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Modern neural sequence models are designed to meet the dual mandate of parallelizable training and fast sequential inference. Recent developments have given rise to various models, such as Gated Linear Attention (GLA) and Mamba, that…
Fast algorithms for the computation of $N$-body problems can be broadly classified into mesh-based interpolation methods, and hierarchical or multiresolution methods. To this last class belongs the well-known fast multipole method (FMM),…
OpenMP is a cross-platform API that extends C, C++ and Fortran and provides shared-memory parallelism platform for those languages. The use of many cores and HPC technologies for scientific computing has been spread since the 1990s, and now…
This paper satisfies the reproducibility challenge of the Student Cluster Competition at Supercomputing 2017. We attempted to reproduce the results of H\"{o}hnerbach et al. (2016) for an implementation of a vectorized code for the Tersoff…
Diagrammatic expansions are a paradigmatic and powerful tool of quantum many-body theory. Their evaluation to high order, e.g., by the Diagrammatic Monte Carlo technique, can provide unbiased results in strongly correlated and challenging…
Previous work has shown that there are two major complexity barriers in the synthesis of fault-tolerant distributed programs: (1) generation of fault-span, the set of states reachable in the presence of faults, and (2) resolving deadlock…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Regions of nested loops are a common feature of High Performance Computing (HPC) codes. In shared memory programming models, such as OpenMP, these structure are the most common source of parallelism. Parallelising these structures requires…
We modified a MPI-friendly density functional theory (DFT) source code within hybrid parallelization including CUDA. Our objective is to find out how simple conversions within the hybrid parallelization with mid-range GPUs affect DFT code…
We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symplectic algorithm in the constant normal pressure and lateral…
State-Space Models (SSMs) have emerged as efficient alternatives to transformers for sequential data tasks, offering linear or near-linear scalability with sequence length, making them ideal for long-sequence applications in NLP, vision,…
This technical report provides an in-depth evaluation of both established and state-of-the-art methods for simulating constrained rigid multi-body systems with hard-contact dynamics, using formulations of Nonlinear Complementarity Problems…
We present a high-fidelity realization of the cosmological $N$-body simulation from the Schneider et al. (2016) code comparison project. The simulation was performed with our Abacus $N$-body code, which offers high force accuracy, high…
Persistent homology is a crucial invariant that is used in many areas to understand data. The $O(N^4)$ run time is a hindrance to its use on most large datasets. We give a parallelization method to utilize multi-core machines and clusters.…
Writing efficient hybrid parallel code is tedious, error-prone, and requires good knowledge of both parallel programming and multithreading such as MPI and OpenMP, resp. Therefore, we present a framework which is based on a job model that…
In this paper we present \texttt{SymOrb.jl}, a software which combines group representation theory and variational methods to provide numerical solutions of singular dynamical systems of paramount relevance in Celestial Mechanics and other…
We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…
Quasiparticle self-consistent many-body perturbation theory (MBPT) methods that update both eigenvalues and eigenvectors can calculate the excited-state properties of molecular systems without depending on the choice of starting points.…
This paper presents an in-depth investigation into the high-performance parallel optimization of the Fish School Behaviour (FSB) algorithm on the Setonix supercomputing platform using the OpenMP framework. Given the increasing demand for…
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave algorithm, the software operates on AMBER generated trajectory data using either UNIX or MPI file IO, and it…