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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.  ...  Specific findings show initial promise in scaling of such applications to larger production deployments targeting large scale computational workloads.  ...  Acknowledgments This work was developed with support from the National Science Foundation (NSF) under grant #0910812 to Indiana University and with support from the Office of Naval Research under grant  ... 
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.  ...  Specific findings show initial promise in scaling of such applications to larger production deployments targeting large scale computational workloads.  ...  Acknowledgments This work was developed with support from the National Science Foundation (NSF) under grant #0910812 to Indiana University and with support from the Office of Naval Research under grant  ... 
doi:10.1145/2817817.2731194 fatcat:t7wjnhvsx5cy5b4ugbb5pvtmie

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

Jitesh M., Sudershan Deshmukh
2016 International Journal of Computer Applications  
MD simulation are used for deeper understating of fluid flows, chemical reaction, and other phenomena due to molecular interaction.  ...  We present the new approach to utilize all heterogeneous resources like CPU cluster, GPU cluster in multi core and multi GPU environment.  ...  CONCLUSION Long CPU idle time and low CPU utilization were observed in current GPU-accelerated Molecular Dynamics simulation due to load not balanced between CPUs and GPUs.  ... 
doi:10.5120/ijca2016908137 fatcat:3katg4x3znd6tosdsfob2xzecm

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vetter
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
In this paper, we explain strategies for optimizing a molecular dynamics (MD) calculation that is used in bio-molecular simulations on three devices: Cell, GPU and MTA-2.  ...  On the other hand, substantial porting and optimization efforts on the Cell and the GPU systems result in a 5x to 6x improvement, respectively, over a 2.2 GHz Opteron system.  ...  Molecular Dynamics Calculations Molecular Dynamics (MD) is a computer simulation technique where the time evolution of a set of interacting atoms is followed by integrating the equations of motion [16  ... 
doi:10.1109/ipdps.2007.370444 dblp:conf/ipps/MeredithAV07 fatcat:kd4yexzdvzbqjmbl4vhachjrbi

Scalable molecular dynamics with NAMD on the Summit system

B. Acun, D. J. Hardy, L. V. Kale, K. Li, J. C. Phillips, J. E. Stone
2018 IBM Journal of Research and Development  
Optimizations for NAMD on Summit include: data layout changes for GPU acceleration and CPU vectorization, improving GPU offload efficiency, increasing performance with PAMI support in Charm++, improving  ...  NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such  ...  late 2016; and Antti-Pekka Hynninen contributed to GPU kernel development in NAMD through the IBM/NVIDIA Center of Excellence program at Oak Ridge National Laboratory and then at NVIDIA until his passing  ... 
doi:10.1147/jrd.2018.2888986 pmid:32154805 pmcid:PMC7059615 fatcat:aobf7zbykvdv7cmrbwccp423tm

Early experiences scaling VMD molecular visualization and analysis jobs on blue waters

John E. Stone, Barry Isralewitz, Klaus Schulten
2013 2013 Extreme Scaling Workshop (xsw 2013)  
Petascale molecular dynamics simulations provide a powerful tool for probing the dynamics of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone.  ...  Finally, we describe the unique capabilities provided by the Cray XK7 GPU-accelerated compute partition of Blue Waters.  ...  The authors wish to thank NCSA, NVIDIA, and Cray for providing system software enabling GPU-accelerated OpenGL rasterization on the Blue Waters XK7 nodes, per our requests.  ... 
doi:10.1109/xsw.2013.10 fatcat:czjno62d5ngb3dnmapwqq5yk6q

GPU-accelerated molecular modeling coming of age

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, Klaus Schulten
2010 Journal of Molecular Graphics and Modelling  
Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations  ...  Hardware acceleration with commodity GPUs is expected to benefit the overall computational biology community by bringing teraflops performance to desktop workstations and in some cases potentially changing  ...  ACEMD-Released as a commercially licensed biomolecular dynamics software package, ACEMD 8 is explicitly designed for execution by a single workstation with multiple GPUs [52] .  ... 
doi:10.1016/j.jmgm.2010.06.010 pmid:20675161 pmcid:PMC2934899 fatcat:kced26vphjb7hpqhf5ygeazwfa

Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

Hun-Joo Myung, Ryuji Sakamaki, Kwang-Jin Oh, Tetsu Narumi, Kenji Yasuoka, Sik Lee
2010 Bulletin of the Korean Chemical Society (Print)  
This suggests that GPU could be a useful hardware for molecular dynamics simulation.  ...  We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU.  ...  Conclusion We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU.  ... 
doi:10.5012/bkcs.2010.31.12.3639 fatcat:li2n6rxxx5bmxi4vbvxmdyrogq

GPU Passthrough Performance: A Comparison of KVM, Xen, VMWare ESXi, and LXC for CUDA and OpenCL Applications

John Paul Walters, Andrew J. Younge, Dong In Kang, Ke Thia Yao, Mikyung Kang, Stephen P. Crago, Geoffrey C. Fox
2014 2014 IEEE 7th International Conference on Cloud Computing  
In this paper we show that low overhead GPU passthrough is achievable across 4 major hypervisors and two processor microarchitectures.  ...  Accelerators such as GPUs offer improvements in both performance and power efficiency over traditional multi-core processors; however, their use in the cloud has been limited.  ...  LAMMPS: The Large-scale Atomic/Molecular Parallel Simulator (LAMMPS), is a parallel molecular dynamics simulator [14] , [17] used for production MD simulation on both CPUs and GPUs [18] .  ... 
doi:10.1109/cloud.2014.90 dblp:conf/IEEEcloud/WaltersYKYKCF14 fatcat:hcxmk4nvsjeudhvqobjdetbkiy

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  
we see for exascale simulation - in particular a very fine-grained task 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  ...  Hence, efficient utilization of Xeon Phi devices in molecular dynamics -especially with typical bio-molecular simulations and strong-scaling in mind -is only possible by treating them as accelerators.  ... 
doi:10.1007/978-3-319-15976-8_1 fatcat:rnekhgugmfe6zgpgwsybw4ywey

Adapting a message-driven parallel application to GPU-accelerated clusters

J.C. Phillips, J.E. Stone, K. Schulten
2008 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis  
We report the adaptation of these techniques to NAMD, a widely-used parallel molecular dynamics simulation package, and present performance results for a 64-core 64-GPU cluster.  ...  Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility of GPU hardware, and due to the availability  ...  In a molecular dynamics simulation, a collection of atoms interact through a set of forces based on atomic physics and quantum chemistry.  ... 
doi:10.1109/sc.2008.5214716 dblp:conf/sc/PhillipsSS08 fatcat:kzunlcf7wbexfnjxij55pcsr2y

Dynamic Scheduling for Work Agglomeration on Heterogeneous Clusters

Jonathan Lifflander, G. Carl Evans, Anshu Arya, Laxmikant V. Kale
2012 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum  
Heterogeneous clusters with highly data-parallel processors, such as GPUs, present unique problems for the application of these techniques.  ...  This paper describes a novel methodology for dynamically agglomerating work units at runtime and scheduling them on accelerators.  ...  NAMD [7] , a molecular dynamics simulation, statically agglomerates patch-pair calculations in a single compute object for the GPU.  ... 
doi:10.1109/ipdpsw.2012.297 dblp:conf/ipps/LifflanderEAK12 fatcat:2caloxbgincufgtktdus6kuea4

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

Tai-Sung Lee, Yuan Hu, Brad Sherborne, Zhuyan Guo, Darrin M. York
2017 Journal of Chemical Theory and Computation  
We demonstrate that pmemdGTI can be used to explore simulation times scales up to 100 times longer, opening the door to more meaningful assessment of errors in free energy estimates, and more practical  ...  abstract Accurate prediction of the binding affinity between a drug candidate and the target protein is one of the biggest challenges for computer-aided drug design (CADD). 1-3 A broad range of We report a GPU-accelerated  ...  We gratefully acknowledge the support of the Nvidia Corporation with the donation of a GTX Titan X (Pascal) GPU and the GPU-time of a GPU-cluster where the reported benchmark results were performed.  ... 
doi:10.1021/acs.jctc.7b00102 pmid:28618232 pmcid:PMC5843186 fatcat:r257m2pzkvcxxkopwsr7tgd5di

GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features

Tai-sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrian E. Roitberg, David A. Case, Ross C Walker, Darrin M. York
2018 Journal of Chemical Information and Modeling  
We report progress in GPU-accelerated molecular dynamics and free energy methods in Amber18.  ...  These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant pH molecular dynamics and new 12-6-4 potentials for metal ions.  ...  We gratefully acknowledge the support of the nVidia Corporation with the donation of several Pascal and Volta GPUs and the GPU-time of a GPU-cluster where the reported benchmark results were performed.  ... 
doi:10.1021/acs.jcim.8b00462 pmid:30199633 pmcid:PMC6226240 fatcat:g5na3zyn7ja63bhy5wwedsy6cu

Cell Charge Approximation For Accelerating Molecular Simulation On Cuda-Enabled Gpu

Jayaraj P B Shyam Mohan K T
2014 Zenodo  
Methods for Molecular Dynamics(MD) simulations are investigated. MD simulation is the widely used computer simulation approach to study the properties of molecular system.  ...  The major aim of this paper is to speed up the MD simulation calculations by/using General Purpose Graphics Processing Unit(GPU) computing paradigm, an efficient and economical way for parallel computing  ...  Force decomposition is rarely used in molecular dynamics simulations. For molecular simulation in GPU the best decomposition method is spatial decomposition [2] .  ... 
doi:10.5281/zenodo.1436258 fatcat:436nqzq7dngczlytj26ml5hrji
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