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Scalability analysis of Dalton, a molecular structure program
KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0001-9693-6265
KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-5415-1248
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-9123-8174
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2013 (English)In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, no 8, 2197-2204 p.Article in journal (Refereed) Published
Abstract [en]

Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.

Place, publisher, year, edition, pages
2013. Vol. 29, no 8, 2197-2204 p.
Keyword [en]
Performance analysis, Optimization, Scalability
National Category
Computer Systems
Research subject
SRA - E-Science (SeRC)
Identifiers
URN: urn:nbn:se:kth:diva-136200DOI: 10.1016/j.future.2013.04.013ISI: 000326613400028Scopus ID: 2-s2.0-84886093468OAI: oai:DiVA.org:kth-136200DiVA: diva2:675573
Funder
Swedish eā€Science Research Center
Note

QC 20131216

Available from: 2013-12-04 Created: 2013-12-04 Last updated: 2017-12-06Bibliographically approved

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Aguilar, XavierSchliephake, MichaelVahtras, OlavLaure, Erwin

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