Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation

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dc.contributor.authorClasca, Marc
dc.contributor.authorGarcia Gasulla, Marta
dc.contributor.authorMontagud, Arnau
dc.contributor.authorCarbonell Caballero, José
dc.contributor.authorValencia, Alfonso
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2024-02-28T10:07:50Z
dc.date.available2024-02-28T10:07:50Z
dc.date.issued2023
dc.description.abstractThis work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and a locality-aware parallelization. The outcome of this paper is not only the speedup of 2.4x achieved by the optimized version with respect to the original PhysiCell code, but also the lessons learned and best practices when developing parallel HPC codes to obtain efficient and highly performant applications, especially in the computational biology field.
dc.description.peerreviewedPeer Reviewed
dc.description.sponsorshipThis work has received funding from the EU Horizon 2020 POP2 (grant agreement No 824080), PerMedCoE (grant agreement No 951773), and by the Spanish Government(PID2019-107255GB).
dc.description.versionPostprint (author's final draft)
dc.identifier.citationClasca, M. [et al.]. Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation. A: Platform for Advanced Scientific Computing Conference. "PASC '23: Platform for Advanced Scientific Computing Conference: June 26 - 28, 2023, Davos Switzerland". New York: Association for Computing Machinery (ACM), 2023, ISBN 979-8-4007-0190-0. DOI 10.1145/3592979.3593403.
dc.identifier.doi10.1145/3592979.3593403
dc.identifier.isbn979-8-4007-0190-0
dc.identifier.otherhttps://arxiv.org/abs/2306.11544
dc.identifier.urihttps://hdl.handle.net/2117/403351
dc.language.isoeng
dc.publisherAssociation for Computing Machinery (ACM)
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/824080/EU/Performance Optimisation and Productivity 2/POP2
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/951773/EU/HPC%2FExascale Centre of Excellence in Personalised Medicine/PerMedCoE
dc.relation.projectidinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-107255GB-C21/ES/BSC - COMPUTACION DE ALTAS PRESTACIONES VIII/
dc.relation.publisherversionhttps://dl.acm.org/doi/proceedings/10.1145/3592979
dc.rights.accessOpen Access
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subject.lcshBioinformatics
dc.subject.lcshComputational biology
dc.subject.lcshPersonalized medicine
dc.subject.lemacSimulació per ordinador
dc.subject.otherLoad balance
dc.subject.otherOptimization
dc.subject.otherMultiscale simulation
dc.subject.otherMemory locality
dc.titleLessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation
dc.typeConference lecture
dspace.entity.typePublication
local.citation.contributorPlatform for Advanced Scientific Computing Conference
local.citation.other4
local.citation.publicationNamePASC '23: Platform for Advanced Scientific Computing Conference: June 26 - 28, 2023, Davos Switzerland
local.citation.pubplaceNew York

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