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Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…

Genomics · Quantitative Biology 2017-03-03 Maciej Dlugosz , Sebastian Deorowicz

Computer models (simulators) are vital tools for investigating physical processes. Despite their utility, the prohibitive run-time of simulators hinders their direct application for uncertainty quantification. Gaussian process emulators…

Computation · Statistics 2024-11-25 Conor Crilly , Oliver Johnson , Alexander Lewis , Jonathan Rougier

In this work we introduce an open source suite of quantum application-oriented performance benchmarks that is designed to measure the effectiveness of quantum computing hardware at executing quantum applications. These benchmarks probe a…

Real-time simulation of a large-scale biologically representative spiking neural network is presented, through the use of a heterogeneous parallelisation scheme and SpiNNaker neuromorphic hardware. A published cortical microcircuit model is…

Emerging Technologies · Computer Science 2021-04-28 Oliver Rhodes , Luca Peres , Andrew G. D. Rowley , Andrew Gait , Luis A. Plana , Christian Brenninkmeijer , Steve B. Furber

This article describes the first public implementation and evaluation of the latest version of the RISC-V hypervisor extension (H-extension v0.6.1) specification in a Rocket chip core. To perform a meaningful evaluation for modern…

Hardware Architecture · Computer Science 2021-08-17 Bruno Sá , José Martins , Sandro Pinto

We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available.…

Astrophysics · Physics 2008-02-03 Robert C. Ferrell , Edmund Bertschinger

Scientific applications are starting to explore the viability of quantum computing. This exploration typically begins with quantum simulations that can run on existing classical platforms, albeit without the performance advantages of real…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-08-16 Amir Shehata , Thomas Naughton , In-Saeng Suh

B-spline based orbital representations are widely used in Quantum Monte Carlo (QMC) simulations of solids, historically taking as much as 50% of the total run time. Random accesses to a large four-dimensional array make it challenging to…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-08-10 Amrita Mathuriya , Ye Luo , Anouar Benali , Luke Shulenburger , Jeongnim Kim

As quantum devices continue to scale, distributed quantum computing emerges as a promising strategy for executing large-scale tasks across modular quantum processors. A central challenge in this paradigm is verifying the correctness of…

Nek5000/RS is a highly-performant open-source spectral element code for simulation of incompressible and low-Mach fluid flow, heat transfer, and combustion with a particular focus on turbulent flows in complex domains. It is based on…

Integration of CPU and GPU technologies is a key enabler for modern AI and graphics workloads, combining control-oriented processing with massive parallel compute capability. As systems evolve toward chiplet-based architectures, pre-silicon…

Distributed, Parallel, and Cluster Computing · Computer Science 2026-03-18 Nij Dorairaj , Debabrata Chatterjee , Hong Wang , Hong Jiang , Alankar Saxena , Altug Koker , Thiam Ern Lim , Cathrane Teoh , Chuan Yin Loo , Bishara Shomar , Anthony Lester

This thesis introduces PEMS2, an improvement to PEMS (Parallel External Memory System). PEMS executes Bulk-Synchronous Parallel (BSP) algorithms in an External Memory (EM) context, enabling computation with very large data sets which exceed…

Distributed, Parallel, and Cluster Computing · Computer Science 2010-01-20 David E. Robillard

The simulation of Systems-on-Chip (SoC) is nowadays a hot topic because, beyond providing many debugging facilities, it allows the development of dedicated software before the hardware is available. Low-consumption CPUs such as ARM play a…

Logic in Computer Science · Computer Science 2012-03-01 Xiaomu Shi , Jean-François Monin , Frederic Tuong , Frédéric Blanqui

A quantum multimeter is a programmable device that can implement measurements of different observables depending on the programming quantum state inserted into it. The advantage of this arrangement over a single purpose device is in its…

Quantum Physics · Physics 2017-05-10 Teiko Heinosaari , Takayuki Miyadera , Mikko Tukiainen

While interest in the open RISC-V instruction set architecture is growing, tools to assess the security of concrete processor implementations are lacking. There are dedicated tools and benchmarks for common microarchitectural side-channel…

Cryptography and Security · Computer Science 2025-10-13 Cédrick Austa , Jan Tobias Mühlberg , Jean-Michel Dricot

The optimal allocation of replicas to a homogeneous or heterogenous set of processors is derived for parallel tempering simulations on multi-processor machines. In the general case, it is possible without substantially increasing wall clock…

Computational Physics · Physics 2007-05-23 David J. Earl , Michael W. Deem

A software model of a reversible processor ReveR with the stack is discussed in this paper. An architecture, the minimal set of elementary reversible operations together with an implementation of the basic control flow structures and…

Emerging Technologies · Computer Science 2011-06-01 Alexander Yu. Vlasov

We have developed a special-purpose computer for gravitational many-body simulations, GRAPE-5. GRAPE-5 is the successor of GRAPE-3. Both consist of eight custom pipeline chips (G5 chip and GRAPE chip). The difference between GRAPE-5 and…

Astrophysics · Physics 2015-06-24 Atsushi Kawai , Toshiyuki Fukushige , Junichiro Makino , Makoto Taiji

Recently, distributed ledger technologies like blockchain have been proliferating and have attracted interest from the academic community, government, and industry. A wide range of blockchain solutions has been introduced, such as Bitcoin,…

Cryptography and Security · Computer Science 2022-08-25 Adel Albshri , Ali Alzubaidi , Bakri Awaji , Ellis Solaiman

For validating low level embedded software, engineers use simulators that take the real binary as input. Like the real hardware, these full-system simulators are organized as a set of components. The main component is the CPU simulator…

Software Engineering · Computer Science 2011-09-21 Frédéric Blanqui , Claude Helmstetter , Vania Joloboff , Jean-François Monin , Xiaomu Shi