24 papers · ranked by Valyu relevance
Sergio Rajsbaum, Michel Raynal
Concurrency, the art of doing many things at the same time is slowly becoming a science. It is very difficult to master, yet it arises all over modern computing systems, both when the communication medium is shared memory and when it is by message passing. Concurrent programming is hard because it requires to cope with…
Himanshu Chauhan, Vijay K. Garg
Partial orders are used extensively for modeling and analyzing concurrent computations. In this paper, we define two properties of partially ordered sets: width-extensibility and interleaving-consistency, and show that a partial order can be a valid state based model: (1) of some synchronous concurrent computation iff…
Vitaly Aksenov, Petr Kuznetsov, Anatoly Shalyto
A parallel batched data structure is designed to process synchronized batches of operations on the data structure using a parallel program. In this paper, we propose parallel combining, a technique that implements a concurrent data structure from a parallel batched one. The idea is that we explicitly synchronize…
Thomas Given-Wilson
Computation can be considered by taking into account two dimensions: extensional versus intensional, and sequential versus concurrent. Traditionally sequential extensional computation can be captured by the λ-calculus. However, recent work shows that there are more expressive intensional calculi such as S F-calculus.…
Pavol Černý, Edmund M. Clarke, Thomas A. Henzinger, Arjun Radhakrishna + 3 more
We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is…
Hao Li, Yi-Cheng Tu, Bo Zeng, Rashid Mehmood
The unrivaled computing capabilities of modern GPUs meet the demand of processing massive amounts of data seen in many application domains. While traditional HPC systems support applications as standalone entities that occupy entire GPUs, there are GPU-based DBMSs where multiple tasks are meant to be run at the same…
Brijender Kahanwal
Nowadays, we are to find out solutions to huge computing problems very rapidly. It brings the idea of parallel computing in which several machines or processors work cooperatively for computational tasks. In the past decades, there are a lot of variations in perceiving the importance of parallelism in computing…
Patrizio Dazzi
Embarrassingly parallel problems are characterised by a very small amount of information to be exchanged among the parts they are split in, during their parallel execution. As a consequence they do not require sophisticated, low-latency, high-bandwidth interconnection networks but can be efficiently computed in…
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…
R. Daniel Kortschak, David L. Adelson
bíogo is a framework designed to ease development and maintenance of computationally intensive bioinformatics applications. The library is written in the Go programming language, a garbage-collected, strictly typed compiled language with built in support for concurrent processing, and performance comparable to C and…
C. Addison Stone, Melissa O'Neill, Sonja A. Bohr, Adam M. Cozzette + 4 more
'M. Joe DeBlasio' 'Julia Matsieva' 'Stuart Pernsteiner' 'Ari D. Schumer'] Programmers benefit because they can reason largely sequentially. Remaining interthread interactions are far less chaotic than in other models, permitting easier reasoning and debugging. Programmers can also defer the choice of…
Eli J. Müller, Kevin Y. Hou, Fulvia Palesi, Joshua Tan + 5 more
A characteristic feature of human cognition is our ability to ‘multi-task’ – performing two or more tasks in parallel – particularly when one task is well-learned. How the brain supports this capacity remains poorly understood. Most past studies have focussed on identifying the areas of the brain – typically the…
Stuart Byma, Akash Dhasade, Adrian Altenhoff, Christophe Dessimoz + 1 more
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find similar pairs in a set of n elements such as protein sequences. Precise…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
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…
Hao Wu, Zhen-Zhou Ji
Concurrent garbage collectors (CGC) have recently obtained extensive concern on multicore platform. Excellent designed CGC can improve the efficiency of runtime systems by exploring the full potential processing resources of multicore computers. Two major performance critical components for designing CGC are studied in…
Bérenger Bramas, Gang Mei
Task-based programming models have demonstrated their efficiency in the development of scientific applications on modern high-performance platforms. They allow delegation of the management of parallelization to the runtime system (RS), which is in charge of the data coherency, the scheduling, and the assignment of the…
Patrick Mukala
| Article Info | ABSTRACT | | --- | --- | | | A myriad of applications ranging from engineering and scientific | | | simulations, image and signal processing as well as high-sensitive data | | | retrieval demand high processing power reaching up to teraflops for their | | | efficient execution. While a standard serial…
Authors not listed
Machine learning models are transforming data-driven research across scientific disciplines, yet their deployment as accessible and reliable web services remains a significant challenge. We introduce the NERDD framework, a scalable, maintainable, and secure microservices platform designed to support the sustainable…
Kuo-Chan Huang, Wei-Ya Wu, Feng-Jian Wang, Hsiao-Ching Liu + 1 more
'Chun-Hao Hung'] Parallel computation has been widely applied in a variety of large-scale scientific and engineering applications. Many studies indicate that exploiting both task and data parallelisms, i.e. mixed-parallel workflows, to solve large computational problems can get better efficacy compared with either pure…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
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…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…