Related papers: Optimized parallel tempering simulations of protei…
We propose an algorithm for generating explicit solutions of multiparametric mixed-integer convex programs to within a given suboptimality tolerance. The algorithm is applicable to a very general class of optimization problems, but is most…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Optimization of searching the best possible action depending on various states like state of environment, system goal etc. has been a major area of study in computer systems. In any search algorithm, searching best possible solution from…
Thermal aware routing and placement algorithms are important in industry. Currently, there are reasonably fast Green's function based algorithms that calculate the temperature distribution in a chip made from a stack of different materials.…
This paper presents implementation details and empirical results for a hybrid message passing and shared memory paralleliziation of the adaptive integral method (AIM). AIM is implemented on a (near) petaflop supercomputing cluster of…
We develop and implement a parallel flatPERM algorithm \cite{G97,PK04} with mutually interacting parallel flatPERM sequences and use it to sample self-avoiding walks in 2 and 3 dimensions. Our data show that the parallel implementation…
Pipeline parallelism is a crucial paradigm for large-scale model training. However, imbalances in memory footprint across stages can lead to significant GPU memory wastage, limiting the model sizes that pipeline parallelism can effectively…
This work presents a statistically principled method for estimating the required number of instances in the experimental comparison of multiple algorithms on a given problem class of interest. This approach generalises earlier results by…
Competing phases or interactions in complex many-particle systems can result in free energy barriers that strongly suppress thermal equilibration. Here we discuss how extended ensemble Monte Carlo simulations can be used to study the…
Neuromorphic or neurally-inspired optimizers rely on local but parallel parameter updates to solve problems that range from quadratic programming to Ising machines. An ideal realization of such an optimizer not only uses a compute-in-memory…
This study was undertaken to develop a system for heat transfer simulation for optimization and treatment planning of magnetic hyperthermia treatment (MHT) using magnetic particle imaging (MPI). First, we performed phantom experiments to…
Parallel algorithms designed for simulation and performance evaluation of single-server tandem queueing systems with both infinite and finite buffers are presented. The algorithms exploit a simple computational procedure based on recursive…
Aligning partially overlapping point sets where there is no prior information about the value of the transformation is a challenging problem in computer vision. To achieve this goal, we first reduce the objective of the robust point…
We consider a hybrid FEM-BEM method to compute approximations of full-space linear elliptic transmission problems. First, we derive a priori and a posteriori error estimates. Then, building on the latter, we present an adaptive algorithm…
We present a new parallel algorithm for probabilistic graphical model optimization. The algorithm relies on data-parallel primitives (DPPs), which provide portable performance over hardware architecture. We evaluate results on CPUs and GPUs…
A solid system consisting of two heat conducting cylinders with a thermoelectric converter (Peltier element) between them is considered. A nonlinear model, which was previously verified by authors, is used to design a constrained control…
In this paper we demonstrate that tempering Markov chain Monte Carlo samplers for Bayesian models by recursively subsampling observations without replacement can improve the performance of baseline samplers in terms of effective sample size…
Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…
Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for…