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Supporting High Performance Molecular Dynamics in Virtualized Clusters using IOMMU, SR-IOV, and GPUDirect
2015
Proceedings of the 11th ACM SIGPLAN/SIGOPS International Conference on Virtual Execution Environments - VEE '15
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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
2015
SIGPLAN notices
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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
2016
International Journal of Computer Applications
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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
2007
2007 IEEE International Parallel and Distributed Processing Symposium
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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
2018
IBM Journal of Research and Development
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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
2013
2013 Extreme Scaling Workshop (xsw 2013)
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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
2010
Journal of Molecular Graphics and Modelling
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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
2010
Bulletin of the Korean Chemical Society (Print)
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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
2014
2014 IEEE 7th International Conference on Cloud Computing
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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]
2015
Lecture Notes in Computer Science
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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
2008
2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis
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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
2012
2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum
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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
2017
Journal of Chemical Theory and Computation
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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
2018
Journal of Chemical Information and Modeling
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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
2014
Zenodo
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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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