I/O limitations in parallel molecular dynamics
Supercomputing '95 Proceedings of the 1995 ACM/IEEE conference on Supercomputing
Lightweight computational steering of very large scale molecular dynamics simulations
Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing
Design of a large scale discrete element soil model for high performance computing systems
Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing
A wrapper generator for wrapping high performance legacy codes as Java/CORBA components
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Scalable molecular dynamics for large biomolecular systems
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Demonstrating the scalability of a molecular dynamics application on a Petaflop computer
ICS '01 Proceedings of the 15th international conference on Supercomputing
Exploiting flexibly assignable work to improve load balance
Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures
Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflops Computer
International Journal of Parallel Programming
Portrait of a Crack: Rapid Fracture Mechanics Using Parallel Molecular Dynamics
IEEE Computational Science & Engineering
Scalable Molecular-Dynamics, Visualization, and Data-Management Algorithms for Materials Simulations
Computing in Science and Engineering
GCSE '99 Proceedings of the First International Symposium on Generative and Component-Based Software Engineering
PPAM '01 Proceedings of the th International Conference on Parallel Processing and Applied Mathematics-Revised Papers
Proceedings of the 9th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface
Comparing high-level and low-level implementations of a molecular dynamics algorithm
HIPS '97 Proceedings of the 1997 Workshop on High-Level Programming Models and Supportive Environments (HIPS '97)
Blue Matter, an application framework for molecular simulation on blue gene
Journal of Parallel and Distributed Computing - High-performance computational biology
Parallel molecular dynamics simulation of Lennard-Jones liquids on a small Beowulf cluster
ICCMSE '03 Proceedings of the international conference on Computational methods in sciences and engineering
Remeshed smoothed particle hydrodynamics for the simulation of laminar chemically reactive flows
Journal of Computational Physics
Engineering high-performance legacy codes as CORBA components for problem-solving environments
Journal of Parallel and Distributed Computing
Comparing various parallelizing approaches for tribology simulations
High performance scientific and engineering computing
Experiments with Parallelizing Tribology Simulations
The Journal of Supercomputing
Characterizing a new class of threads in scientific applications for high end supercomputers
Proceedings of the 18th annual international conference on Supercomputing
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
Parallel Particle Simulations of Thin-Film Deposition
International Journal of High Performance Computing Applications
Using AMDAHL's Law as a Metric to Drive Code Parallelization: Two Case Studies
International Journal of High Performance Computing Applications
The implications of working set analysis on supercomputing memory hierarchy design
Proceedings of the 19th annual international conference on Supercomputing
Massively parallel implementation of a fast multipole method for distributed memory machines
Journal of Parallel and Distributed Computing
Improving Load Balance with Flexibly Assignable Tasks
IEEE Transactions on Parallel and Distributed Systems
Revisiting and parallelizing SHAKE
Journal of Computational Physics
Parallel molecular dynamics simulation in NPT ensemble and its application to general anesthesia
HPCASIA '05 Proceedings of the Eighth International Conference on High-Performance Computing in Asia-Pacific Region
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
First Experiences with Group Projects in CSE Education
Computing in Science and Engineering
Proceedings of the 2006 ACM SIGGRAPH symposium on Videogames
Scalable algorithms for molecular dynamics simulations on commodity clusters
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Architectures and APIs: assessing requirements for delivering FPGA performance to applications
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Multiscale diffusion Monte Carlo simulation of epitaxial growth
Journal of Computational Physics
Using the GA and TAO toolkits for solving large-scale optimization problems on parallel computers
ACM Transactions on Mathematical Software (TOMS)
Scalable molecular dynamics for large biomolecular systems
Scientific Programming
Anton, a special-purpose machine for molecular dynamics simulation
Proceedings of the 34th annual international symposium on Computer architecture
IEEE Transactions on Computers
Proceedings of the 21st annual international conference on Supercomputing
An Evaluation of the Oak Ridge National Laboratory Cray XT3
International Journal of High Performance Computing Applications
Implications of application usage characteristics for collective communication offload
International Journal of High Performance Computing and Networking
General purpose molecular dynamics simulations fully implemented on graphics processing units
Journal of Computational Physics
Proceedings of the 22nd annual international conference on Supercomputing
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Asymmetric interactions in symmetric multi-core systems: analysis, enhancements and evaluation
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Early evaluation of IBM BlueGene/P
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Numerical study of segregation using multiscale models
International Journal of Computational Fluid Dynamics - Mining and Mineral Processing
Alternative ways of coupling particle behaviour with fluid dynamics in mineral processing
International Journal of Computational Fluid Dynamics - Mining and Mineral Processing
Proceedings of the 3rd ACM Workshop on System-level Virtualization for High Performance Computing
Numerical study of segregation using multiscale models
International Journal of Computational Fluid Dynamics - CFD Methods of Mining and Mineral Processing
Alternative ways of coupling particle behaviour with fluid dynamics in mineral processing
International Journal of Computational Fluid Dynamics - CFD Methods of Mining and Mineral Processing
Dynamic Resizing of Parallel Scientific Simulations: A Case Study Using LAMMPS
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
Free Energy Correction to Rigid Body Docking: Application to the Colicin E7 and Im7 Complex
ICCS 2009 Proceedings of the 9th International Conference on Computational Science
Parallelization Strategies for Mixed Regular-Irregular Applications on Multicore-Systems
APPT '09 Proceedings of the 8th International Symposium on Advanced Parallel Processing Technologies
Parallel discrete element simulation of poly-dispersed granular material
Advances in Engineering Software
Instruction-level simulation of a cluster at scale
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Proceedings of the 5th Grid Computing Environments Workshop
Nanoaggregation and solubility of crude oil asphaltenes from molecular dynamics simulations
BIOCOMPUCHEM'09 Proceedings of the 3rd WSEAS International Conference on Computational Chemistry
International Journal of High Performance Computing Applications
Molecular dynamics simulations on commodity GPUs with CUDA
HiPC'07 Proceedings of the 14th international conference on High performance computing
HiPC'07 Proceedings of the 14th international conference on High performance computing
Asynchronous parallel molecular dynamics simulations
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Experimental evaluation of molecular dynamics simulations on multi-core systems
HiPC'08 Proceedings of the 15th international conference on High performance computing
HieraAnalyses – a tool for hierarchical analysis of parallel programs
International Journal of High Performance Systems Architecture
Identifying software usage at HPC centers with the automatic library tracking database
Proceedings of the 2010 TeraGrid Conference
Computer modeling and simulation of the nanoaggregation and solubility of crude oil asphaltenes
WSEAS Transactions on Computers
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Early evaluation of the cray XT3
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
CMC'10 Proceedings of the 11th international conference on Membrane computing
Quantifying NUMA and contention effects in multi-GPU systems
Proceedings of the Fourth Workshop on General Purpose Processing on Graphics Processing Units
Just in time: adding value to the IO pipelines of high performance applications with JITStaging
Proceedings of the 20th international symposium on High performance distributed computing
Proceedings of the 8th ACM International Conference on Computing Frontiers
Parallelising computational microstructure simulations for metallic materials with OpenMP
IWOMP'11 Proceedings of the 7th international conference on OpenMP in the Petascale era
The effect of interatomic potentials on the molecular dynamics simulation of nanometric machining
International Journal of Automation and Computing
libhashckpt: hash-based incremental checkpointing using GPU's
EuroMPI'11 Proceedings of the 18th European MPI Users' Group conference on Recent advances in the message passing interface
A survey of the practice of computational science
State of the Practice Reports
Evaluating the viability of process replication reliability for exascale systems
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
Journal of Computational Physics
Symmetrical data sieving for noncontiguous i/o accesses in molecular dynamics simulations
PVM/MPI'05 Proceedings of the 12th European PVM/MPI users' group conference on Recent Advances in Parallel Virtual Machine and Message Passing Interface
A hybrid molecular continuum method using point wise coupling
Advances in Engineering Software
Cluster-Based parallel simulation for large scale molecular dynamics in microscale thermophysics
ISPA'04 Proceedings of the Second international conference on Parallel and Distributed Processing and Applications
A new scalable parallel method for molecular dynamics based on cell-block data structure
ISPA'04 Proceedings of the Second international conference on Parallel and Distributed Processing and Applications
Learning by doing: software projects in CSE education
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Parallelization algorithms for three-body interactions in molecular dynamics simulation
ISPA'06 Proceedings of the 4th international conference on Parallel and Distributed Processing and Applications
Mathematical and Computer Modelling: An International Journal
Proper orthogonal decomposition of atomistic flow simulations
Journal of Computational Physics
Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations
Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond
Energy based performance tuning for large scale high performance computing systems
Proceedings of the 2012 Symposium on High Performance Computing
Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques
SIAM Journal on Scientific Computing
A parallel Lowe-Andersen thermostat for soft matter simulations
Proceedings of the ATIP/A*CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way?
βSn grain boundary structure and self-diffusivity via molecular dynamics simulation
Proceedings of the 2011 Grand Challenges on Modeling and Simulation Conference
High-resolution simulation of turbulent collision of cloud droplets
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part II
Boundary treatment effects on molecular dynamics simulations of interface thermal resistance
Journal of Computational Physics
Alleviating scalability issues of checkpointing protocols
SC '12 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Application data prefetching on the IBM blue gene/Q supercomputer
SC '12 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Distributed Infrastructure for Multiscale Computing
DS-RT '12 Proceedings of the 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications
Micro-applications for communication data access patterns and MPI datatypes
EuroMPI'12 Proceedings of the 19th European conference on Recent Advances in the Message Passing Interface
Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces
Journal of Computational Physics
MIC acceleration of short-range molecular dynamics simulations
Proceedings of the First International Workshop on Code OptimiSation for MultI and many Cores
The viability of using compression to decrease message log sizes
Euro-Par'12 Proceedings of the 18th international conference on Parallel processing workshops
Automatically mining program build information via signature matching
Proceedings of the 11th ACM SIGPLAN-SIGSOFT Workshop on Program Analysis for Software Tools and Engineering
Fault tolerance using lower fidelity data in adaptive mesh applications
Proceedings of the 3rd Workshop on Fault-tolerance for HPC at extreme scale
Determination of performance characteristics of scientific applications on IBM Blue Gene/Q
IBM Journal of Research and Development
Smoothed particle hydrodynamics non-Newtonian model for ice-sheet and ice-shelf dynamics
Journal of Computational Physics
Parallel multiscale simulations of a brain aneurysm
Journal of Computational Physics
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Hybrid MPI: efficient message passing for multi-core systems
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Effective sampling-driven performance tools for GPU-accelerated supercomputers
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
On-Board Multi-GPU molecular dynamics
Euro-Par'13 Proceedings of the 19th international conference on Parallel Processing
A study of application-level recovery methods for transient network faults
ScalA '13 Proceedings of the Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems
Scalability study of molecular dynamics simulation on Godson-T many-core architecture
Journal of Parallel and Distributed Computing
Evaluating energy savings for checkpoint/restart
E2SC '13 Proceedings of the 1st International Workshop on Energy Efficient Supercomputing
Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system
Journal of Parallel and Distributed Computing
Efficient parallel CFD-DEM simulations using OpenMP
Journal of Computational Physics
Proceedings of Annual IEEE/ACM International Symposium on Code Generation and Optimization
Accelerating incremental checkpointing for extreme-scale computing
Future Generation Computer Systems
Journal of Computational Physics
Parameterizing the Morse potential for coarse-grained modeling of blood plasma
Journal of Computational Physics
Journal of Parallel and Distributed Computing
From atoms to product reliability: toward a generalized multiscale simulation approach
Journal of Computational Electronics
Process modeling for advanced device technologies
Journal of Computational Electronics
Multiscale modelling of irradiation in nanostructures
Journal of Computational Electronics
Multiscale modeling and uncertainty quantification in nanoparticle-mediated drug/gene delivery
Computational Mechanics
The archetype-genome exemplar in molecular dynamics and continuum mechanics
Computational Mechanics
Analysis of Pd-Ni nanobelts melting process using molecular dynamics simulation
Journal of Nanomaterials - Special issue on Bimetallic Nanomaterials: Functional Efficacy towards Synthesis, Photocatalytic Degradation, and Biomedical Catalysts
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