research-article

Performance optimization of large non-negatively constrained least squares problems with an application in biophysics

Authors:

Emre H. Brookes,

Borries DemelerAuthors Info & Claims

TG '10: Proceedings of the 2010 TeraGrid Conference

Article No.: 5, Pages 1 - 9

https://doi.org/10.1145/1838574.1838579

Published: 02 August 2010 Publication History

Abstract

Solving large non-negatively constrained least squares systems is frequently used in the physical sciences to estimate model parameters which best fit experimental data. Analytical Ultracentrifugation (AUC) is an important hydrodynamic experimental technique used in biophysics to characterize macromolecules and to determine parameters such as molecular weight and shape. We previously developed a parallel divide and conquer method to facilitate solving the large systems obtained from AUC experiments. New AUC instruments equipped with multi-wavelength (MWL) detectors have recently increased the data sizes by three orders of magnitude. Analyzing the MWL data requires significant compute resources. To better utilize these resources, we introduce a procedure allowing the researcher to optimize the divide and conquer scheme along a continuum from minimum wall time to minimum compute service units. We achieve our results by implementing a preprocessing stage performed on a local workstation before job submission.

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Cited By

Krueger SCurtis JScott DGrishaev AGlenn GSmith GEllingsworth LBorisov OMaynard E(2020)Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in SolutionMolecular Pharmaceutics10.1021/acs.molpharmaceut.0c0098618:1(359-376)Online publication date: 16-Dec-2020
https://doi.org/10.1021/acs.molpharmaceut.0c00986
Kim HBrookes EDemeler BPeterson G(2015)A performance predictor for UltraScan supercomputer calculationsProceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure10.1145/2792745.2792787(1-5)Online publication date: 26-Jul-2015
https://dl.acm.org/doi/10.1145/2792745.2792787
Luers LBannach OStöhr JWördehoff MWolff MNagel-Steger LRiesner DWillbold DBirkmann E(2013)Seeded Fibrillation as Molecular Basis of the Species Barrier in Human Prion DiseasesPLoS ONE10.1371/journal.pone.00726238:8(e72623)Online publication date: 20-Aug-2013
https://doi.org/10.1371/journal.pone.0072623
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Performance optimization of large non-negatively constrained least squares problems with an application in biophysics

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cover image ACM Other conferences

TG '10: Proceedings of the 2010 TeraGrid Conference

August 2010

177 pages

ISBN:9781605588186

DOI:10.1145/1838574

Co-chairs:
Richard Moore
SDSC
,
Daniel S. Katz
UC/ANL
,
Program Chair:
Shawn Brown
PSC

Copyright © 2010 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 02 August 2010

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TG '10: TeraGrid 2010

August 2 - 5, 2010

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Cited By

Krueger SCurtis JScott DGrishaev AGlenn GSmith GEllingsworth LBorisov OMaynard E(2020)Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in SolutionMolecular Pharmaceutics10.1021/acs.molpharmaceut.0c0098618:1(359-376)Online publication date: 16-Dec-2020
https://doi.org/10.1021/acs.molpharmaceut.0c00986
Kim HBrookes EDemeler BPeterson G(2015)A performance predictor for UltraScan supercomputer calculationsProceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure10.1145/2792745.2792787(1-5)Online publication date: 26-Jul-2015
https://dl.acm.org/doi/10.1145/2792745.2792787
Luers LBannach OStöhr JWördehoff MWolff MNagel-Steger LRiesner DWillbold DBirkmann E(2013)Seeded Fibrillation as Molecular Basis of the Species Barrier in Human Prion DiseasesPLoS ONE10.1371/journal.pone.00726238:8(e72623)Online publication date: 20-Aug-2013
https://doi.org/10.1371/journal.pone.0072623
Brookes ESingh RPierce MMarru SDemeler BRocco MStewart C(2012)Ultrascan solution modelerProceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond10.1145/2335755.2335839(1-8)Online publication date: 16-Jul-2012
https://dl.acm.org/doi/10.1145/2335755.2335839
Demeler BSingh RPierce MBrookes EMarru SDubbs BTowns JBrown SKatz D(2011)UltraScan gateway enhancementsProceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery10.1145/2016741.2016778(1-8)Online publication date: 18-Jul-2011
https://dl.acm.org/doi/10.1145/2016741.2016778

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