Maximizing resource usage in multifold molecular dynamics with rCUDA

[EN] The full-understanding of the dynamics of molecular systems at the atomic scale is of great relevance in the fields of chemistry, physics, materials science, and drug discovery just to name a few. Molecular dynamics (MD) is a widely used computer tool for simulating the dynamical behavior of mo...

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Authors: Prades, Javier|||0000-0003-3349-2200, Silla, Federico|||0000-0002-6435-1200, Imbernon, Baldomero, Reaño González, Carlos, Peña-García, Jorge, Cerón-Carrasco, Jose Pedro, Pérez-Sánchez, Horacio
Format: article
Publication Date:2020
Country:España
Institution:Universitat Politècnica de València (UPV)
Repository:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
Language:English
OAI Identifier:oai:riunet.upv.es:10251/151657
Online Access:https://riunet.upv.es/handle/10251/151657
Access Level:Open access
Keyword:Molecular dynamics
GPU virtualization
RCUDA
GROMACS
GPU
ARQUITECTURA Y TECNOLOGIA DE COMPUTADORES
id ES_3ff69d1b9182e9de0b6f9577b8cd9e31
oai_identifier_str oai:riunet.upv.es:10251/151657
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Maximizing resource usage in multifold molecular dynamics with rCUDA
title Maximizing resource usage in multifold molecular dynamics with rCUDA
spellingShingle Maximizing resource usage in multifold molecular dynamics with rCUDA
Prades, Javier|||0000-0003-3349-2200
Molecular dynamics
GPU virtualization
RCUDA
GROMACS
GPU
ARQUITECTURA Y TECNOLOGIA DE COMPUTADORES
title_short Maximizing resource usage in multifold molecular dynamics with rCUDA
title_full Maximizing resource usage in multifold molecular dynamics with rCUDA
title_fullStr Maximizing resource usage in multifold molecular dynamics with rCUDA
title_full_unstemmed Maximizing resource usage in multifold molecular dynamics with rCUDA
title_sort Maximizing resource usage in multifold molecular dynamics with rCUDA
dc.creator.none.fl_str_mv Prades, Javier|||0000-0003-3349-2200
Silla, Federico|||0000-0002-6435-1200
Imbernon, Baldomero
Reaño González, Carlos
Peña-García, Jorge
Cerón-Carrasco, Jose Pedro
Pérez-Sánchez, Horacio
author Prades, Javier|||0000-0003-3349-2200
author_facet Prades, Javier|||0000-0003-3349-2200
Silla, Federico|||0000-0002-6435-1200
Imbernon, Baldomero
Reaño González, Carlos
Peña-García, Jorge
Cerón-Carrasco, Jose Pedro
Pérez-Sánchez, Horacio
author_role author
author2 Silla, Federico|||0000-0002-6435-1200
Imbernon, Baldomero
Reaño González, Carlos
Peña-García, Jorge
Cerón-Carrasco, Jose Pedro
Pérez-Sánchez, Horacio
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Departamento de Informática de Sistemas y Computadores
Escuela Técnica Superior de Ingeniería Informática
Grupo de Redes de Computadores
Grupo de Arquitecturas Paralelas
European Regional Development Fund
Ministerio de Educación y Ciencia
Ministerio de Ciencia e Innovación
Universitat Politècnica de València
Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia
Generalitat Valenciana
Ministerio de Economía y Competitividad
Agencia Estatal de Investigación
Repositorio Institucional de la Universitat Politècnica de València Riunet
dc.subject.none.fl_str_mv Molecular dynamics
GPU virtualization
RCUDA
GROMACS
GPU
ARQUITECTURA Y TECNOLOGIA DE COMPUTADORES
topic Molecular dynamics
GPU virtualization
RCUDA
GROMACS
GPU
ARQUITECTURA Y TECNOLOGIA DE COMPUTADORES
description [EN] The full-understanding of the dynamics of molecular systems at the atomic scale is of great relevance in the fields of chemistry, physics, materials science, and drug discovery just to name a few. Molecular dynamics (MD) is a widely used computer tool for simulating the dynamical behavior of molecules. However, the computational horsepower required by MD simulations is too high to obtain conclusive results in real-world scenarios. This is mainly motivated by two factors: (1) the long execution time required by each MD simulation (usually in the nanoseconds and microseconds scale, and beyond) and (2) the large number of simulations required in drug discovery to study the interactions between a large library of compounds and a given protein target. To deal with the former, graphics processing units (GPUs) have come up into the scene. The latter has been traditionally approached by launching large amounts of simulations in computing clusters that may contain several GPUs on each node. However, GPUs are targeted as a single node that only runs one MD instance at a time, which translates into low GPU occupancy ratios and therefore low throughput. In this work, we propose a strategy to increase the overall throughput of MD simulations by increasing the GPU occupancy through virtualized GPUs. We use the remote CUDA (rCUDA) middleware as a tool to decouple GPUs from CPUs, and thus enabling multi-tenancy of the virtual GPUs. As a working test in the drug discovery field, we studied the binding process of a novel flavonol to DNA with the GROningen MAchine for Chemical Simulations (GROMACS) MD package. Our results show that the use of rCUDA provides with a 1.21x speed-up factor compared to the CUDA counterpart version while requiring a similar power budget.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-01-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://riunet.upv.es/handle/10251/151657
url https://riunet.upv.es/handle/10251/151657
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 TIN2016-78799-P DESARROLLO HOLISTICO DE APLICACIONES EMERGENTES EN SISTEMAS HETEROGENEOS
Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia https://doi.org/10.13039/100007801 20813%2FPI%2F18
Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia https://doi.org/10.13039/100007801 20524%2FPDC%2F18
Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia https://doi.org/10.13039/100007801 20988%2FPI%2F18
Ministerio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 TIN2015-66972-C5-3-R TECNICAS PARA LA MEJORA DE LAS PRESTACIONES, FIABILIDAD Y CONSUMO DE ENERGIA DE LOS SERVIDORES. OPTIMIZACION DE APLICACIONES CIENTIFICAS, MEDICAS Y DE VISION ARTIFICIAL
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016 CTQ2017-87974-R DESARROLLO DE TECNICAS AVANZADAS DE DESCUBRIMIENTO DE FARMACOS, SU IMPLEMENTACION EN HERRAMIENTAS SOFTWARE Y WEB, Y SU APLICACION A CONTEXTOS DE RELEVANCIA FARMACOLOGICA
Generalitat Valenciana https://doi.org/10.13039/501100003359 PROMETEO%2F2017%2F077
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reserva de todos los derechos
http://rightsstatements.org/vocab/InC/1.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reserva de todos los derechos
http://rightsstatements.org/vocab/InC/1.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv SAGE Publications
publisher.none.fl_str_mv SAGE Publications
dc.source.none.fl_str_mv reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
instname:Universitat Politècnica de València (UPV)
instname_str Universitat Politècnica de València (UPV)
reponame_str RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
collection RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
repository.name.fl_str_mv
repository.mail.fl_str_mv
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spelling Maximizing resource usage in multifold molecular dynamics with rCUDAPrades, Javier|||0000-0003-3349-2200Silla, Federico|||0000-0002-6435-1200Imbernon, BaldomeroReaño González, CarlosPeña-García, JorgeCerón-Carrasco, Jose PedroPérez-Sánchez, HoracioMolecular dynamicsGPU virtualizationRCUDAGROMACSGPUARQUITECTURA Y TECNOLOGIA DE COMPUTADORES[EN] The full-understanding of the dynamics of molecular systems at the atomic scale is of great relevance in the fields of chemistry, physics, materials science, and drug discovery just to name a few. Molecular dynamics (MD) is a widely used computer tool for simulating the dynamical behavior of molecules. However, the computational horsepower required by MD simulations is too high to obtain conclusive results in real-world scenarios. This is mainly motivated by two factors: (1) the long execution time required by each MD simulation (usually in the nanoseconds and microseconds scale, and beyond) and (2) the large number of simulations required in drug discovery to study the interactions between a large library of compounds and a given protein target. To deal with the former, graphics processing units (GPUs) have come up into the scene. The latter has been traditionally approached by launching large amounts of simulations in computing clusters that may contain several GPUs on each node. However, GPUs are targeted as a single node that only runs one MD instance at a time, which translates into low GPU occupancy ratios and therefore low throughput. In this work, we propose a strategy to increase the overall throughput of MD simulations by increasing the GPU occupancy through virtualized GPUs. We use the remote CUDA (rCUDA) middleware as a tool to decouple GPUs from CPUs, and thus enabling multi-tenancy of the virtual GPUs. As a working test in the drug discovery field, we studied the binding process of a novel flavonol to DNA with the GROningen MAchine for Chemical Simulations (GROMACS) MD package. Our results show that the use of rCUDA provides with a 1.21x speed-up factor compared to the CUDA counterpart version while requiring a similar power budget.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was jointly supported by the Fundación Séneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants (20524/PDC/18, 20813/PI/ 18, and 20988/PI/18) and by the Spanish MEC and Eur-opean Commission FEDER under grants TIN2015-66972-C5-3-R, TIN2016-78799-P, and CTQ2017-87974-R (AEI/FEDER, UE). Researchers from the Universitat Politècnica de València are supported by the Generalitat Valenciana under grant PROMETEO/2017/077.SAGE PublicationsDepartamento de Informática de Sistemas y ComputadoresEscuela Técnica Superior de Ingeniería InformáticaGrupo de Redes de ComputadoresGrupo de Arquitecturas ParalelasEuropean Regional Development FundMinisterio de Educación y CienciaMinisterio de Ciencia e InnovaciónUniversitat Politècnica de ValènciaFundación Séneca-Agencia de Ciencia y Tecnología de la Región de MurciaGeneralitat ValencianaMinisterio de Economía y CompetitividadAgencia Estatal de InvestigaciónRepositorio Institucional de la Universitat Politècnica de València Riunet20202020-01-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfapplication/pdfhttps://riunet.upv.es/handle/10251/151657reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengMinisterio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 TIN2016-78799-P DESARROLLO HOLISTICO DE APLICACIONES EMERGENTES EN SISTEMAS HETEROGENEOSFundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia https://doi.org/10.13039/100007801 20813%2FPI%2F18Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia https://doi.org/10.13039/100007801 20524%2FPDC%2F18Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia https://doi.org/10.13039/100007801 20988%2FPI%2F18Ministerio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 TIN2015-66972-C5-3-R TECNICAS PARA LA MEJORA DE LAS PRESTACIONES, FIABILIDAD Y CONSUMO DE ENERGIA DE LOS SERVIDORES. OPTIMIZACION DE APLICACIONES CIENTIFICAS, MEDICAS Y DE VISION ARTIFICIALAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016 CTQ2017-87974-R DESARROLLO DE TECNICAS AVANZADAS DE DESCUBRIMIENTO DE FARMACOS, SU IMPLEMENTACION EN HERRAMIENTAS SOFTWARE Y WEB, Y SU APLICACION A CONTEXTOS DE RELEVANCIA FARMACOLOGICAGeneralitat Valenciana https://doi.org/10.13039/501100003359 PROMETEO%2F2017%2F077open accesshttp://purl.org/coar/access_right/c_abf2Reserva de todos los derechoshttp://rightsstatements.org/vocab/InC/1.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/1516572026-06-13T07:49:27Z
score 15.198674

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