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Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
This paper presents a realization of the approach to spatial 3D stereo of visualization of 3D images with use parallel Graphics processing unit (GPU). The experiments of realization of synthesis of images of a 3D stage by a method of trace…
In this paper we present an optimized parallel implementation of a flexible MAP decoder for synchronization error correcting codes, supporting a very wide range of code sizes and channel conditions. On mid-range GPUs we demonstrate decoding…
The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on…
Generation of optimal codes is a well known problem in coding theory. Many computational approaches exist in the literature for finding record breaking codes. However generating codes with long lengths $n$ using serial algorithms is…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
Maximizing parallelism level in applications can be achieved by minimizing overheads due to load imbalances and waiting time due to memory latencies. Compiler optimization is one of the most effective solutions to tackle this problem. The…
We present a simple and easy to apply methodology for using high-level self-submitting parallel job queues in an MPI environment. Using C++, we implemented a library of functions, MPQueue, both for testing our concepts and for use in real…
Sequential computation is well understood but does not scale well with current technology. Within the next decade, systems will contain large numbers of processors with potentially thousands of processors per chip. Despite this, many…
Graphics Processing Units (GPUs) have become the standard in accelerating scientific applications on heterogeneous systems. However, as GPUs are getting faster, one potential performance bottleneck with GPU-accelerated applications is the…
We investigate GPU-based parallelization of Iterative-Deepening A* (IDA*). We show that straightforward thread-based parallelization techniques which were previously proposed for massively parallel SIMD processors perform poorly due to warp…
We study parallel algorithms for the minimisation and equivalence checking of Deterministic Finite Automata (DFAs). Regarding DFA minimisation, we implement four different massively parallel algorithms on Graphics Processing Units~(GPUs).…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
There has been considerable research into improving Fast Fourier Transform (FFT) performance through parallelization and optimization for specialized hardware. However, even with those advancements, processing of very large files, over 1TB…
To effectively control large-scale distributed systems online, model predictive control (MPC) has to swiftly solve the underlying high-dimensional optimization. There are multiple techniques applied to accelerate the solving process in the…
MPI derived datatypes are an abstraction that simplifies handling of non-contiguous data in MPI applications. These datatypes are recursively constructed at runtime from primitive Named Types defined in the MPI standard. More recently, the…
Compactly expressing large-scale datasets through Multivariate Functional Approximations (MFA) can be critically important for analysis and visualization to drive scientific discovery. Tackling such problems requires scalable data…
We study parallel algorithms for the minimization of Deterministic Finite Automata (DFAs). In particular, we implement four different massively parallel algorithms on Graphics Processing Units (GPUs). Our results confirm the expectations…
We present four high performance hybrid sorting methods developed for various parallel platforms: shared memory multiprocessors, distributed multiprocessors, and clusters taking advantage of existence of both shared and distributed memory.…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…