19 papers · ranked by Valyu relevance
Muhammad Osama, Serban D. Porumbescu, John D. Owens
We propose a GPU fine-grained load-balancing abstraction that decouples load balancing from work processing and aims to support both static and dynamic schedules with a programmable interface to implement new load-balancing schedules. Prior to our work, the only way to unleash the GPU's potential on irregular problems…
Harisankar Sadasivan, Milos Maric, Eric Dawson, Vishanth Iyer + 2 more
Long read sequencing technology is becoming increasingly popular for Precision Medicine applications like variant calling from Whole Genome Sequencing (WGS) and for metagenomics applications like microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing…
Michael Rowan, Axel Huebl, Kevin Gott, Jack Deslippe + 3 more
'Maxence Thévenet' 'Remi Lehé' 'Jean-Luc Vay'] Maintaining computational load balance is important to the performant behavior of codes which operate under a distributed computing model. This is especially true for GPU architectures, which can suffer from memory oversubscription if improperly load balanced. We present…
Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon + 3 more
Nanopore sequencing has the potential to revolutionise genomics by realising portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these applications requires efficient bioinformatic algorithms for the analysis of raw nanopore signal data. For instance…
Chun-Yuan Lin, Chung-Hung Wang, Che-Lun Hung, Yu-Shiang Lin
Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n2), where n is the maximal length of compounds. In general, the length of…
Ananya Raval, Rupesh Nasre, Vivek Kumar, Rama K. Vasudevan + 2 more
'Sathish Vadhiyar' 'Keshav Pingali'] Abstract—Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this…
Jeongmin Bae, Hajin Jeon, Min-Soo Kim
Background Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target sequences. It takes an entire sequence DB as input and returns all feasible and valid primer pairs…
Georgios Koutsoumpakis, Iakovos Koutsoumpakis, Anastasios Gounaris
Nowadays, the data to be processed by database systems has grown so large that any conventional, centralized technique is inadequate. At the same time, general purpose computation on GPU (GPGPU) recently has successfully drawn attention from the data management community due to its ability to achieve significant…
Álvaro Luiz Fazenda, Celso L. Mendes, Laxmikant V. Kalé, Jairo Panetta + 1 more
'Jairo Panetta' 'Eduardo R. Rodrigues'] The dynamic load-balancing framework in Charm++/AMPI, developed at the University of Illinois, is based on using processor virtualization to allow thread migration across processors. This framework has been successfully applied to many scientific applications in the past, such as…
Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann + 2 more
'Bert L. de Groot' 'Helmut Grubmüller'] The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and…
Juechu Dong, Xueshen Liu, Harisankar Sadasivan, Sriranjani Sitaraman + 1 more
Long-read DNA sequencing is becoming increasingly popular for genetic diagnostics. Minimap2 is the state-of-the-art long-read aligner. However, Minimap2’s chaining step is slow on the CPU and takes 40-68% of the time especially for long DNA reads. Prior works in accelerating Minimap2 either lose mapping accuracy, are…
Maksudul Alam, Kalyan Perumalla
Synthetically generated, large graph networks serve as useful proxies to real-world networks for many graph-based applications. The ability to generate such networks helps overcome several limitations of real-world networks regarding their number, availability, and access. Here, we present the design, implementation…
Heeseung Jo, Jinkyu Jeong, Myoungho Lee, Dong Hoon Choi
Recently, biological applications start to be reimplemented into the applications which exploit many cores of GPUs for better computation performance. Therefore, by providing virtualized GPUs to VMs in cloud computing environment, many biological applications will willingly move into cloud environment to enhance their…
Moises Hernandez-Fernandez, Istvan Reguly, Saad Jbabdi, Mike Giles + 2 more
The great potential of computational diffusion MRI (dMRI) relies on indirect inference of tissue microstructure and brain connections, since modelling and tractography frameworks map diffusion measurements to neuroanatomical features. This mapping however can be computationally highly expensive, particularly given the…
Shanky Goyal, Shashi Bhushan, Yogesh Kumar, Abu ul Hassan S. Rana + 3 more
'Muhammad Raheel Bhutta' 'Muhammad Fazal Ijaz' 'Youngdoo Son'] Cloud computing offers the services to access, manipulate and configure data online over the web. The cloud term refers to an internet network which is remotely available and accessible at anytime from anywhere. Cloud computing is undoubtedly an innovation…
Authors not listed
Modeling multimetallic systems efficiently enables faster prediction of desirable chemical properties and design of new materials. This work describes an initial implementation for performing multireference wave function method localized active space self-consistent field (LASSCF) calculations through the use of…
Quim Aguado-Puig, Max Doblas, Christos Matzoros, Antonio Espinosa + 3 more
Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like…
Authors not listed
The complete active space self-consistent field (CASSCF) method is essential for describing complex photochemical processes, but its application in ab initio molecular dynamics is often limited by the computational cost associated with four-center two-electron repulsion integrals (ERIs). We present the first…
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Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…