25 papers · ranked by Valyu relevance
Jun Shirako, Akihiro Hayashi, Sri Raj Paul, Alexey Tumanov + 1 more
'Vivek Sarkar'] Abstract. This paper introduces a novel approach to automatic aheadof-time (AOT) parallelization and optimization of sequential Python programs for execution on distributed heterogeneous platforms. Our approach enables AOT source-to-source transformation of Python programs, driven by the inclusion of…
Clément Aubert, Thomas Rubiano, Neea Rusch, Thomas Seiller
This work explores an unexpected application of Implicit Computational Complexity (ICC) to parallelize loops in imperative programs. Thanks to a lightweight dependency analysis, our algorithm allows splitting a loop into multiple loops that can be run in parallel, resulting in gains in terms of execution time similar…
Tal Kadosh, Niranjan Hasabnis, Prema Soundararajan, Vy A. Vo + 4 more
Compilation Authors: ['Tal Kadosh' 'Niranjan Hasabnis' 'Prema Soundararajan' 'Vy A. Vo' 'Mihai Capotă' 'Nesreen K. Ahmed' 'Yuval Pinter' 'Gal Oren'] Manual parallelization of code remains a significant challenge due to the complexities of modern software systems and the widespread adoption of multi-core architectures.…
Quazi Ishtiaque Mahmud, Ali TehraniJamsaz, Hung Phan, Nesreen K. Ahmed + 1 more
'Nesreen K. Ahmed' 'Ali Jannesari'] Parallelizing sequentially written programs is a challenging task. Even experienced developers need to spend considerable time finding parallelism opportunities and then actually writing parallel versions of sequentially written programs. To address this issue, we present AUTOPARLLM…
Parinaz Barakhshan, Rudolf Eigenmann
We compare automatically and manually parallelized NAS Benchmarks in order to identify code sections that differ. We discuss opportunities for advancing automatic parallelizers. We find ten patterns that pose challenges for current parallelization technology. We also measure the potential impact of advanced techniques…
Pavel Telegin, Anton Baranov, B. M. Shabanov, Artem Tikhomirov
Usage of multiprocessor and multicore computers implies parallel programming. Tools for preparing parallel programs include parallel languages and libraries as well as parallelizing compilers and convertors that can perform automatic parallelization. The basic approach for parallelism detection is analysis of data…
Krzysztof Stuglik, Piotr Listkiewicz, Mateusz Kulczyk, Marcin Pietroń
'Marcin Pietroń'] Manual translation of the algorithms from sequential version to its parallel counterpart is time consuming and can be done only with the specific knowledge of hardware accelerator architecture, parallel programming or programming environment. The automation of this process makes porting the code much…
Alvaro Estebanez, Diego R. Llanos, David Orden, Belen Palop + 1 more
'Rafael Sachetto Oliveira'] Loops are a rich source of parallelism. Unfortunately, many loops cannot be safely parallelized at compile time because the compiler is not able to guarantee that there will be no dependence violations. Thread-Level Speculation (TLS) techniques, either hardware or software-based, allow the…
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…
Clément Flint, Ludovic Paillat, Bérenger Bramas, Muhammad Aleem
High-performance computing (HPC) relies increasingly on heterogeneous hardware and especially on the combination of central and graphical processing units. The task-based method has demonstrated promising potential for parallelizing applications on such computing nodes. With this approach, the scheduling strategy…
Authors not listed
With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
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.…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
Paul Cardosi, Bérenger Bramas, Bilal Alatas
Parallelization is needed everywhere, from laptops and mobile phones to supercomputers. Among parallel programming models, task-based programming has demonstrated a powerful potential and is widely used in high-performance scientific computing. Not only does it allow efficient parallelization across distributed…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Seth Stadick
Filtering records using command line tools is a staple of Bioin-formatics. In analysis pipelines and in day-to-day research tools such as awk, grep, and cut are the workhorses of much of our data crunching. To date, there is no command line utility for performing index-free alignment-based filtering of records. Ish is…
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Vladislav Skorpil, Vaclav Oujezsky, Arcangelo Castiglione, Gianni D’Angelo
'Gianni D’Angelo'] This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt
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 quadratic…
Riley Hickman, Malcolm Sim, Sergio Pablo-García, Ivan Woolhouse + 6 more
Self-driving laboratories (SDLs) are next-generation research and development platforms for closed-loop, autonomous experimentation that combine ideas from artificial intelligence, robotics, and high-performance computing. A critical component of SDLs is the decision-making algorithm used to prioritize experiments to…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Christoph Stelz, Lukas Hübner, Alexandros Stamatakis
Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum Likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between…
Alejandro Santana-Bonilla, Raquel Lopez-Rios De Castro, Peike Sun, Robert Ziolek + 1 more
Machine learning methods offer the opportunity to design new functional materials on an unprecedented scale however building the large, diverse databases of molecules on which to train such methods remains a daunting task. Automated computational chemistry modelling workflows are therefore becoming essential tools in…
Authors not listed
Molecular Dynamics (MD) simulations are essential for studying the time evolution of molecular systems. Still, their efficiency is often bottlenecked by file-based Inter-Process Communication (IPC) between MD and Electronic Structure (ES) programs. We present a socket-based IPC implementation that dramatically…