Related papers: A hybrid algorithm for parallel molecular dynamics…
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…
Simulators are a primary tool in computer architecture research but are extremely computationally intensive. Simulating modern architectures with increased core counts and recent workloads can be challenging, even on modern hardware. This…
Arrival of multicore systems has enforced a new scenario in computing, the parallel and distributed algorithms are fast replacing the older sequential algorithms, with many challenges of these techniques. The distributed algorithms provide…
We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant…
We provide algorithms for efficiently addressing quantum memory in parallel. These imply that the standard circuit model can be simulated with low overhead by the more realistic model of a distributed quantum computer. As a result, the…
In this paper we analyze, evaluate, and improve the performance of training generalized linear models on modern CPUs. We start with a state-of-the-art asynchronous parallel training algorithm, identify system-level performance bottlenecks,…
The high cost of sequential time integration is one major constraint that limits the speedup of a time-parallel algorithm like the Parareal algorithm due to the difficulty of coarsening time steps in a stiff numerical problem. To address…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
A parallelized quantum dynamics package using the Smolyak algorithm for general molecular simulation is introduced in this work. The program has no limitation of the Hamiltonian form and provides high flexibility on the simulation setup to…
In this work, we investigate the potential utility of parallelization for meeting real-time constraints and minimizing energy. We consider malleable Gang scheduling of implicit-deadline sporadic tasks upon multiprocessors. We first show the…
Parallel tempering simulates at many quark masses simultaneously, by changing the mass during the simulation while remaining in equilibrium. The algorithm is faster than pure HMC if more than one mass is needed, and works better the smaller…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
In this study, we have developed a parallel version of the random time simulation algorithm. Firstly, we gave a rigorous basis of the random time description of the stochastic process of chemical reaction network time evolution. And then we…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Manufacturers have been developing new graphics processing unit (GPU) nodes with large capacity, high bandwidth memory and very high bandwidth intra-node interconnects. This enables moving large amounts of data between GPUs on the same node…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step…
Coupled models are set to become increasingly important in all aspects of science and engineering as tools with which to study complex systems in an integrated manner. Such coupled, hybrid simulations typically communicate data between the…
We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication…
Breadth-first search (BFS) is a fundamental graph algorithm that presents significant challenges for parallel implementation due to irregular memory access patterns, load imbalance and synchronization overhead. In this paper, we introduce a…