Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

doi:10.1103/PhysRevE.96.053311

Title: Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Abstract

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

Authors:

Guzman, Horacio V. ^[1]; Junghans, Christoph ^[2]; Kremer, Kurt ^[1]; Stuehn, Torsten ^[1]

Max Planck Inst. for Polymer Research, Mainz (Germany)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Publication Date:: Mon Nov 27 00:00:00 EST 2017

Research Org.:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Org.:: USDOE; German Research Foundation (DFG)

OSTI Identifier:: 1412879

Report Number(s):: LA-UR-17-30265
Journal ID: ISSN 2470-0045; TRN: US1800388

Grant/Contract Number:: AC52-06NA25396

Resource Type:: Accepted Manuscript

Journal Name:: Physical Review E

Additional Journal Information:: Journal Volume: 96; Journal Issue: 5; Journal ID: ISSN 2470-0045

Publisher:: American Physical Society (APS)

Country of Publication:: United States

Language:: English

Subject:: 36 MATERIALS SCIENCE; 97 MATHEMATICS AND COMPUTING; Atomic and Nuclear Physics

Citation Formats


                    Guzman, Horacio V., Junghans, Christoph, Kremer, Kurt, and Stuehn, Torsten. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes.  United States: N. p., 2017. 
Web.  doi:10.1103/PhysRevE.96.053311.

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                    Guzman, Horacio V., Junghans, Christoph, Kremer, Kurt, & Stuehn, Torsten. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes.  United States.  https://doi.org/10.1103/PhysRevE.96.053311

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                    Guzman, Horacio V., Junghans, Christoph, Kremer, Kurt, and Stuehn, Torsten. Mon .  
"Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes".  United States.  https://doi.org/10.1103/PhysRevE.96.053311.  https://www.osti.gov/servlets/purl/1412879.

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@article{osti_1412879,

  title        = {Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes},

  author       = {Guzman, Horacio V. and Junghans, Christoph and Kremer, Kurt and Stuehn, Torsten},

  abstractNote = {Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.},

  doi          = {10.1103/PhysRevE.96.053311},

  journal      = {Physical Review E},

  number       = 5,

  volume       = 96,

  place        = {United States},

  year         = {Mon Nov 27 00:00:00 EST 2017},

  month        = {Mon Nov 27 00:00:00 EST 2017}

}

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Works referenced in this record:

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Works referencing / citing this record:

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids
journal, April 2019

Zavadlav, Julija; Marrink, Siewert J.; Praprotnik, Matej
Interface Focus, Vol. 9, Issue 3
DOI: 10.1098/rsfs.2018.0075

Molecular Dynamics Simulation of High Density DNA Arrays
journal, January 2018

Podgornik, Rudolf; Zavadlav, Julija; Praprotnik, Matej
Computation, Vol. 6, Issue 1
DOI: 10.3390/computation6010003

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Title: Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Abstract

Citation Formats

Multi-million particle molecular dynamics I. Design considerations for vector processing journal, March 1991

Biomembranes in atomistic and coarse-grained simulations journal, July 2015

Allocating Independent Subtasks on Parallel Processors journal, October 1985

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution journal, May 2008

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: Application to liquid water journal, December 2009

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations journal, June 2015

Network-aware optimization of communications for parallel matrix multiplication on hierarchical HPC platforms: NETWORK-AWARE OPTIMIZATION OF COMMUNICATIONS... journal, August 2015

Small Activity Differences Drive Phase Separation in Active-Passive Polymer Mixtures journal, March 2017

Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates journal, February 1998

A Review of Multiscale Computational Methods in Polymeric Materials journal, January 2017

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions journal, January 2005

Adaptive resolution simulation of an atomistic protein in MARTINI water journal, February 2014

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal, February 2008

Adaptive resolution simulation of liquid water journal, December 2008

Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids journal, August 2013

Adaptive Resolution Simulation of a DNA Molecule in Salt Solution journal, September 2015

Concurrent triple-scale simulation of molecular liquids journal, March 2008

Challenges in Multiscale Modeling of Polymer Dynamics journal, June 2013

A unified framework for force-based and energy-based adaptive resolution simulations journal, November 2014

From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations journal, June 2016

ESPResSo++: A modern multiscale simulation package for soft matter systems journal, April 2013

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations journal, February 2014

Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange journal, October 2014

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Fast Parallel Algorithms for Short-Range Molecular Dynamics journal, March 1995

Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling journal, January 2011

Hamiltonian Adaptive Resolution Simulation for Molecular Liquids journal, March 2013

Idle waves in high-performance computing journal, January 2015

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly journal, December 2005

Adaptive resolution simulation of liquid water journal, July 2007

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties journal, May 2015

Guided Self-Scheduling: A Practical Scheduling Scheme for Parallel Supercomputers journal, December 1987

Multiscale simulation in polymer science journal, August 2002

Multiscale simulation of soft matter systems journal, January 2010

Empirical potential Monte Carlo simulation of fluid structure journal, January 1996

Technical advances in molecular simulation since the 1980s journal, September 2015

Molecular dynamics simulation: a tool for exploration and discovery using simple models journal, November 2014

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations journal, August 2003

Enhanced Crystal Growth in Binary Lennard-Jones Mixtures journal, January 2017

Challenges in Multiscale Modeling of Polymer Dynamics text, January 2013

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water text, January 2009

Small activity differences drive phase separation in active-passive polymer mixtures text, January 2017

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids journal, April 2019

Molecular Dynamics Simulation of High Density DNA Arrays journal, January 2018

Multi-million particle molecular dynamics I. Design considerations for vector processing
journal, March 1991

Biomembranes in atomistic and coarse-grained simulations
journal, July 2015

Allocating Independent Subtasks on Parallel Processors
journal, October 1985

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
journal, May 2008

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: Application to liquid water
journal, December 2009

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
journal, June 2015

Network-aware optimization of communications for parallel matrix multiplication on hierarchical HPC platforms: NETWORK-AWARE OPTIMIZATION OF COMMUNICATIONS...
journal, August 2015

Small Activity Differences Drive Phase Separation in Active-Passive Polymer Mixtures
journal, March 2017

Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates
journal, February 1998

A Review of Multiscale Computational Methods in Polymeric Materials
journal, January 2017

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions
journal, January 2005

Adaptive resolution simulation of an atomistic protein in MARTINI water
journal, February 2014

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008

Adaptive resolution simulation of liquid water
journal, December 2008

Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids
journal, August 2013

Adaptive Resolution Simulation of a DNA Molecule in Salt Solution
journal, September 2015

Concurrent triple-scale simulation of molecular liquids
journal, March 2008

Challenges in Multiscale Modeling of Polymer Dynamics
journal, June 2013

A unified framework for force-based and energy-based adaptive resolution simulations
journal, November 2014

From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations
journal, June 2016

ESPResSo++: A modern multiscale simulation package for soft matter systems
journal, April 2013

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
journal, February 2014

Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange
journal, October 2014

Opportunities in theoretical and computational polymeric materials and soft matter
journal, January 2015

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling
journal, January 2011

Hamiltonian Adaptive Resolution Simulation for Molecular Liquids
journal, March 2013

Idle waves in high-performance computing
journal, January 2015

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
journal, December 2005

Adaptive resolution simulation of liquid water
journal, July 2007

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties
journal, May 2015

Guided Self-Scheduling: A Practical Scheduling Scheme for Parallel Supercomputers
journal, December 1987

Multiscale simulation in polymer science
journal, August 2002

Multiscale simulation of soft matter systems
journal, January 2010

Empirical potential Monte Carlo simulation of fluid structure
journal, January 1996

Technical advances in molecular simulation since the 1980s
journal, September 2015

Molecular dynamics simulation: a tool for exploration and discovery using simple models
journal, November 2014

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003

Enhanced Crystal Growth in Binary Lennard-Jones Mixtures
journal, January 2017

Challenges in Multiscale Modeling of Polymer Dynamics
text, January 2013

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water
text, January 2009

Small activity differences drive phase separation in active-passive polymer mixtures
text, January 2017

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids
journal, April 2019

Molecular Dynamics Simulation of High Density DNA Arrays
journal, January 2018