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Integrating multi-level molecular simulations across heterogeneous resources

Yudong Sun, Steve McKeever, Kia Balali-Mood, Mark S. P. Sansom
2007 2007 8th IEEE/ACM International Conference on Grid Computing  
This work made use of the UK Grid resources of NGS and HPCx.  ...  The authors thank all collaborators including Graham Riley and Rupert Ford for the proposed hybrid MD simulation model, and Adrian Mulholland and Christo Christov for the QM/MM simulation and data.  ...  That is, each simulation is resource-dependent, whereas the entire simulation infrastructure ought to be resource-neutral to allow seamless integration of the simulations on all levels and across heterogeneous  ... 
doi:10.1109/grid.2007.4354129 dblp:conf/grid/SunMBS07 fatcat:kn74346kf5cojeputgnmkeuoii

Comparative Study: MD Simulation with different Load Balancing Technique on Heterogeneous Environment

Jitesh M., Sudershan Deshmukh
2016 International Journal of Computer Applications  
We present the new approach to utilize all heterogeneous resources like CPU cluster, GPU cluster in multi core and multi GPU environment.  ...  MD simulation are used for deeper understating of fluid flows, chemical reaction, and other phenomena due to molecular interaction.  ...  Therefore, it enables the workload to be balanced across heterogeneous resources and efficiently utilize all resources.  ... 
doi:10.5120/ijca2016908137 fatcat:3katg4x3znd6tosdsfob2xzecm

A Grid-Based Bridging Domain Multiple-Scale Method for Computational Nanotechnology [chapter]

Shaowen Wang, Shaoping Xiao, Jun Ni
2005 Lecture Notes in Computer Science  
This paper presents an application-level Grid middleware framework to support a bridging domain multi-scale method fornumerical modeling and simulation in nanotechnology.  ...  The framework is designed to enable researchers to conductlarge-scale computing in computational nanotechnology through the use of Grid resources for exploring microscopic physical properties of materials  ...  The workflow demonstrates the integration of computational nanotechnology and computer science in this multi-disciplinary project.  ... 
doi:10.1007/11428862_45 fatcat:xmch76aqynfyhk4736dc645lni

Detailed author index

2007 2007 8th IEEE/ACM International Conference on Grid Computing  
Platform for High Availability Grid Operations McKeever, Steve 161 Integrating Multi-Level Molecular Simulations Across Heterogeneous Resources Mehta, Gaurang 267 Data Placement for Scientific  ...  Multi-Level Molecular Simulations Across Heterogeneous Resources Suter, Frédéric 2 Scheduling Δ-Critical Tasks in Mixed-Parallel Applications on a National Grid Swany, Martin 226 Log Summarization  ... 
doi:10.1109/grid.2007.4354098 fatcat:bdepm2c3ajc2llfrcmioopsxve

Toward an integrated software platform for systems pharmacology

Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin, Hiroaki Kitano
2013 Biopharmaceutics & drug disposition  
Establishing an integrated software platform will be the next important step in the field.  ...  A series of software and data resources are used for model development, verification and exploration of the possible behaviors of biological systems using the model that may not be possible or not cost  ...  While a cellular level model often plays a pivotal role, integration from the molecular level to the whole body level is critical because changes in the molecular and genetic level may affect the physiological  ... 
doi:10.1002/bdd.1875 pmid:24150748 pmcid:PMC4253131 fatcat:l4dvxrd4qzeqro75ysop35j4b4

AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing

Tanmoy Bhattacharya, Thomas Brettin, James H. Doroshow, Yvonne A. Evrard, Emily J. Greenspan, Amy L. Gryshuk, Thuc T. Hoang, Carolyn B. Vea Lauzon, Dwight Nissley, Lynne Penberthy, Eric Stahlberg, Rick Stevens (+4 others)
2019 Frontiers in Oncology  
Unique challenges persist, however, in building ML models related to cancer, including: (1) access, sharing, labeling, and integration of multimodal and multi-institutional data across different cancer  ...  effort focused on advancing computing and data technologies to accelerate cancer research on three levels: molecular, cellular, and population.  ...  human-AI workflow integration for broad and standardized technology integration across registries.  ... 
doi:10.3389/fonc.2019.00984 pmid:31632915 pmcid:PMC6783509 fatcat:7n67izqty5gz7icvxmqrbwmora

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action [article]

Anda Trifan, Defne Gorgun, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin R Clyde, David A Clark, Michael Salim, David Hardy, Tom Burnley, Lei Huang (+21 others)
2021 bioRxiv   pre-print
We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers.  ...  Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.  ...  Multiscale biological simulations Integrating data across diverse spatial, temporal, and functional scales has played an important role in understanding the role of molecular interactions in various diseases  ... 
doi:10.1101/2021.10.09.463779 fatcat:4oluasz3jbgnvhwryercs6jts4

Preparing GROMACS for Heterogeneous Exascale HPC Systems

Szilárd Páll, Andrey Alekseenko
2022 figshare.com  
At its core, it was a bottom-up redesign of the simulation engine, starting with reformulating key MD algorithms for modern processor microarchitectures combined with a heterogeneous multi-level parallelisation  ...  To do so, the integration was offloaded, allowing the molecular simulation state to remain resident on the GPU for tens to hundreds of iterations.  ... 
doi:10.6084/m9.figshare.19945430.v1 fatcat:fwpryvllqzgw5aeg55orkoynim

D7.6: Numerical Libraries for Heterogeneous/Hybrid Architectures

Prashanth Kanduri, Victor Holanda Rusu, Raffaele Solcà
2019 Zenodo  
This integration involves significant refactor to separate concerns along with multi-level APIs for integration of new features for developers, as well as for comp [...]  ...  Non-Bonded Interactions (NBI) in Classical Molecular Dynamics In any molecular dynamics (MD) simulation, computation of the NBI between various particles overwhelmingly dominate the compute loads.  ...  This integration involves significant refactor to separate concerns along with multi-level APIs for integration of new features for developers, as well as for composing high level workflows for end-users  ... 
doi:10.5281/zenodo.6806001 fatcat:hpulniancbh6fomojhgbvtrfim

CyberInfrastructures of cyber-applications-systems

Frederica Darema
2010 Procedia Computer Science  
The paper discusses considerations of dynamic invocation of multi-scale models, uncertainty quantification, uncertainty propagation, and dynamic runtime systems support on heterogeneous, distributed, end-to-end  ...  dynamically integrated high-end, real-time and instrumentation and control systems.  ...  support on heterogeneous, distributed, end-to-end dynamically integrated high-end, real-time and instrumentation and control systems.  ... 
doi:10.1016/j.procs.2010.04.143 fatcat:a6umb62gufcbnogzz7d26osmae

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS [chapter]

Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
2015 Lecture Notes in Computer Science  
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism  ...  The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges  ...  Computational resources were provided by the Swedish National Infrastructure for computing (grants SNIC 025/12-32 & 2013-26/24) and the Leibniz Supercomputing Center.  ... 
doi:10.1007/978-3-319-15976-8_1 fatcat:rnekhgugmfe6zgpgwsybw4ywey

Developing a European grid infrastructure for cancer research: vision, architecture, and services

M Tsiknakis
2015 ecancermedicalscience  
Data integration across heterogeneous data sources and data aggregation across different aspects of the biomedical spectrum, therefore, is at the centre of current biomedical and pharmaceutical R&D.  ...  Post-genomic CTs use multi-level clinical and genomic data and advanced computational analysis and visualization tools to test hypotheses in trying to identify the molecular reasons for a disease and the  ...  modelling and simulation, considering and integrating from the molecular to the systems biology level and from the organ to the living organism level; 4. standards for exposing the properties of local  ... 
doi:10.3332/ecancer.2007.56 fatcat:c4imtkihsrh3djksxu6frunesu

Developing a European Grid Infrastructure for Cancer Research: Vision, Architecture, and Services

M Tsiknakis
2007 ecancermedicalscience  
Data integration across heterogeneous data sources and data aggregation across different aspects of the biomedical spectrum, therefore, is at the centre of current biomedical and pharmaceutical R&D.  ...  Post-genomic CTs use multi-level clinical and genomic data and advanced computational analysis and visualization tools to test hypotheses in trying to identify the molecular reasons for a disease and the  ...  modelling and simulation, considering and integrating from the molecular to the systems biology level and from the organ to the living organism level; 4. standards for exposing the properties of local  ... 
doi:10.3332/ecms.2007.56 pmid:22275955 pmcid:PMC3223975 fatcat:w5drhkauzneafiwiuhzaeavtfa

Supporting High Performance Molecular Dynamics in Virtualized Clusters using IOMMU, SR-IOV, and GPUDirect

Andrew J. Younge, John Paul Walters, Stephen P. Crago, Geoffrey C. Fox
2015 Proceedings of the 11th ACM SIGPLAN/SIGOPS International Conference on Virtual Execution Environments - VEE '15  
By using KVM virtual machines that leverage both Nvidia GPUs and InfiniBand, we show that molecular dynamics simulations with LAMMPS and HOOMD run at near-native speeds.  ...  In this model, the cloud level scheduler dispatches jobs to nodes based on resource requirements (e.g. Kepler GPU) and node level resource availability.  ...  In our earlier work, we have developed a cloud level heterogeneous scheduler for OpenStack that allows scheduling based on architectures and resources [14] .  ... 
doi:10.1145/2731186.2731194 dblp:conf/vee/YoungeWCF15 fatcat:s6pvv43ahrgvplr4zwwpvmcvqi

Supporting High Performance Molecular Dynamics in Virtualized Clusters using IOMMU, SR-IOV, and GPUDirect

Andrew J. Younge, John Paul Walters, Stephen P. Crago, Geoffrey C. Fox
2015 SIGPLAN notices  
By using KVM virtual machines that leverage both Nvidia GPUs and InfiniBand, we show that molecular dynamics simulations with LAMMPS and HOOMD run at near-native speeds.  ...  In this model, the cloud level scheduler dispatches jobs to nodes based on resource requirements (e.g. Kepler GPU) and node level resource availability.  ...  In our earlier work, we have developed a cloud level heterogeneous scheduler for OpenStack that allows scheduling based on architectures and resources [14] .  ... 
doi:10.1145/2817817.2731194 fatcat:t7wjnhvsx5cy5b4ugbb5pvtmie
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