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In this work, we survey the role of GPUs in real-time systems. Originally designed for parallel graphics workloads, GPUs are now widely used in time-critical applications such as machine learning, autonomous vehicles, and robotics due to…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
GPUs are the most popular platform for accelerating HPC workloads, such as artificial intelligence and science simulations. However, most microarchitectural research in academia relies on GPU core pipeline designs based on architectures…
Structural parameters are normally extracted from observed galaxies by fitting analytic light profiles to the observations. Obtaining accurate fits to high-resolution images is a computationally expensive task, requiring many model…
Dynamic Parallelism (DP) is a runtime feature of the GPU programming model that allows GPU threads to execute additional GPU kernels, recursively. Apart from making the programming of parallel hierarchical patterns easier, DP can also…
The Random Phase Approximation (RPA) for correlation energy in the grid-based projector augmented wave (gpaw) code is accelerated by porting to the Graphics Processing Unit (GPU) architecture. The acceleration is achieved by grouping…
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…
The answers to data assimilation questions can be expressed as path integrals over all possible state and parameter histories. We show how these path integrals can be evaluated numerically using a Markov Chain Monte Carlo method designed to…
Simulating large-scale microswimmer dynamics in viscous fluid poses significant challenges due to the coupled high spatial and temporal complexity. Conventional high-performance computing (HPC) methods often address these two dimensions in…
Cycle-level simulators such as gem5 are widely used in microarchitecture design, but they are prohibitively slow for large-scale design space explorations. We present Concorde, a new methodology for learning fast and accurate performance…
Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…
We carry out a comparative performance study of multi-core CPUs, GPUs and Intel Xeon Phi (Many Integrated Core - MIC) with a microscopy image analysis application. We experimentally evaluate the performance of computing devices on core…
Many techniques in program synthesis, superoptimization, and array programming require parallel rollouts of general-purpose programs. GPUs, while capable targets for domain-specific parallelism, are traditionally underutilized by such…
In this work, we present an extension of Gaussian process (GP) models with sophisticated parallelization and GPU acceleration. The parallelization scheme arises naturally from the modular computational structure w.r.t. datapoints in the…
Principal component analysis (PCA) is a statistical technique commonly used in multivariate data analysis. However, PCA can be difficult to interpret and explain since the principal components (PCs) are linear combinations of the original…
Graphics Processing Unit (GPU) computing is becoming an alternate computing platform for numerical simulations. However, it is not clear which numerical scheme will provide the highest computational efficiency for different types of…
This paper investigates the application of a robust CPU-based power modelling methodology that performs an automatic search of explanatory events derived from performance counters to embedded GPUs. A 64-bit Tegra TX1 SoC is configured with…
Graphics Processing Units (GPUs) are becoming popular accelerators in modern High-Performance Computing (HPC) clusters. Installing GPUs on each node of the cluster is not efficient resulting in high costs and power consumption as well as…
Principal component analysis (PCA) is a key statistical technique for multivariate data analysis. For large data sets the common approach to PCA computation is based on the standard NIPALS-PCA algorithm, which unfortunately suffers from…