in any other physical way, and transmission or information
storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynow
knownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication
doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant
protectivelawsandregulationsandthereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookare
believedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditors
give a warranty, expressed or implied, with respect to the material contained herein or for any errors or
omissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaimsin
publishedmapsandinstitutionalaffiliations.
ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG
Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland
Preface
This volume comprises the proceedings of the 4th International Conference on High
Performance Computing in Science and Engineering – HPCSE 2019, which was held
intheHotelSoláňintheheartoftheBeskydyMountains,CzechRepublic,onMay20–
23, 2019. The biennial conference was organized by the IT4Innovations National
Supercomputing Center at VSB - Technical University of Ostrava with the support of
partner institutions: Brno University of Technology, Charles University, Czech
TechnicalUniversityinPrague,InstituteofGeonicsandInstituteofMathematicsofthe
CAS,andCzechNetworkforMathematicsinIndustryeu-maths-in.cz.Theaimwasto
bring together specialists in high performance computing from fields such as applied
mathematics, numerical methods, and parallel computing, toexchange experience and
toinitiatenewresearchcollaborations.Wearegladthatourinvitationwasacceptedby
distinguished experts from world-leading research institutions.
This conference has become an international forum for exchanging ideas among
researchers involved in scientific and parallel computing, including theory and appli-
cations,aswellasappliedandcomputationalmathematics.ThefocusofHPCSE2019
was on models, algorithms, and software tools that facilitate efficient and convenient
utilization of modern parallel and distributed computing architectures, as well as on
large-scale applications.
The members of the Scientific Committee of HPCSE 2019 were Radim Blaheta,
Martin Čermák, Zdeněk Dostál, Jaroslav Hron, Jiří Jaroš, Tomáš Kozubek, Jaroslav
Kruis, Tomáš Oberhuber, Ivan Šimeček, Jakub Šístek, Petr Tichý, and Vít Vondrák.
The invited plenary talks were presented by:
(cid:129) Andrea Bartolini (University of Bologna),
(cid:129) Steffen Börm (Christian-Albrechts-Universität zu Kiel),
(cid:129) Ben T. Cox (University College London),
(cid:129) Dominik Göddeke (University of Stuttgart),
(cid:129) Frédéric Hecht (Université Pierre et Marie Curie),
(cid:129) Jakub Kurzak (University of Tennessee),
(cid:129) Günther Of (Technische Universität Graz),
(cid:129) Daniela di Serafino (University of Campania Luigi Vanvitelli),
(cid:129) Garth Wells (University of Cambridge),
(cid:129) Stefano Zampini (KAUST).
We gratefully acknowledge the support of the Ministry of Education, Youth and
Sports from the National Programme of Sustainability (NPU II) through project
“IT4Innovations excellence in science – LQ1602”.
The HPCSE 2019 conference was a fruitful event, providing interesting lectures,
showcasing new ideas, demonstrating the beauty of applied mathematics, presenting
numericallinearalgebra,optimizationmethods,andhighperformancecomputing,and
starting or strengthening collaborations and friendships.
vi Preface
This meeting attracted about 100 participants from 10 countries. All participants
were invited to submit an original paper to this book of proceedings. We give thanks
forallcontributionsaswellasfortheworkofthereviewers,andhopethatthisvolume
will be useful for readers. The proceedings were edited by Tomáš Kozubek, Peter
Arbenz, Jiří Jaroš, Lubomír Říha, Jakub Šístek, and Petr Tichý.
Finally, we would like to cordially invite readers to participate in the next HPCSE
conference, which is planned to be held at the same place on May 17–20, 2021.
On behalf of the organizers, Tomáš Kozubek.
Tomáš Kozubek
Peter Arbenz
Jiří Jaroš
Lubomír Říha
Jakub Šístek
Petr Tichý
Organization
Conference Chair
Tomáš Kozubek VSB - Technical University of Ostrava,
Czech Republic
Scientific Committee
Radim Blaheta Institute of Geonics of the CAS, Czech Republic
Martin Čermák VSB - Technical University of Ostrava,
Czech Republic
Zdeněk Dostál VSB - Technical University of Ostrava,
Czech Republic
Jaroslav Hron Charles University, Czech Republic
Jiří Jaroš Brno University of Technology, Czech Republic
Tomáš Kozubek VSB - Technical University of Ostrava,
Czech Republic
Jaroslav Kruis CzechTechnicalUniversityinPrague,CzechRepublic
Tomáš Oberhuber CzechTechnicalUniversityinPrague,CzechRepublic
Ivan Šimeček CzechTechnicalUniversityinPrague,CzechRepublic
Jakub Šístek Institute of Mathematics of the CAS, Czech Republic
Petr Tichý Charles University, Czech Republic
Vít Vondrák VSB - Technical University of Ostrava,
Czech Republic
Contents
Thermal Characterization of a Tier0 Datacenter Room in Normal
and Thermal Emergency Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Mohsen Seyedkazemi Ardebili, Carlo Cavazzoni, Luca Benini,
and Andrea Bartolini
Towards Local-Failure Local-Recovery in PDE Frameworks:
The Case of Linear Solvers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Mirco Altenbernd, Nils-Arne Dreier, Christian Engwer,
and Dominik Göddeke
Complexity Analysis of a Fast Directional Matrix-Vector Multiplication . . . . 39
Günther Of and Raphael Watschinger
Fast Large-Scale Boundary Element Algorithms . . . . . . . . . . . . . . . . . . . . . 60
Steffen Börm
Solving Large-Scale Interior Eigenvalue Problems to Investigate
the Vibrational Properties of the Boson Peak Regime
in Amorphous Materials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Giuseppe Accaputo, Peter M. Derlet, and Peter Arbenz
Performance Evaluation of Pseudospectral Ultrasound Simulations
on a Cluster of Xeon Phi Accelerators. . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Filip Vaverka, Bradley E. Treeby, and Jiri Jaros
Estimation of Execution Parameters for k-Wave Simulations . . . . . . . . . . . . 116
Marta Jaros, Tomas Sasak, Bradley E. Treeby, and Jiri Jaros
Analysis and Visualization of the Dynamic Behavior of HPC Applications. . . 135
Ondrej Vysocky, Ivo Peterek, Martin Beseda, Matej Spetko,
David Ulcak, and Lubomir Riha
A Convenient Graph Connectedness for Digital Imagery . . . . . . . . . . . . . . . 150
Josef Šlapal
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Thermal Characterization of a Tier0
Datacenter Room in Normal and Thermal
Emergency Conditions
B
Mohsen Seyedkazemi Ardebili1( ) , Carlo Cavazzoni2 , Luca Benini1,3 ,
and Andrea Bartolini1
1 Universit´a degli Studi di Bologna, Viale Risorgimento, 2, 40136 Bologna, Italy
{mohsen.seyedkazemi,luca.benini,a.bartolini}@unibo.it
2 CINECA, Via Magnanelli 6/3, Casalecchio di Reno, 40033 Bologna, Italy
[email protected]
3 Eidgen¨ossische Technische Hochschule Zu¨rich, Gloriastrasse 35,
8092 Zu¨rich, Switzerland
[email protected]
https://ee.ethz.ch/
https://www.dei.unibo.it/
https://www.cineca.it/
Abstract. Datacenters are at the heart of the AI, Industry 4.0 and
cloud revolution. A datacenter contains a large number of computing
nodeshostedinalargetemperature-controlledroom.Duetotheincreas-
ing total power and power density of computing nodes, the overall dat-
acenter compute capacity is often capped by peak power consumption
andtemperaturebottlenecks.Topreservethehomogeneousperformance
assumptionbetweenallthenodes,complexcoolingsolutionarerequired,
but they might not be sufficient. In this work, we analysed and charac-
terisedthethermalpropertiesofaTier0datacenterdeployingadvanced
hybridcoolingtechnologies:specifically,westudiedthespatialandtem-
poral heterogeneity during production and cooling emergency hazards.
This paper gives first quantitative evidence of thermal bottlenecks in
real-life production workload, showing the presence of significant spa-
tial thermal heterogeneity which could be exploited by thermal-aware
job scheduling and datacenter-room run-time workload adaptation and
distribution.
· ·
Keywords: HPC Thermal characterization Power consumption
1 Introduction and Related Works
Withthegrowthofthecomputingdemandfromabroadsetofsocietal,industrial
and science application, datacenter have become a key component of the whole
This work has been partially supported by the EU H2020 ICT/2018 project IoTwins
(g.a. 857191).
(cid:2)c SpringerNatureSwitzerlandAG2021
T.Kozubeketal.(Eds.):HPCSE2019,LNCS12456,pp.1–16,2021.
https://doi.org/10.1007/978-3-030-67077-1_1