Search results for "Supercomputer"
showing 5 items of 45 documents
The Dynamical Kernel Scheduler - Part 1
2015
Emerging processor architectures such as GPUs and Intel MICs provide a huge performance potential for high performance computing. However developing software using these hardware accelerators introduces additional challenges for the developer such as exposing additional parallelism, dealing with different hardware designs and using multiple development frameworks in order to use devices from different vendors. The Dynamic Kernel Scheduler (DKS) is being developed in order to provide a software layer between host application and different hardware accelerators. DKS handles the communication between the host and device, schedules task execution, and provides a library of built-in algorithms. …
Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions
2022
Molecular dynamics (MD) simulations are playing an increasingly important role in many areas ranging from chemical materials to biological molecules. With the continuing development of MD models, the potentials are getting larger and more complex. In this article, we focus on the reactive force field (ReaxFF) potential from LAMMPS to optimize the computation of interactions. We present our efforts on refactoring for neighbor list building, bond order computation, as well as valence angles and torsion angles computation. After redesigning these kernels, we develop a vectorized implementation for non-bonded interactions, which is nearly $100 \times$ 100 × faster than the management processing…
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures
2018
Abstract Motivation Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. Results BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance perf…
A Simulation Based Analysis of an Multi Objective Diffusive Load Balancing Algorithm
2018
In this paper, we presented a further development of our research on developing an optimal software-hardware mapping framework. We used the Petri Net model of the complete hardware and software High Performance Computing (HPC) system running a Computational Fluid Dynamics (CFD) application, to simulate the behaviour of the proposed diffusive two level multi-objective load-balancing algorithm. We developed an meta-heuristic algorithm for generating an approximation of the Pareto-optimal set to be used as reference. The simulations showed the advantages of this algorithm over other diffusive algorithms: reduced computational and communication overhead and robustness due to low dependence on u…
Grid production with the ATLAS Event Service
2018
ATLAS has developed and previously presented a new computing architecture, the Event Service, that allows real time delivery of fine grained workloads which process dispatched events (or event ranges) and immediately streams outputs. The principal aim was to profit from opportunistic resources such as commercial cloud, supercomputing, and volunteer computing, and otherwise unused cycles on clusters and grids. During the development and deployment phase, its utility also on the grid and conventional clusters for the exploitation of otherwise unused cycles became apparent. Here we describe our experience commissioning the Event Service on the grid in the ATLAS production system. We study the …