NDLI: Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations

Please wait, while we are loading the content...

A distributed memory out-of-core method on HPC clusters and its application to quantum chemistry applications

High accuracy gravitational waveforms from black hole binary inspirals using OpenCL

Exploring similarities among many species distributions

Computational science certificates for the current workforce: lessons learned

Security for science gateways and campus bridging: XSEDE12 panel

Running many molecular dynamics simulations on many supercomputers

Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations: sampling for the 99%

The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources

A blended, multimodal access eTextBook in computational physics

SaaS for science: the path to reality for research in the cloud

Gordon: design, performance, and experiences deploying and supporting a data intensive supercomputer

Membrane protein simulations under asymmetric ionic concentrations

Roadmaps, not blueprints: paving the way to science gateway success

Longitudinal user and usage patterns in the XSEDE user community

Campus bridging pilot project reports: XSEDE12 panel

Radiation modeling using the Uintah heterogeneous CPU/GPU runtime system

Benchmark calculations for multi-photon ionization of the hydrogen molecule and the hydrogen molecular ion by short-pulse intense laser radiation

Offline parallel debugging: a case study report

Cloud-enabling biological simulations for scalable and sustainable access: an experience report

Managing the long tail of science: data and communities

An analysis of GPU utilization trends on the Keeneland initial delivery system

Electrostatic screening effects on a model system for molecular electronics

Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools

Conducting K-12 outreach to evoke early interest in IT, science, and advanced technology

A tale of two systems: flexibility of usage of Kraken and Nautilus at the National Institute for Computational Sciences

Exploiting HPC resources for the 3D-time series analysis of caries lesion activity

The Prickly Pear Archive: a portable hypermedia for scholarly publication

Computing MATTERS: building pathways to cyberinfrastructure

A framework for federated two-factor authentication enabling cost-effective secure access to distributed cyberinfrastructure

Multiscale simulations of Langmuir cells and submesoscale eddies using XSEDE resources

Mojave: a development environment for the Cactus computational framework

Enhancing chemistry teaching and learning through cyberinfrastructure

A systematic process for efficient execution on Intel's heterogeneous computation nodes

Comparing the performance of group detection algorithm in serial and parallel processing environments

Trinity RNA-Seq assembler performance optimization

Using stereoscopic 3D videos to inform the public about the benefits of computational science

Evaluation of parallel and distributed file system technologies for XSEDE

High performance mining of social media data

The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDE

WaterHUB: a resource for students and educators for learning hydrology

Achieve better performance with PEAK on XSEDE resources

Massively parallel direct numerical simulations of forced compressible turbulence: a hybrid MPI/OpenMP approach

What is campus bridging and what is XSEDE doing about it?

A learning outcome driven cyber infrastructure for thermodynamics education

Analyzing throughput and utilization on trestles

Quantum algorithms for predicting the properties of complex materials

The Eclipse parallel tools platform: toward an integrated development environment for XSEDE resources

FutureGrid education: using case studies to develop a curriculum for communicating parallel and distributed computing concepts

Using kerberized lustre over the WAN for high energy physics data

Monte Carlo strategies for first-principles simulations of elemental systems

Enabling large-scale scientific workflows on petascale resources using MPI master/worker

The initial role of evaluation in a large-scale multi-site project

The data supercell

Computational challenges in nanoparticle partition function calculation

Campus bridging made easy via Globus services

Minority student involvement in computational science research at Texas Southern University

Ensemble modeling of storm interaction with XSEDE

Building a partnership for computer science education

Excited states in lattice QCD using the stochastic LapH method

Multiple concurrent queries on demand: large scale video analysis in a flash memory environment as a case for humanities supercomputing

A toolkit for the analysis and visualization of free volume in materials

Three-dimensional simulations of geometrically complex subduction with large viscosity variations

Multiscale modeling of high explosives for transportation accidents

Multiscale simulations of blood-flow: from a platelet to an artery

A high throughput workflow environment for cosmological simulations

Using the XSEDE supercomputing and visualization resources to improve tornado prediction using data mining

Optimization of density functional tight-binding and classical reactive molecular dynamics for high-throughput simulations of carbon materials

Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations

Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations

Content Provider	ACM Digital Library
Author	Crosby, Lonnie Voth, Gregory A. Knight, Chris Blood, Philip Peng, Yuxing
Abstract	Conducting molecular dynamics (MD) simulations involving chemical reactions in large-scale condensed phase systems (liquids, proteins, fuel cells, etc.) is a computationally prohibitive task even though many new ab initio based methodologies (i.e., AIMD, QM/MM) have been developed. Chemical processes occur over a range of length scales and are coupled to slow (long time scale) system motions, which make adequate sampling a challenge. Multistate methodologies, such as the multistate empirical valence bond (MS-EVB) method, which are based on effective force fields, are more computationally efficient and enable the simulation of chemical reactions over the necessary time and length scales to properly converge statistical properties. The typical parallel scaling bottleneck in both reactive and nonreactive all-atom MD simulations is the accurate treatment of long-range electrostatic interactions. Currently, Ewald-type algorithms rely on three-dimensional Fast Fourier Transform (3D-FFT) calculations. The parallel scaling of these 3D-FFT calculations can be severely degraded at higher processor counts due to necessary MPI all-to-all communication. This poses an even bigger problem in MS-EVB calculations, since the electrostatics, and hence the 3D-FFT, must be evaluated many times during a single time step. Due to the limited scaling of the 3D-FFT in MD simulations, the traditional single-program-multiple-data (SPMD) parallelism model is only able to utilize several hundred CPU cores, even for very large systems. However, with a proper implementation of a multi-program (MP) model, large systems can scale to thousands of CPU cores. This paper will discuss recent efforts in collaboration with XSEDE advanced support to implement the MS-EVB model in the scalable LAMMPS MD code, and to further improve parallel scaling by implementing MP parallelization algorithms in LAMMPS. These algorithms improve parallel scaling in both the standard LAMMPS code and LAMMPS with MS-EVB, thus facilitating the efficient simulation of large-scale condensed phase systems, which include the ability to model chemical reactions.
Starting Page	1
Ending Page	7
Page Count	7
File Format	PDF
ISBN	9781450316026
DOI	10.1145/2335755.2335833
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-07-16
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Lammps Ms-evb Reactive molecular dynamics
Content Type	Text
Resource Type	Article

Central Library (ISO-9001:2015 Certified)
Indian Institute of Technology Kharagpur
Kharagpur, West Bengal, India | PIN - 721302

See location in the Map
03222 282435
Mail: support@ndl.gov.in

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in