25 papers · ranked by Valyu relevance
Cristian Ramon-Cortes, Ramon Amela, Jorge Ejarque, Philippe Clauss + 1 more
'Rosa Badia'] Abstract—The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory management and garbage collection, which simplifies code…
Alcides Fonseca, Bruno Cabral, João Rafael, Ivo Correia
This work proposes a new approach for achieving such goal. We created a new parallelizing compiler that analyses the read and write instructions, and control-flow modifications in programs to identify a set of dependencies between the instructions in the program. Afterwards, the compiler, based on the generated…
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.…
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…
Garip Kusoglu, Bérenger Bramas, Stéphane Genaud
Currently, multi/many-core CPUs are considered standard in most types of computers including, mobile phones, PCs or supercomputers. However, the parallelization of applications as well as refactoring/design of applications for efficient hardware usage remains restricted to experts who have advanced technical knowledge…
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…
Ashwani Jha, K. M. Flurchick, Marwan Bikdash, Dukka B. KC
Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10-15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a…
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…
Muhammad Adnan, Faisal Aslam, Zubair Nawaz, Syed Mansoor Sarwar + 1 more
'Maciej Huk'] Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional…
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…
Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis
Coalescent- and reconciliation-based methods are now widely used to infer species phylogenies from genomic data. They typically use per-gene phylogenies as input, which requires conducting multiple individual tree inferences on a large set of multiple sequence alignments (MSAs). At present, no easy-to-use parallel tool…
Pau Andrio, Adam Hospital, Cristian Ramon-Cortes, Javier Conejero + 4 more
The usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data.…
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…
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…
Daniel Langenkämper, Tobias Jakobi, Dustin Feld, Lukas Jelonek + 2 more
'Alexander Goesmann' 'Tim W. Nattkemper'] Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data…
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…
Alessandro Petrini, Marco Mesiti, Max Schubach, Marco Frasca + 7 more
Several prediction problems in Computational Biology and Genomic Medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are…
Ling-Hong Hung, Wes Lloyd, Radhika Agumbe Sridhar, Saranya Devi Athmalingam Ravishankar + 3 more
For many next-generation sequencing pipelines, the most computationally intensive step is the alignment of reads to a reference sequence. As a result, alignment software such as the Burrows-Wheeler Aligner (BWA) is optimized for speed and and is often executed in parallel on the cloud. However, there are other less…
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…
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
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…
Charly Empereur-mot, Luca Pesce, Davide Bochicchio, Claudio Perego + 1 more
We present Swarm-CG, a versatile software for the automatic parametrization of bonded parameters incoarse-grained (CG) models. By coupling state-of-the-art metaheuristics to Boltzmann inversion, Swarm-CG performs accurate parametrization of bonded terms in CG models composed of up to 200 pseudoatomswithin 4h-24h on…
Charly Empereur-mot, Luca Pesce, Davide Bochicchio, Claudio Perego + 1 more
We present Swarm-CG, a versatile software for the automatic parametrization of bonded parameters in coarse-grained (CG) models. By coupling state-of-the-art metaheuristics to Boltzmann inversion, Swarm-CG performs accurate parametrization of bonded terms in CG models composed of up to 200 pseudoatoms within 4h-24h on…