21 papers · ranked by Valyu relevance
Xiandong Meng, Yanqing Ji
This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications-hidden Markov models (HMM). We show the detailed performance…
Dirk Beyer, Karlheinz Friedberger
Verifying multi-threaded programs is becoming more and more important, because of the strong trend to increase the number of processing units per CPU socket. We introduce a new configurable program analysis for verifying multi-threaded programs with a bounded number of threads. We present a simple and yet efficient…
Shuvendu K. Lahiri, Chao Wang, Daniel Schemmel, Julian Büning + 3 more
'César Rodríguez' 'David Laprell' 'Klaus Wehrle'] We describe a technique for systematic testing of multi-threaded programs. We combine Quasi-Optimal Partial-Order Reduction, a state-of-the-art technique that tackles path explosion due to interleaving non-determinism, with symbolic execution to handle data…
Parosh Aziz Abdulla, Mohamed Faouzi Atig, Frederik Meyer Bønneland, Sarbojit Das + 3 more
'Sarbojit Das' 'Bengt Jönsson' 'Magnus Lång' 'Konstantinos Sagonas'] Abstract. Event-driven multi-threaded programming is an important idiom for structuring concurrent computations. Stateless Model Checking (SMC) is an effective verification technique for multi-threaded programs, especially when coupled with Dynamic…
T. Murata, Hiroaki Hashiura
—Multi-threaded programs are expected to improve responsiveness and conserve resources by dividing an application process into multiple threads for concurrent processing. However, due to scheduling and the interaction of multiple threads, their runtime behavior is more complex than that of single-threaded programs…
Erickson H. da S. Alves, Lucas C. Cordeiro, Eddie B. de Lima Filho
—Software debugging is a very time-consuming process, which is even worse for multi-threaded programs, due to the non-deterministic behavior of thread-scheduling algorithms. However, the debugging time may be greatly reduced, if automatic methods are used for localizing faults. In this study, a new method for fault…
Abraham Chan, Stefan Winter, Habib Saissi, Karthik Pattabiraman + 1 more
'Neeraj Suri'] Fault injection is a technique to measure the robustness of a program to errors by introducing faults into the program under test. Following a fault injection experiment, Error Propagation Analysis (EPA) is deployed to understand how errors affect a program's execution. EPA typically compares the traces…
Thomas Nagler
Calling multi-threaded C++ code from R has its perils. Since the R interpreter is single-threaded, one must not check for user interruptions or print to the R console from multiple threads. One can, however, synchronize with R from the main thread. The R package RcppThread (current version 0.5.3) contains a header only…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…
Eunjae Kim, Sukwon Choi, Cheong Ghil Kim, Woo-Chan Park + 1 more
We propose a multi-threaded algorithm that can improve the performance of geometric acoustic (GA)-based sound propagation algorithms in mobile devices. In general, sound propagation algorithms require high computational cost because they perform based on ray tracing algorithms. For this reason, it is difficult to…
Tao Liu, Yi Liu, Chen Qian, Depei Qian + 1 more
With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of…
Yu David Liu
This paper describes an operational semantics for futures, with the primary target on energy efficiency. The work in progress is built around an insight that different threads can coordinate by running at different "paces," so that the time for synchronization and the resulting wasteful energy consumption can be…
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…
Min Shuai, Xin Chen
Weighted gene co-expression network analysis (WGCNA) is an R package that can search highly related gene modules. The most time-consuming step of the whole analysis is to calculate the Topological Overlap Matrix (TOM) from the Adjacency Matrix in a single thread. This study changes it to multithreading. This paper uses…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
J.A. Bergstra
| 1 | Introduction, PMTh | | 2 | | --- | --- | --- | --- | | | 1.1 | Concurrency, multi-tasking, multi-threading, arbitrary interleav | | | | | ing, and strategic interleaving | 3 | | | 1.2 | Multi-threading in psychology versus multi-threading in computing | 4 | | | 1.3 | Designing a story on PMTh | 6 | | | 1.4 | A…
Pierre Carrier, Bill Long, Richard Walsh, Jef Dawson + 4 more
High Performance Computing (HPC) Best Practice offers opportunities to implement lessons learned in areas such as computational chemistry and physics in genomics workflows, specifically Next-Generation Sequencing (NGS) workflows. In this study we will briefly describe how distributed-memory parallelism can be an…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Shumpei Morita, Jay T. Groves
T cells can recognize a few molecules of cognate antigen amongst vastly outnumbering non-cognate ligands. The T cell receptor (TCR) differentiates antigens based on antigen-TCR binding dwell time through a kinetic proofreading process. Historically, this has been modeled as the ligated receptor undergoing a series of…
Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti + 3 more
We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the…
Xinwei Zhao, Eberhard Korsching
DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) provided in this study offers a user-friendly platform for sequence…