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In recent years, there has been increasing interest in network diffusion models and related problems. The most popular of these are the independent cascade and linear threshold models. Much of the recent experimental work done on these…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Efficiently solving nonlinear equations underpins numerous scientific and engineering disciplines, yet scaling these solutions for challenging system models remains a challenge. This paper presents NonlinearSolve.jl -- a suite of…
There is a growing need for distributed graph processing systems that are capable of gracefully scaling to very large graph datasets. Unfortunately, this challenge has not been easily met due to the intense memory pressure imposed by…
Linear Programs (LPs) appear in a large number of applications and offloading them to a GPU is viable to gain performance. Existing work on offloading and solving an LP on a GPU suggests that there is performance gain generally on large…
Robot motion can have many goals. Depending on the task, we might optimize for pose error, speed, collision, or similarity to a human demonstration. Motivated by this, we present PyRoki: a modular, extensible, and cross-platform toolkit for…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
The Epiphany is a many-core, low power, low on-chip memory architecture and one can very cheaply gain access to a number of parallel cores which is beneficial for HPC education and prototyping. The very low power nature of these…
Over the past few years machine learning has seen a renewed explosion of interest, following a number of studies showing the effectiveness of neural networks in a range of tasks which had previously been considered incredibly hard. Neural…
Automated data-driven modeling, the process of directly discovering the governing equations of a system from data, is increasingly being used across the scientific community. PySINDy is a Python package that provides tools for applying the…
Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…
High Energy Physics (HEP) experiments are making increasing use of GPUs and GPU dominated High Performance Computer facilities. Both the software and hardware of these systems are rapidly evolving, creating challenges for experiments to…
State of art DL models are growing in size and complexity, with many modern models also increasing in heterogeneity of behavior. GPUs are still the dominant platform for DL applications, relying on a bulk-synchronous execution model which…
Evolutionary computing (EC) has proven to be effective in solving complex optimization and robotics problems. Unfortunately, typical Evolutionary Algorithms (EAs) are constrained by the computational capacity available to researchers. More…
A high-performance gas kinetic solver using multi-level parallelization is developed to enable pore-scale simulations of rarefied flows in porous media. The Boltzmann model equation is solved by the discrete velocity method with an…
The pyFAI package has been designed to reduce X-ray diffraction images into powder diffraction curves to be further processed by scientists. This contribution describes how to convert an image into a radial profile using the Numpy package,…
We propose, implement, and experimentally evaluate a runtime middleware to support high-throughput execution on hybrid cluster machines of large-scale analysis applications. A hybrid cluster machine consists of computation nodes which have…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…