High Performance Computer Applications. 6th International Conference, ISUM 2015

575 Pages·2016·172.296 MB·English

by  Isidoro Gitler and Jaime Klapp

Isidoro Gitler
Jaime Klapp (Eds.)
Communications in Computer and Information Science 595
High Performance
Computer Applications
6th International Conference, ISUM 2015
Mexico City, Mexico, March 9–13, 2015
Revised Selected Papers
123
Communications
in Computer and Information Science 595
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Isidoro Gitler Jaime Klapp (Eds.)
(cid:129)
High Performance
Computer Applications
6th International Conference, ISUM 2015
–
Mexico City, Mexico, March 9 13, 2015
Revised Selected Papers
123
Editors
Isidoro Gitler Jaime Klapp
CINVESTAV-IPN Instituto Nacional deInvestigaciones
ABACUSCentrodeMatemáticasAplicadas Nucleares
y Cómputo deAlto Rendimiento LaMarquesa
LaMarquesa Mexico
Mexico
ISSN 1865-0929 ISSN 1865-0937 (electronic)
Communications inComputer andInformationScience
ISBN 978-3-319-32242-1 ISBN978-3-319-32243-8 (eBook)
DOI 10.1007/978-3-319-32243-8
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Preface
Supercomputingisrapidlybeingrecognizedasmorethananessentialtoolandinstrument
for contemporary science and technology. It has turned out to be, together with the
development of basic theory and experimentation, the third crucial pillar for the
improvement of our understanding of nature, the analysis of society, and technological
advancement. Nowadays, current research in applied mathematics, physics, biology,
engineering, medicine, and environmental sciences relies more and more on supercom-
puting, allowing us to expand basic research and experimentation in areas such as
astrophysics,cosmology,fluiddynamics,elementaryparticlephysics,medicine,andlife
sciences. Supercomputing has proven to be equally essential for developing and under-
standingawiderangeofadvancedscienceandtechnologytopicsthataredirectlyrelated
toourdailylives,includingscientificglobalwarmingforecasting,simulationsofnatural
disasters that help minimize the damage from events such as earthquakes, tsunamis,
torrentialrains,andtyphoonsamongothers.Otherareasbenefitingfromsupercomputing
aregenomeanalysisforgenetherapyandproteinanalysisfordrugdesign,thedevelop-
ment of new devices and materials, car crash simulations, jet engine design, and many
more. High-performance computing (HPC) enables the design of models and running
computersimulationsofphenomenabeforepassingthroughanexperimentalphase,with
greateconomicsavings,butmoreimportantlyallowingustoprovideresultswithindays
orweekswhenmonthsorevenyearswererequiredinthepast.
Technologytodayismorethancomputers;modernapplicationscombinenetworks,
visualization, data storage, data mining, remote instruments, sensors, supercomputers,
servers, laptops, etc. Science is increasingly driven by data (large and small). Data
come from everywhere: scientific instruments, experiments, sensors, new devices, and
are used by everyone: scientists, technologists, consumers, educators, and the general
public.Wefindstrongparallelsbetweengenomicstodayandastronomy20yearsago,
similarities between turbulence/CFD, N-body, ocean circulation, and material science,
and on the future exascale everything will be a big data problem. Progress in super-
computing has become an everyday challenge for human endeavors.
The6thInternationalConferenceonSupercomputinginMexico—ISUM2015—
washeldinMexicoCity,duringMarch9–13,2015.Theorganizationwasajointeffort
of various research institutions and universities in Mexico City and the State of
Mexico: the Centro de Investigación y Estudios Avanzados (CINVESTAV), the
Universidad Nacional Autónoma de México (UNAM), the Universidad Autónoma
Metropolitana (UAM), the Instituto Politécnico Nacional (IPN), the Instituto Nacional
deInvestigacionesNucleares(ININ),theUniversidadAutónomadelEstadodeMéxico
(UAEMEX),theCorporaciónUniversitariaparaelDesarrollodelInternet(CUDI),and
the Consejo Nacional de Ciencia y Tecnología (CONACYT).
Building on the success of the five previous ISUM Meetings, the 2015 edition was
heldinMexicoCity,wheremostresearchcenters,universities,enterprises,government
agencies, and businesses in the country are found. This is the most important event in
VI Preface
Mexico organized to discuss progress, problems, and challenges at a national and
internationallevelregardingthefutureofsupercomputing.TheobjectivesofISUM,in
its various editions, have been about upgrading technology and information exchange
amongleadersofmajorprojects(bothdomesticandforeign),linkingactionscapableof
enhancingexistinginfrastructure,andincreasingthenumberofpeopletrainedinHPC.
The main objective of the 2015 ISUM edition was to make the conference a
world-classforumthroughtheexchangeanddisseminationofnewideas,research,and
expertiseinHPC.TheISUMConferenceisorganizedeveryyearoveraperiodoffive
days. During these days, it features internationally and nationally renowned speakers
from both academia and industry, concurrent sessions holding frontier research and
new ideas in both scientific and industrial applications, as well as poster sessions,
workshops (keeping in mind the importance of training human resources), and dis-
cussion panels on key issues in the future of HPC. The ISUM Conference also orga-
nizes an exhibition floor and an exhibitor’s forum where attendees can see and learn
about the latest innovations in HPC, hardware, software, applications, networking,
storage, and related technologies available in distinct fields of the supercomputing
industry. The exhibition attracted groups of scientists, researchers, department man-
agers, laboratory directors, decision makers, and vendors from all corners of the HPC
community and networking industry involved in the HPC development in Mexico.
ISUM 2015 was attended by roughly 350 participants; among them, a considerable
numberwereresearchers,academics,engineers, graduate,andundergraduate students.
ISUM2015cameacrosswithnewconditionsfortheHPCenvironmentinMexico.
NewlaboratoriesforHPCareupandworking.Furthermore,Mexicoisnowbackinthe
Top 500 list of the 500 most powerful supercomputers in the world. The ISUM 2015
conference was hosted by ABACUS, the recently created Centro de Matemáticas
Aplicadas y Cómputo de Alto Rendimiento (Centre for Applied Mathematics and
High-Performance Computing) of CINVESTAV, which from early 2015 has hosted
one of the largest supercomputers in Latin America, where scientists and engineers in
Mexicoandothercountriesareabletodevelopcomputationalprojectsthatrequirevery
large HPC facilities.
ItisworthnotingthatMexicohassignificantexperienceintheuseofsupercomputers,
beginning in 1991, when UNAM installed a Cray YMP supercomputer. Afterwards,
Mexico appeared in the Top 500 supercomputing list several times: the case of the oil
industry(Top83,Top84,andTop85inthelistofNovember2003).Afewyearslater,
UNAM and UAM placed computers in slots 126 (2006) and 225 (2008), respectively.
OtheroutstandingprojectsinMexicoaretheNationalLaboratoryforHigh-Performance
Computing in Mexico City (UNAM-UAM-CINVESTAV), the National Supercomput-
ingCenterofSanLuisPotosiwithintheInstitutoPotosinodeInvestigaciónCientíficay
Tecnológica (IPICYT), the Grids National Laboratory, the National Supercomputing
Laboratory of the Southeast, and ABACUS-CINVESTAV, which recently placed its
supercomputer ABACUS-I in the 255 slot of the top 500 list of June 2015.
Although we have a platform and experience in supercomputing, it is still very
scarce for the needs of a country like Mexico. Hence the importance of ISUM 2015,
where we had the opportunity to discuss the currently installed platforms and defined
some of the possible growth policies regarding the acquisition and use of these
technologies.
Preface VII
The topics of interest included, but were not limited to: use of high-performance
computingsystemstosolvecomplexproblemsinacademicandscientificresearchfields,
applications for science and engineering, scientific visualization, simulation and model-
ing, parallel processing, algorithms and techniques, GPU, Xeon Phi and other accelera-
tors, cluster, grid, and cloud computing, tools and environments for high-performance
system engineering, software tools, programming tools, virtualization, architectures,
component technologies, infrastructure, emerging and new technologies for HPC, big
data, advance networking, petascale/exascale technologies, high-performance technical
and business computing (HPTC/HPBC), energy, cooling/green computing, resource
provisioningandoptimization,HPCinhealth,education,andgovernment,HPCfortheoil
andgasindustry,andinnovationanddevelopmentofHPCtechnologiesinMexico.
The plenary lectures were given by directors and researchers from major super-
computing centers: “Words of Data Science in the Presence of Heterogeneous Com-
puting Architectures” by Ilkay Altintas, San Diego Supercomputer Center (SDSC),
USA,“TheStateoftheArtin3DSeismicImaging”byJoséM.CelaEspín,Barcelona
SupercomputingCenter(BSC),Spain,“TamingBigData”byIanFoster,Universityof
Chicago,USA,“EnergyEfficiencyinEmbeddedSystemDesign”byJeanLucGaudiot,
UniversityofCalifornia–Irvine,USA,“TheFutureoftheMessage-PassingInterface”
by William Gropp, University of Illinois Urbana-Champaign, USA, “HPC in Japan:
More in Application and Utilized in Production Design in Industries” by Ryutaro
Himeno, Advanced Center for Computing and Communication (ACCC), RIKEN,
Japan, “Supercomputing for the European Human Brain Project” by Thomas Lippert,
Forschungszentrum Jülich, Germany, “Towards Exascale Machines” by Philippe Oli-
vier Alexandre Navaux, Federal University of Rio Grande do Sul, Brazil, “The
Data-Enabled Revolution in Science and Society: A Need for (Inter)National Data
Services and Policies” by Edward Seidel, National Center for Supercomputing
Applications, USA, “Runtime Aware Architectures” by Mateo Valero, Barcelona
Supercomputing Centre (BSC), Barcelona, Spain, “Efficiency of Exascale Supercom-
puter Centers” by Vladimir Voevodin, Moscow State University, Russia, and “The
XSEDEExtendedCollaborativeSupportProgram:3YearsofHighlightsandLessons”
by Nancy Wilkins Diehr, San Diego Supercomputing Center, USA.
ISUM 2015 also had eight technological plenary lectures: “Addressing Challenges
of Exascale Systems Usability” by Lim Goh, Silicon Graphics, “Programmability for
HPCIstheKey”byJamesReinders,IntelCorporation,“InterconnectYourFuture”by
Scot Schultz, Mellanox, “Technologies, Cloud and HPC Systems and Solutions” by
Robert Anderson, Seagate, “Transformational technologies of the new style of IT”
by Javier Flores, HP, “Trends in Processing and Storage Solutions” by Guillermo
Sandoval García, CADGRAFICS, “Benefits of the Cloud to Virtualize HPC Envi-
ronments” by Eduardo Marin Grijalva, VMware, and “RHEL and Supercomputing.
The Value of Community” by Rolando Cedillo, RedHat.
In addition to the plenary and technological lectures, over 100 contributions were
presented in oral parallel sessions. A very important activity during ISUM 2015 were
the10workshopsoffered:(1)IntroductorycoursetoparallelcomputingwithMPIand
CUDA, Frédéic Massets, UNAM; (2) A Practical Introduction to Numerical Hydro-
dynamics,AlejandroEsquivel,ICN-UNAM;(3)CentralizedHPCClusterManagement
with CFEngine, Eduardo Ortega and Yolanda Flores, DGTIC-UNAM; (4) Distributed
VIII Preface
High-Performance Scientific Computing, Sergio Nesmachnow, Universidad de la
República, Uruguay; (5) Management of NWChem in HPC Infrastructures, Marcos
RiveraAlmazo,UAM-I;(6)ParallelProgrammingwithIntelCluster StudioXE2013,
Carlos Antonio Sánchez Sevilla, UAM-I; (7) Building a Lustre Storage System, Luis
Arturo Nuñez Pablo, UAM-I; (8) HPC Applications Development assisted by Eclipse
for Parallel Application Developers, Apolinar Martínez Melchor, UAM-I; (9) Under-
standing Performance in Modern High-Performance Computers, Irving Álvarez, Julio
César Clemente, José Luis Gordillo and Leobardo Itehua, DGTIC-UNAM;
(10) Development and Visualization Training Using CUDA, Carlos Jaime Barrios
Hernández, Industrial University of Santander, Colombia.
This book contains selected contributions presented during the ISUM 2015 con-
ferenceandincludesplenaryandothercontributions.Thebookcontainsthreeparts.In
Part 1, we have included four contributions on perspectives in supercomputer infras-
tructure and applications, two of which describe previous experience on how to build
anadequatenetworkingenvironmentsothatpeopleinHPCcanfurthercollaborateand
addonworkalreadydonewithemphasisontheMexicancase.Also,itofferstwomore
papers,whichgiveanoverviewoncurrentcollaborativesupportprogramsaswellasa
glimpse ofsomerelations between anexascalesupercomputingsystemandeducation.
In Part 2, the contributions focus on parallel algorithms and optimization for both
CPUsandGPUs.GPUcomputingwasintroducedtoHPCusersin2007.Sincethenthe
technology has advanced rapidly, largely driven by HPC practitioners looking for
greater performance and improved energy efficiencies. Performance has been a fun-
damental driver in the HPC market since its inception, while energy efficiency is a
more recent demand that has come about as a result of the breakdown of Dennard
scaling. GPUs are able to offer a better performance and performance-per-watt com-
paredwithCPUsonparallelsoftwarethankstotheirthroughput-optimizeddesignand
considerable floating point capability if certain conditions are fulfilled. As a result,
accelerators are now found in nearly half of all new HPC systems deployed, thus
havingaprofoundimpactontheimplementationofparallelalgorithms,particularlyfor
those looking for optimal solutions for a given problem. We have included several
contributions that use CPUs and/or GPUs architectures.
In Part 3, we have included contributions in HPC applications and simulations.
Nowadays,as aconsequenceofthegrowth insupercomputer performance,there isan
increase in the development of data-intensive predictive science as a solution to sci-
entific problems via simulations that generate large amounts of data. Generally, the
problems that are studied are multiscale and multidisciplinary simulations such as:
digital engineering, rocket engine design, electrical energy storage, solar energy fixa-
tion, fusion, genome networks, human body simulations, hemodynamics, protein
function analysis, protein folding, protein control, virus, anti-cancer drugs,
nano-devices and nano-science modeling and fragmentation, material design, astro-
physical simulations, cosmological simulations, disaster prevention, volcano simula-
tions,earthquakewavepropagation,cloudanalysis,climateprediction,high-resolution
atmospheric circulation, melted rock simulations, engineering, non-steady flow, com-
pressible flow, large eddy simulation, and structural analysis, among many others.
For many of these simulations, we find fluid dynamics in their core, which is a
highly developed branch of science that has been subject to continued and expanding
Preface IX
researchactivityboththeoreticallyandexperimentallysincemorethanacenturyanda
half ago. Mexico has a strong and active community in this area. At ISUM 2015, a
widevarietyoffluiddynamicstopicswerepresentedthatincluded:asymptoticmethods
in fluids, convection, computational methods for biological systems, interfacial fluid
dynamics, colloidal dispersion, and flow in fractured porous media.
The book is aimed at senior undergraduate and graduate students, as well as sci-
entists in the fields of HPC, computer sciences, physics, biology, mathematics, engi-
neering,andchemistrywhohaveinterestinthesolutionofalargevarietyofproblems
that make use of supercomputers. The material included in this book is adequate for
both teaching and research.
The editors are very grateful to the institutions and people that made possible the
realizationofthe6thInternationalConferenceonSupercomputinginMexico—ISUM
2015, especially Julia Tagüeña Parga and Elías Micha Zaga from CONACYT, Felipe
Bracho Carpizo from UNAM, Luis A. Villa Vargas from IPN, José Mustre de León
from CINVESTAV, Lydia Concepción Paredes Gutiérrez and Federico Puente Espel
from ININ, Axel Aviles Pallaresfrom UAM, and Carlos Casasús LópezHermosa and
Salma Leticia Jaliffe Villalón from CUDI.
The following individuals were instrumental in organizing the ISUM 2015:
ABACUS-CINVESTAV:RuslanGabbasov,FranciscoOrtizArango,AlejandroFlores
Méndez, Juan Antonio Vega, Olivia Lazcano, Daniel Ortiz, Omar Nieto, Estela Her-
nández, Adriana Aranda, Alberto Trejo; ININ: Jorge Luis Cervantes Cota, Estela
Mayoral Villa; UNAM: Alfredo Santillán, Fabián Romo, José Luis Gordillo, José de
Jesús Cruz, Liliana Hernández; IPN: René Luna García, Juan Carlos Chimal; UAM:
Apolinar Martínez Melchor, Luis Arturo Núñez Pablo, Juan Carlos Rosas Cabrera;
UAEMEX: Luis Enrique Díaz, Roberto López Rendón; CUDI: Salma Leticia Jaliffe
Villalón, Hans Ludwing Reyes, Martha Ávila.
ISUM 2015 was organized by the following institutions: ABACUS-CINVESTAV,
CONACYT, CUDI, ININ, IPN, UAM, UNAM, LNS-SURESTE, CICESE,
LANGEBIO-CINVESTAV, CIMAT, UAEMEX, UAEM, CNS-IPICYT, UCOL,
UDG, UNISON, UV, and The National Committee ISUM; it was sponsored by: SGI,
Fujitsu,Intel,HP,Cray,Dell,ATOS,Seagate,Mellanox,Huawei,B-CAUSE,Penguin
Computing, Red Hat, Enter, VMware, ENLACE, and CADGRAFICS.
WeacknowledgethehelpoftheEditionCommitteefortheirimportantandvaluable
contribution to the final manuscript, in particular Ruslan Gabbasov, Salvador Galindo
Uribarri, Julian Becerra Sagredo, Nathan Weinstein, Leonardo Di G. Sigalotti, Ale-
jandro Aviles Cervantes, and Carlos Jaime Barrios Hernández.
We thank Estela Hernández Juárez and Adriana Aranda for their valuable contri-
bution to the production of this book.
February 2016 Isidoro Gitler
Jaime Klapp