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This paper considers decentralized consensus optimization problems where nodes of a network have access to different summands of a global objective function. Nodes cooperate to minimize the global objective by exchanging information with…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
The discretization of elliptic PDEs leads to large coupled systems of equations. Domain decomposition methods (DDMs) are one approach to the solution of these systems, and can split the problem in a way that allows for parallel computing.…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
Context parallelism has emerged as a key technique to support long-context training, a growing trend in generative AI for modern large models. However, existing context parallel methods rely on static parallelization configurations that…
Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the…
The development of tailored materials for specific applications is an active field of research in chemistry, material science and drug discovery. The number of possible molecules that can be obtained from a set of atomic species grow…
Video diffusion models (VDMs) perform attention computation over the 3D spatio-temporal domain. Compared to large language models (LLMs) processing 1D sequences, their memory consumption scales cubically, necessitating parallel serving…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
The use of deep learning methods for solving PDEs is a field in full expansion. In particular, Physical Informed Neural Networks, that implement a sampling of the physical domain and use a loss function that penalizes the violation of the…
High-performance computing (HPC) requires resilience techniques such as checkpointing in order to tolerate failures in supercomputers. As the number of nodes and memory in supercomputers keeps on increasing, the size of checkpoint data also…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…
We introduce the so called DeepParticle method to learn and generate invariant measures of stochastic dynamical systems with physical parameters based on data computed from an interacting particle method (IPM). We utilize the expressiveness…
Simulations of quantum dynamics are a key application of near term quantum computing, but are hindered by the twin challenges of noise and small device scale, which limit the executable circuit depths and the number of qubits the algorithm…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
We consider the coupled system of equations that describe flow in fractured porous media. To describe such types of problems, multicontinuum and multiscale approaches are used. Because in multicontinuum models, the permeability of each…
The emergence of huge-scale, data-intensive linear optimization (LO) problems in applications such as machine learning has driven the need for more computationally efficient interior point methods (IPMs). While conventional IPMs are…
This paper was prompted by numerical experiments we performed, in which algorithms already available in the literature (DVS-BDDM) yielded accelerations (or speedups) many times larger (more than seventy in some examples already treated, but…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…