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Maxime Maria

Publications and source records attributed to Maxime Maria.

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Advancing RT Core-Accelerated Fixed-Radius Nearest Neighbor Search

In this work we introduce three ideas that can further improve particle FRNN physics simulations running on RT Cores; i) a real-time update/rebuild ratio optimizer for the bounding volume hierarchy (BVH) structure, ii) a new RT core use, with two variants, that eliminates the need of a neighbor list and iii) a technique that enables RT cores for FRNN with periodic boundary conditions (BC). Experimental evaluation using the Lennard-Jones FRNN interaction model as a case study shows that the proposed update/rebuild ratio optimizer is capable of adapting to the different dynamics that emerge during a simulation, leading to a RT core pipeline up to $\sim 3.4\times$ faster than with other known approaches to manage the BVH. In terms of simulation step performance, the proposed variants can significantly improve the speedup and energy efficiency (EE) of the base RT core idea; from $\sim1.3\times$ at small radius to $\sim2.0\times$ for log normal radius distributions. Furthermore, the proposed variants manage to simulate cases that would otherwise not fit in memory because of the use of neighbor lists, such as clusters of particles with log normal radius distribution. The proposed RT Core technique to support periodic BC is indeed effective as it does not introduce any significant penalty in performance. In terms of scaling, the proposed methods scale both their performance and EE across GPU generations. Throughout the experimental evaluation, we also identify the simulation cases were regular GPU computation should still be preferred, contributing to the understanding of the strengths and limitations of RT cores.

cs.DC

Pushing the Accuracy Limit of Foundation Neural Network Models with Quantum Monte Carlo Forces and Path Integrals

We propose an end-to-end integrated strategy to produce highly accurate quantum chemistry (QC) synthetic datasets (energies and forces) aimed at deriving Foundation Machine Learning models for molecular simulation. Starting from Density Functional Theory (DFT), a "Jacob's Ladder" approach leverages computationally-optimized layers of massively GPU-accelerated software with increasing accuracy. Thanks to Exascale, this is the first time that the computationally intensive calculation of Quantum Monte Carlo forces (QMC), and the combination of multi-determinant QMC energies and forces with selected-Configuration Interaction wavefunctions, are computed at such scale at the complete basis-set limit. To bridge the gap between accurate QC and condensed-phase Molecular Dynamics, we leverage transfer learning to improve the DFT-based FeNNix-Bio1 foundation model. The resulting approach is coupled to path integrals adaptive sampling quantum dynamics to perform nanosecond reactive simulations at unprecedented accuracy. These results demonstrate the promise of Exascale to deepen our understanding of the inner machinery of complex biosystems.

physics.chem-ph

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model

VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics engine utilizing impostor-based techniques and adaptive level-of-detail (LOD) rendering. This approach significantly reduces memory usage and enables real-time visualization and manipulation of large molecular systems. Performance benchmarks against VMD, PyMOL, and ChimeraX using a 114-million-bead Martini minimal whole-cell model demonstrate VTX's efficiency, maintaining consistent frame rates even under interactive manipulation on standard computer hardware. VTX incorporates features such as screen-space ambient occlusion (SSAO) for enhanced depth perception and free-fly navigation for intuitive exploration of large molecular systems. VTX is open-source and free for non commercial use. Binaries for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. VTX source code is available at https://github.com/VTX-Molecular-Visualization.

physics.chem-ph

VTX: Real-time high-performance molecular structure and dynamics visualization software

Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for the visualization of massive molecular systems and molecular dynamics trajectories. VTX includes multiple interactive camera and user interaction features, notably free-fly navigation and a fully modular graphical user interface designed for increased usability. It allows the production of high-resolution images for presentations and posters with custom background. VTX design is focused on performance and usability for research, teaching and educative purposes. Availability and implementation: VTX is open source and free for non commercial use. Builds for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. The source code is available at https://github.com/VTX-Molecular-Visualization . Supplementary Information: A video displaying free-fly navigation in a whole-cell model is available

cs.GR