Related papers: An Efficient SIMD Implementation of Pseudo-Verlet …
An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition…
This paper describes a new fast and implicitly parallel approach to neighbour-finding in multi-resolution Smoothed Particle Hydrodynamics (SPH) simulations. This new approach is based on hierarchical cell decompositions and sorted…
Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…
This paper describes a novel approach to neighbour-finding in Smoothed Particle Hydrodynamics (SPH) simulations with large dynamic range in smoothing length. This approach is based on hierarchical cell decompositions, sorted interactions,…
In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (10pJ/word on-die to 10,000pJ/word on the network). To increase memory locality at the hardware level and reduce…
We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a…
Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…
The Extended Discrete Element Method (XDEM) is an innovative numerical simulation technique that extends the dynamics of granular materials known as Discrete Element Method (DEM) by additional properties such as the thermodynamic state,…
Interactive exploration of large, multidimensional datasets plays a very important role in various scientific fields. It makes it possible not only to identify important structural features and forms, such as clusters of vertices and their…
We propose Partition Dimensions Across (PDX), a data layout for vectors (e.g., embeddings) that, similar to PAX [6], stores multiple vectors in one block, using a vertical layout for the dimensions (Figure 1). PDX accelerates exact and…
Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…
Hardware/Software (HW/SW) co-designed processors provide a promising solution to the power and complexity problems of the modern microprocessors by keeping their hardware simple. Moreover, they employ several runtime optimizations to…
The Discrete Element Method is widely employed for simulating granular flows, but conventional integration techniques may produce unphysical results for simulations with static friction when particle size ratios exceed $R \approx 3$. These…
We present a 'two-fluid' implementation of dust in smoothed particle hydrodynamics (SPH) in the test particle limit. The scheme is able to handle both short and long stopping times and reproduces the short friction time limit, which is not…
Neighbour embeddings (NE) allow the representation of high dimensional datasets into lower dimensional spaces and are often used in data visualisation. In practice, accelerated approximations are employed to handle very large datasets.…
Finding the exact close neighbors of each fluid element in mesh-free computational hydrodynamical methods, such as the Smoothed Particle Hydrodynamics (SPH), often becomes a main bottleneck for scaling their performance beyond a few million…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
We present an algorithm for neighbor search in molecular simulations on graphics processing units (GPUs) based on bounding volume hierarchies (BVHs). The BVH is compressed into a low-precision, quantized representation to increase the BVH…
With high computation power and memory bandwidth, graphics processing units (GPUs) lend themselves to accelerate data-intensive analytics, especially when such applications fit the single instruction multiple data (SIMD) model. However,…