Related papers: A simple asynchronous replica-exchange implementat…
We evaluate optimized parallel sparse matrix-vector operations for two representative application areas on widespread multicore-based cluster configurations. First the single-socket baseline performance is analyzed and modeled with respect…
Applications to process seismic data employ scalable parallel systems to produce timely results. To fully exploit emerging processor architectures, application will need to employ threaded parallelism within a node and message passing…
Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly…
Now days, manufacturers are focusing on increasing the concurrency in multiprocessor system-on-a-chip (MPSoC) architecture instead of increasing clock speed, for embedded systems. Traditionally lock-based synchronization is provided to…
Comprehending the performance bottlenecks at the core of the intricate hardware-software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Replica exchange Monte Carlo (reMC), also known as parallel tempering, is an important technique for accelerating the convergence of the conventional Markov Chain Monte Carlo (MCMC) algorithms. However, such a method requires the evaluation…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
We propose an efficient Monte Carlo algorithm for simulating a ``hardly-relaxing" system, in which many replicas with different temperatures are simultaneously simulated and a virtual process exchanging configurations of these replica is…
In this paper, we present STAR, a new distributed in-memory database with asymmetric replication. By employing a single-node non-partitioned architecture for some replicas and a partitioned architecture for other replicas, STAR is able to…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
In order to increase availability in a distributed system some or all of the data items are replicated and stored at separate sites. This is an issue of key concern especially since there is such a proliferation of wireless technologies and…
We present here two novel algorithms for simulated tempering simulations, which break detailed balance condition (DBC) but satisfy the skewed detailed balance to ensure invariance of the target distribution. The irreversible methods we…
Markov Chain Monte Carlo (MCMC) algorithms are essential tools in computational statistics for sampling from unnormalised probability distributions, but can be fragile when targeting high-dimensional, multimodal, or complex target…
Parallel tempering (PT) is a class of Markov chain Monte Carlo algorithms that constructs a path of distributions annealing between a tractable reference and an intractable target, and then interchanges states along the path to improve…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
State machine replication is standard approach to fault tolerance. One of the key assumptions of state machine replication is that replicas must execute operations deterministically and thus serially. To benefit from multi-core servers,…
In the near future, massively parallel computing systems will be necessary to solve computation intensive applications. The key bottleneck in massively parallel implementation of numerical algorithms is the synchronization of data across…
This paper introduces a framework for distributed parallel image signal extrapolation. Since high-quality image signal processing often comes along with a high computational complexity, a parallel execution is desirable. The proposed…