Scaling read aligners to hundreds of threads on general-purpose processors

B Langmead, C Wilks, V Antonescu, R Charles - Bioinformatics, 2019 - academic.oup.com
Motivation General-purpose processors can now contain many dozens of processor cores
and support hundreds of simultaneous threads of execution. To make best use of these …

[HTML][HTML] A taxonomy of task-based parallel programming technologies for high-performance computing

P Thoman, K Dichev, T Heller, R Iakymchuk… - The Journal of …, 2018 - Springer
Task-based programming models for shared memory—such as Cilk Plus and OpenMP 3—
are well established and documented. However, with the increase in parallel, many-core …

A survey of algorithmic skeleton frameworks: high‐level structured parallel programming enablers

H González‐Vélez, M Leyton - Software: Practice and …, 2010 - Wiley Online Library
Structured parallel programs ought to be conceived as two separate and complementary
entities: computation, which expresses the calculations in a procedural manner, and …

A massively parallel and scalable multi-GPU material point method

X Wang, Y Qiu, SR Slattery, Y Fang, M Li… - ACM Transactions on …, 2020 - dl.acm.org
Harnessing the power of modern multi-GPU architectures, we present a massively parallel
simulation system based on the Material Point Method (MPM) for simulating physical …

[HTML][HTML] PARMA-CC: A family of parallel multiphase approximate cluster combining algorithms

A Keramatian, V Gulisano, M Papatriantafilou… - Journal of Parallel and …, 2023 - Elsevier
Clustering is a common task in data analysis applications. Despite the extensive literature,
the continuously increasing volumes of data produced by sensors (eg, rates of several MB/s …

Tasking framework for adaptive speculative parallel mesh generation

C Tsolakis, P Thomadakis, N Chrisochoides - The Journal of …, 2022 - Springer
Handling the ever-increasing complexity of mesh generation codes along with the intricacies
of newer hardware often results in codes that are both difficult to comprehend and maintain …

The challenges of elastic in situ analysis and visualization

M Dorier, O Yildiz, T Peterka, R Ross - … of the Workshop on In Situ …, 2019 - dl.acm.org
In situ analysis and visualization have been proposed in high-performance computing
(HPC) to enable executing analysis tasks while a simulation is running, bypassing the …

Parallel planning of Marine Observation Tasks Based on threading building blocks

Z Zhang, D Li, M Zhao, Y Yao, SY Lee - International Journal of …, 2021 - ijpe-online.com
Marine monitoring has diverse targets. How to complete the observation over marine targets
to the largest extent by reasonably and efficiently allocating various observation platform …

ZNNi: maximizing the inference throughput of 3D convolutional networks on CPUs and GPUs

A Zlateski, K Lee, HS Seung - SC'16: Proceedings of the …, 2016 - ieeexplore.ieee.org
Sliding window convolutional networks (ConvNets) have become a popular approach to
computer vision problems such as image segmentation and object detection and …

SLPA-based parallel overlap** community detection approach in large complex social networks

A Mahabadi, M Hosseini - Multimedia tools and applications, 2021 - Springer
Performance improvement of community detection is an NP problem in large social networks
analysis where by integrating the overlapped communities' information and modularity …