14 papers · ranked by Valyu relevance
Fabian Woller, Lis Arend, Christian Fuchsberger, Markus List + 1 more
To demonstrate the practical applicability of NApy on a real-world dataset, all statistical tests were performed on the CHRIS study data both without any parallelization (single thread) and with heavy parallelization (64 threads). For correlations, pandas was used as comparison as it was the fastest compared to other…
Laouen Belloli, Pedro A. M. Mediano, Rodrigo Cofré, Diego Fernandez Slezak + 2 more
Complex systems are characterized by nonlinear dynamics, multi-level interactions, and emergent collective behaviors. Traditional analyses that focus solely on pairwise interactions often oversimplify these systems, neglecting the higher-order interactions critical for understanding their full collective dynamics.…
Zeyi Zhang, Carlos Mora Perez, Patrick Kwon, Martin Head‐Gordon + 1 more
PARSEC.py is a Python-based real-space Kohn-Sham density functional theory (real-space KS-DFT) framework designed to provide a user- and developer-friendly platform for first-principles electronic-structure simulations. Discretization on real-space grids eliminates basis-set approximations, while enabling systematic…
Bahman Arasteh, Seyed Salar Sefati, Huseyin Kusetogullari, Farzad Kiani + 3 more
Efficient task scheduling remains a key challenge in High-Performance Computing and Internet of Things (IoT) systems, where the sequential execution of nested loops often limits parallelism. This paper proposes a hybrid approach that dynamically parallelizes nested loops in heterogeneous IoT environments. The suggested…
Jiaming Cao, Samuel Montero-Hernandez, Rickson C. Mesquita, Adam T. Eggebrecht + 1 more
Significance Accurate and efficient photon modeling plays an essential role in the rapidly developing field of diffuse optical imaging, whereby the use of model-based analysis and image reconstruction can provide both educational and research benefits. Aim NIRFASTerFF is a cross-platform (Linux, macOS, and Windows)…
Ainur Abukaev, Constantin Völter, Mikhail Romodin, Sebastian Schwartzkopff + 6 more
A new Python package, pygid, enables fast batch processing of X-ray scattering data, with a particular focus on grazing-incidence geometries.
Arsham Mikaeili Namini, Ali Saberi, Hamed S Najafabadi, Peter Robinson
Runtime benchmarking demonstrated substantial improvements from both architectural redesign and parallelization ([btag334-F1]). Even without parallelism, GEDI 2.0 ran up to $∼$3 $\times$ faster than the legacy implementation, confirming substantial performance gains from improved algorithms and memory access patterns…
Mohammed Alaa Ala’anzy, Nurdaulet Tolendi, Baizhan Baubek, Abdulmohsen Algarni + 1 more
Sorting can be approached in two main ways: sequentially and in parallel. In sequential sorting, data is processed in a single-threaded manner, which can be slow for large datasets. However, parallel sorting divides the task across multiple processing units, enabling faster results by processing data simultaneously.…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…
Fernando Martínez-García, Francisco Revson F. Pereira, Pedro Parrado-Rodríguez, Yauhen Yakimenka + 1 more
The development and use of large-scale quantum computers relies on integrating quantum error-correcting (QEC) schemes into the quantum computing pipeline. A fundamental part of the QEC protocol is the decoding of the syndrome to identify a recovery operation with a high success rate. In this work, we implement a…
Christoph Stelz, Lukas Hübner, Alexandros Stamatakis, Russell Schwartz
Next to disseminating results, scientific publications also aim to convince the reader of their validity (). While reproducibility is crucial for validating scientific claims (), practical attempts to reproduce computational findings frequently fail, e.g. in climate and weather modeling (), power grid analysis (), or…
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt
Background The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated…
Kevin Garner, Polykarpos Thomadakis, Nikos Chrisochoides
This paper presents a distributed memory method for anisotropic mesh adaptation that is designed to avoid the use of collective communication and global synchronization techniques. In the presented method, meshing functionality is separated from performance aspects by utilizing a separate entity for each - a multicore…
Tomasz Chady, Zuzanna Karolina Filutowska, Zhiyong Lu
GTF/GFF version 2 and FASTA file formats are widely used in genomics owing to their simplicity and ease of use. Consequently, parsing these files is often the first step in many projects, and can become a bottleneck. Indeed, this was the experience of the authors, who found a Python-based parser to be too slow and…