22 papers · ranked by Valyu relevance
Yi Song, Xiaoyuan Xie, Quanming Liu, Xihao Zhang + 1 more
The clustering technique has attracted a lot of attention as a promising strategy for parallel debugging in multi-fault scenarios, this heuristic approach (i.e., failure indexing or fault isolation) enables developers to perform multiple debugging tasks simultaneously through dividing failed test cases into several…
God'salvation F. Oguibe, Vinodh Kumaran Jayakumar, Tongping Liu, Andrew Lan + 1 more
Concurrent programming is a core component of Computer Science curricula, yet remains notoriously difficult for students to master due to its inherent complexity and the nondeterministic nature of concurrency bugs such as deadlocks and race conditions. In this work, we present ParaView, an educational tool designed to…
Sabbir Hussain Meraj, Riham Chowdhury, Shimul Debnath, Wei Wang
Debugging data races is a major challenge for students learning parallel programming due to the non-deterministic nature of concurrent execution and the complexity of shared-memory semantics. Recent advances in Large Language Models (LLMs) suggest that they could serve as AI teaching assistants, but the capabilities of…
Temitayo Adefemi
—Parallelization has become a cornerstone of modern computing, influencing everything from high-performance supercomputers to everyday mobile devices. This paper presents a comprehensive guide on the fundamentals of parallelization that every computer scientist should know, beginning with a historical perspective that…
Jiri Dokulil, Siegfried Benkner
Task-based runtime systems are an important branch of parallel programming research, since tasks decouple computation from the compute units, giving the runtime systems greater flexibility than a thread-based solution. This makes it easier to deal with the ever-increasing complexity of parallel architectures by…
Utpal Bora, Shraiysh Vaishay, Saurabh Joshi, Ramakrishna Upadrasta
—Data races, a major source of bugs in concurrent programs, can result in loss of manpower and time as well as data loss due to system failures. OpenMP, the de facto shared memory parallelism framework used in the HPC community, also suffers from data races. To detect race conditions in OpenMP programs and improve…
Authors not listed
Recent advances in machine learning force fields (MLFF) have significantly extended the reach of atomistic simulations. Continuous progress in this field requires reliable reference datasets, accurate MLFF architectures, and efficient active learning strategies to enable robust modeling of complex molecular and…
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…
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…
David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
The Structure and TOpology Replica Molecular Mechanics (STORMM) code is a next-generation molecular simulation engine and associated libraries optimized for performance on fast, multicore central processor units (CPUs) and graphics processing units (GPUs) with independent memory and tens of thousands of threads. STORMM…
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…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. 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…
Paul Leger, Felipe Ruiz, Hiroaki Fukuda, Nicolás Cardozo + 1 more
'Muhammad Aleem'] JavaScript Web applications are a common product in industry. As with most applications, Web applications can acquire software flaws (known as bugs), whose symptoms are seen during the development stage and, even worse, in production. The use of debuggers is beneficial for detecting bugs.…
Manuel Carrer, Henrique Musseli Cezar, Sigbjørn Løland Bore, Morten Ledum + 1 more
We develop #-HylleraasMD (#-HyMD), a fully end-to-end differentiable molecular dynamics software based on the Hamiltonian hybrid particle-field formalism, and use it to establish a protocol for automated optimization of force field parameters. #-HyMD is templated on the recently established HylleraaasMD software, while…
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
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…
A. Lucas Martins, Alexandre Laborde, Michael Orger
We present Sardine, a software framework built with.NET to control experimental setups through the reliable execution of dynamic networks of independent modules, where each module can interface with a hardware device (e.g., camera, motor) or represent an operation over data (e.g., image filter, data stream). The…
Marco Savioli, Paolo Calligari, Ugo Locatelli, Gianfranco Bocchinfuso
We introduce GROMODEX, a novel tool designed to optimise GROMACS molecular dynamics (MD) simulations using a structured Design of Experiments (DoE) approach. GROMACS, though efficient, requires extensive tuning of parameters to perform optimally on different hardware and molecular systems. Manual tuning is tedious and…
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…
Yeongung Park, Seokwoo Choi, Un Yeong Choi, Haimin Jin + 2 more
'Nurul Harzira Mohamad Nor' 'Yongsu Park'] As IoT devices are being widely used, malicious code is increasingly appearing in Linux environments. Sophisticated Linux malware employs various evasive techniques to deter analysis. The embedded trace microcell (ETM) supported by modern Arm CPUs is a suitable hardware tracer…
Cristian Vidal-Silva, Vannessa Duarte, Jesennia Cárdenas-Cobo, Iván Veas
Parallel computing is a current algorithmic approach to looking for efficient solutions; that is, to define a set of processes in charge of performing at the same time the same task. Advances in hardware permit the massification of accessibility to and applications of parallel computing. Nonetheless, some algorithms…