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- ArticleAugust 2024
VLASPH: Smoothed Particle Hydrodynamics on VLA SIMD Architectures
AbstractIn the domain of Computational Fluid Dynamics (CFD), Smoothed Particle Hydrodynamics (SPH) has gained increasing popularity compared with traditional grid-based methods. We have seen an increasing demand to accelerate the SPH method with new ...
- research-articleJuly 2024
HFN: Heterogeneous feature network for multivariate time series anomaly detection
Information Sciences: an International Journal (ISCI), Volume 670, Issue Chttps://doi.org/10.1016/j.ins.2024.120626AbstractAs the key step of anomaly detection for multivariate time-series (MTS) data, learning the relations among different variables has been explored by many approaches. However, most existing approaches overlook the heterogeneity among variables, ...
- research-articleJanuary 2023
Free energy perturbation–based large-scale virtual screening for effective drug discovery against COVID-19
- Zhe Li,
- Chengkun Wu,
- Yishui Li,
- Runduo Liu,
- Kai Lu,
- Ruibo Wang,
- Jie Liu,
- Chunye Gong,
- Canqun Yang,
- Xin Wang,
- Chang-Guo Zhan,
- Hai-Bin Luo,
- Mark Parsons
International Journal of High Performance Computing Applications (SAGE-HPCA), Volume 37, Issue 1Pages 45–57https://doi.org/10.1177/10943420221117797As a theoretically rigorous and accurate method, FEP-ABFE (Free Energy Perturbation-Absolute Binding Free Energy) calculations showed great potential in drug discovery, but its practical application was difficult due to high computational cost. To ...
- research-articleAugust 2022
VecDualSPHysics: A vectorized implementation of Smoothed Particle Hydrodynamics method for simulating fluid flows on multi-core processors
Journal of Computational Physics (JOCP), Volume 463, Issue Chttps://doi.org/10.1016/j.jcp.2022.111234AbstractAs one of the most promising mesh-free numerical approaches, the Smoothed Particle Hydrodynamics (SPH) algorithm can be used for simulating many engineering problems. However, it is necessary to fully exploit the performance of computing ...
- ArticleDecember 2021
Large-Scale Parallel Alignment Algorithm for SMRT Reads
- Zeyu Xia,
- Yingbo Cui,
- Ang Zhang,
- Peng Zhang,
- Sifan Long,
- Tao Tang,
- Lin Peng,
- Chun Huang,
- Canqun Yang,
- Xiangke Liao
Algorithms and Architectures for Parallel ProcessingPages 213–229https://doi.org/10.1007/978-3-030-95388-1_14AbstractSingle Molecule Real-Time (SMRT) sequencing is one of the popular issues in third-generation sequencing technology. Compared with next-generation sequencing technology, SMRT can detect single molecules and has much longer read lengths, which also ...
- research-articleFebruary 2020
Correlation maximization machine for multi-modalities multiclass classification
Pattern Analysis & Applications (PAAS), Volume 23, Issue 1Pages 349–358https://doi.org/10.1007/s10044-019-00795-2AbstractSupport vector machine (SVM) learns the maximum margin to separate training examples that belong to two classes and has been widely used in many pattern recognition tasks due to its high effectiveness. However, conventional SVM suffers from the ...
- research-articleAugust 2019
Application-aware NoC management in GPUs multitasking
The Journal of Supercomputing (JSCO), Volume 75, Issue 8Pages 4710–4730https://doi.org/10.1007/s11227-018-2694-xAbstractCurrent network-on-chip (NoC) designs in GPUs are agnostic to application requirements, and this leads to wasted performance in GPUs multitasking. We observe that applications can generally be classified as either network-sensitive or network-...
- ArticleOctober 2016
Streaming Applications on Heterogeneous Platforms
AbstractUsing multiple streams can improve the overall system performance by mitigating the data transfer overhead on heterogeneous systems. Currently, very few cases have been streamed to demonstrate the streaming performance impact and a systematic ...
- ArticleNovember 2008
Low Power Optimization for MPI Collective Operations
ICYCS '08: Proceedings of the 2008 The 9th International Conference for Young Computer ScientistsPages 1047–1052https://doi.org/10.1109/ICYCS.2008.500DVFS-available (Dynamic Voltage/Frequency Scaling) processors make it possible for a system to reduce the energy consumption by scaling down the frequency/voltage of the processors in high performance computing. For MPI collective operations, network ...
- ArticleMay 2008
Exploiting Energy Saving Opportunity of Barrier Operation in MPI Programs
AMS '08: Proceedings of the 2008 Second Asia International Conference on Modelling & Simulation (AMS)Pages 144–149https://doi.org/10.1109/AMS.2008.80In high performance parallel computing, energy consumption has become a more and more important problem. Under the support of the voltage scaling-available processors, reducing CPU voltage/frequency in the non-critical path is an efficient energy ...
- ArticleMarch 2008
OSS: Efficient Compiler Approach for Selecting Optimal Strip Size on the Imagine Stream Processor
AINAW '08: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications - WorkshopsPages 337–342https://doi.org/10.1109/WAINA.2008.63Strip-mining technique is critical for improving performance of large-scale scientific applications on Imagine. In this paper, we present a model-guided strip size selection approach (OSS) for finding the optimal strip size to minimize the execution ...