0000000000589861
AUTHOR
Lin Gan
showing 5 related works from this author
Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight
2020
Large-scale molecular dynamics (MD) simulations on supercomputers play an increasingly important role in many research areas. With the capability of simulating charge equilibration (QEq), bonds and so on, Reactive force field (ReaxFF) enables the precise simulation of chemical reactions. Compared to the first principle molecular dynamics (FPMD), ReaxFF has far lower requirements on computational resources so that it can achieve higher efficiencies for large-scale simulations. In this article, we present our efforts on scaling ReaxFF on the Sunway TaihuLight Supercomputer (TaihuLight). We have carefully redesigned the force analysis and neighbor list building steps. By applying fine-grained …
Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer
2020
Molecular dynamics (MD) simulations are playing an increasingly important role in many research areas. Pair-wise potentials are widely used in MD simulations of bio-molecules, polymers, and nano-scale materials. Due to a low compute-to-memory-access ratio, their calculation is often bounded by memory transfer speeds. Sunway TaihuLight is one of the fastest supercomputers featuring a custom SW26010 many-core processor. Since the SW26010 has some critical limitations regarding main memory bandwidth and scratchpad memory size, it is considered as a good platform to investigate the optimization of pair-wise potentials especially in terms of data reusage. MD algorithms often use a neighbor-list …
BLBP-expression in astrocytes during experimental demyelination and in human multiple sclerosis lesions
2011
Several lines of evidence indicate that remyelination represents one of the most effective mechanisms to achieve axonal protection. For reasons that are not yet understood, this process is often incomplete or fails in multiple sclerosis (MS). Activated astrocytes appear to be able to boost or inhibit endogenous repair processes. A better understanding of remyelination in MS and possible reasons for its failure is needed. Using the well-established toxic demyelination cuprizone model, we created lesions with either robust or impaired endogenous remyelination capacity. Lesions were analyzed for mRNA expression levels by Affymetrix GeneChip® arrays. One finding was the predominance of immune a…
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…
Cell-List based Molecular Dynamics on Many-Core Processors: A Case Study on Sunway TaihuLight Supercomputer
2020
Molecular dynamics (MD) simulations are playing an increasingly important role in several research areas. The most frequently used potentials in MD simulations are pair-wise potentials. Due to the memory wall, computing pair-wise potentials on many-core processors are usually memory bounded. In this paper, we take the SW26010 processor as an exemplary platform to explore the possibility to break the memory bottleneck by improving data reusage via cell-list-based methods. We use cell-lists instead of neighbor-lists in the potential computation, and apply a number of novel optimization methods. Theses methods include: an adaptive replica arrangement strategy, a parameter profile data structur…