arXiv subjects

Pietro Incardona

Publications and source records attributed to Pietro Incardona.

8 recordsLinked to original sources

arXiv2025

Integrating Odeint Time Stepping into OpenFPM for Distributed and GPU Accelerated Numerical Solvers

We present a software implementation integrating the time-integration library Odeint from Boost with the OpenFPM framework for scalable scientific computing. This enables compact and scalable codes for multi-stage, multi-step, and adaptive explicit time integration on distributed-memory parallel computers and on Graphics Processing Units (GPUs). The present implementation is based on extending OpenFPM's metaprogramming system to Odeint data types. This makes the time-integration methods from Odeint available in a concise template-expression language for numerical simulations distributed and parallelized using OpenFPM. We benchmark the present software for exponential and sigmoidal dynamics and present application examples to the 3D Gray-Scott reaction-diffusion problem and the "dam break" problem from fluid mechanics. We find a strong-scaling efficiency of 80% on up to 512 CPU cores and a five-fold speedup on a single GPU.

cs.MS↗

arXiv2025

TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter

We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications across the biomedical sciences. Addressing these problems will require flexible, cross-scale models of tissue shape, development, and dysfunction that can be tuned to understand, model, and predict relevant individual cases. Current approaches to simulating anatomical or cellular subsystems tend to rely on static, assumed shapes. Meanwhile, the potential for topology to provide natural dimensionality reduction and organization of shape and dynamical outcomes is not fully exploited. TopoSPAM combines ease of use with powerful simulation algorithms and methodological advances, including active nematic gels, topological-defect-driven shape dynamics, and an active 3D vertex model of tissues. It is capable of determining emergent flows and shapes across scales.

physics.bio-ph↗

arXiv2024

Parallel Compositing of Volumetric Depth Images for Interactive Visualization of Distributed Volumes at High Frame Rates

We present a parallel compositing algorithm for Volumetric Depth Images (VDIs) of large three-dimensional volume data. Large distributed volume data are routinely produced in both numerical simulations and experiments, yet it remains challenging to visualize them at smooth, interactive frame rates. VDIs are view-dependent piecewise constant representations of volume data that offer a potential solution. They are more compact and less expensive to render than the original data. So far, however, there is no method for generating VDIs from distributed data. We propose an algorithm that enables this by sort-last parallel generation and compositing of VDIs with automatically chosen content-adaptive parameters. The resulting composited VDI can then be streamed for remote display, providing responsive visualization of large, distributed volume data.

cs.GR↗

arXiv2023

A meshfree collocation scheme for surface differential operators on point clouds

We present a meshfree collocation scheme to discretize intrinsic surface differential operators over scalar fields on smooth curved surfaces with given normal vectors and a non-intersecting tubular neighborhood. The method is based on Discretization-Corrected Particle Strength Exchange (DC-PSE), which generalizes finite difference methods to meshfree point clouds. The proposed Surface DC-PSE method is derived from an embedding theorem, but we analytically reduce the operator kernels along surface normals to obtain a purely intrinsic computational scheme over surface point clouds. We benchmark Surface DC-PSE by discretizing the Laplace-Beltrami operator on a circle and a sphere, and we present convergence results for both explicit and implicit solvers. We then showcase the algorithm on the problem of computing Gauss and mean curvature of an ellipsoid and of the Stanford Bunny by approximating the intrinsic divergence of the normal vector field. Finally, we compare Surface DC-PSE with Surface Finite Elements (SFEM) and Diffuse-Interface Finite Elements (DI FEM) in a validation case.

math.NA↗

arXiv2023

Efficient Raycasting of Volumetric Depth Images for Remote Visualization of Large Volumes at High Frame Rates

We present an efficient raycasting algorithm for rendering Volumetric Depth Images (VDIs), and we show how it can be used in a remote visualization setting with VDIs generated and streamed from a remote server. VDIs are compact view-dependent volume representations that enable interactive visualization of large volumes at high frame rates by decoupling viewpoint changes from expensive rendering calculations. However, current rendering approaches for VDIs struggle with achieving interactive frame rates at high image resolutions. Here, we exploit the properties of perspective projection to simplify intersections of rays with the view-dependent frustums in a VDI and leverage spatial smoothness in the volume data to minimize memory accesses. Benchmarks show that responsive frame rates can be achieved close to the viewpoint of generation for HD display resolutions, providing high-fidelity approximate renderings of Gigabyte-sized volumes. We also propose a method to subsample the VDI for preview rendering, maintaining high frame rates even for large viewpoint deviations. We provide our implementation as an extension of an established open-source visualization library.

cs.GR↗

arXiv2019

A Proposed Framework for Interactive Virtual Reality In Situ Visualization of Parallel Numerical Simulations

As computer simulations progress to increasingly complex, non-linear, and three-dimensional systems and phenomena, intuitive and immediate visualization of their results is becoming crucial. While Virtual Reality (VR) and Natural User Interfaces (NUIs) have been shown to improve understanding of complex 3D data, their application to live in situ visualization and computational steering is hampered by performance requirements. Here, we present the design of a software framework for interactive VR in situ visualization of parallel numerical simulations, as well as a working prototype implementation. Our design is targeted towards meeting the performance requirements for VR, and our work is packaged in a framework that allows for easy instrumentation of simulations. Our preliminary results inform about the technical feasibility of the architecture, as well as the challenges that remain.

cs.DC↗

arXiv2018

OpenFPM: A scalable open framework for particle and particle-mesh codes on parallel computers

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through increasing heterogeneous parallelism, enabling simulations of ever more complex models. However, efficiently implementing scalable codes on heterogeneous, distributed hardware systems becomes the bottleneck. This bottleneck can be alleviated by intermediate software layers that provide higher-level abstractions closer to the problem domain, hence allowing the computational scientist to focus on the simulation. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of particles-only and hybrid particle-mesh simulations of both discrete and continuous models, as well as non-simulation codes. This infrastructure is complemented with portable implementations of frequently used numerical routines, as well as interfaces to third-party libraries. We present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed-Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), Vortex Methods, stencil codes, high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing software frameworks.

cs.DC↗

arXiv2011

QCD simulations with staggered fermions on GPUs

We report on our implementation of the RHMC algorithm for the simulation of lattice QCD with two staggered flavors on Graphics Processing Units, using the NVIDIA CUDA programming language. The main feature of our code is that the GPU is not used just as an accelerator, but instead the whole Molecular Dynamics trajectory is performed on it. After pointing out the main bottlenecks and how to circumvent them, we discuss the obtained performances. We present some preliminary results regarding OpenCL and multiGPU extensions of our code and discuss future perspectives.

hep-lat↗