Constructing a Bioinformatics Platform with Web and Mobile Services Based on NVIDIA Jetson TK1

2015 ◽  
Vol 7 (4) ◽  
pp. 57-73 ◽  
Author(s):  
Chun-Yuan Lin ◽  
Jin Ye ◽  
Che-Lun Hung ◽  
Chung-Hung Wang ◽  
Min Su ◽  
...  
Keyword(s):  
Power Consumption ◽  
High Performance Computing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Low Cost ◽  
Research Direction ◽  
Mobile Services ◽  
Performance Ratio ◽  
The Cost ◽  
Performance Computing

Current high-end graphics processing units (abbreviate to GPUs), such as NVIDIA Tesla, Fermi, Kepler series cards which contain up to thousand cores per-chip, are widely used in the high performance computing fields. These GPU cards (called desktop GPUs) should be installed in personal computers/servers with desktop CPUs; moreover, the cost and power consumption of constructing a high performance computing platform with these desktop CPUs and GPUs are high. NVIDIA releases Tegra K1, called Jetson TK1, which contains 4 ARM Cortex-A15 CPUs and 192 CUDA cores (Kepler GPU) and is an embedded board with low cost, low power consumption and high applicability advantages for embedded applications. NVIDIA Jetson TK1 becomes a new research direction. Hence, in this paper, a bioinformatics platform was constructed based on NVIDIA Jetson TK1. ClustalWtk and MCCtk tools for sequence alignment and compound comparison were designed on this platform, respectively. Moreover, the web and mobile services for these two tools with user friendly interfaces also were provided. The experimental results showed that the cost-performance ratio by NVIDIA Jetson TK1 is higher than that by Intel XEON E5-2650 CPU and NVIDIA Tesla K20m GPU card.

Constructing a Bioinformatics Platform with Web and Mobile Services Based on NVIDIA Jetson TK1

2020 ◽  
pp. 629-644
Author(s):  
Chun-Yuan Lin ◽  
Jin Ye ◽  
Che-Lun Hung ◽  
Chung-Hung Wang ◽  
Min Su ◽  
...  
Keyword(s):  
Power Consumption ◽  
High Performance Computing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Low Cost ◽  
Research Direction ◽  
Mobile Services ◽  
Computing Platform ◽  
The Cost ◽  
Performance Computing

Current high-end graphics processing units (abbreviate to GPUs), such as NVIDIA Tesla, Fermi, Kepler series cards which contain up to thousand cores per-chip, are widely used in the high performance computing fields. These GPU cards (called desktop GPUs) should be installed in personal computers/servers with desktop CPUs; moreover, the cost and power consumption of constructing a high performance computing platform with these desktop CPUs and GPUs are high. NVIDIA releases Tegra K1, called Jetson TK1, which contains 4 ARM Cortex-A15 CPUs and 192 CUDA cores (Kepler GPU) and is an embedded board with low cost, low power consumption and high applicability advantages for embedded applications. NVIDIA Jetson TK1 becomes a new research direction. Hence, in this paper, a bioinformatics platform was constructed based on NVIDIA Jetson TK1. ClustalWtk and MCCtk tools for sequence alignment and compound comparison were designed on this platform, respectively. Moreover, the web and mobile services for these two tools with user friendly interfaces also were provided. The experimental results showed that the cost-performance ratio by NVIDIA Jetson TK1 is higher than that by Intel XEON E5-2650 CPU and NVIDIA Tesla K20m GPU card.

High-performance computing for computational modelling in built environment-related studies – a scientometric review

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Emmanuel Imuetinyan Aghimien ◽  
Lerato Millicent Aghimien ◽  
Olutomilayo Olayemi Petinrin ◽  
Douglas Omoregie Aghimien
Keyword(s):  
High Performance Computing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Computational Models ◽  
Computational Modelling ◽  
Scientometric Analysis ◽  
Content Type ◽  
Performance Computing ◽  
Aec Industry

Purpose This paper aims to present the result of a scientometric analysis conducted using studies on high-performance computing in computational modelling. This was done with a view to showcasing the need for high-performance computers (HPC) within the architecture, engineering and construction (AEC) industry in developing countries, particularly in Africa, where the use of HPC in developing computational models (CMs) for effective problem solving is still low. Design/methodology/approach An interpretivism philosophical stance was adopted for the study which informed a scientometric review of existing studies gathered from the Scopus database. Keywords such as high-performance computing, and computational modelling were used to extract papers from the database. Visualisation of Similarities viewer (VOSviewer) was used to prepare co-occurrence maps based on the bibliographic data gathered. Findings Findings revealed the scarcity of research emanating from Africa in this area of study. Furthermore, past studies had placed focus on high-performance computing in the development of computational modelling and theory, parallel computing and improved visualisation, large-scale application software, computer simulations and computational mathematical modelling. Future studies can also explore areas such as cloud computing, optimisation, high-level programming language, natural science computing, computer graphics equipment and Graphics Processing Units as they relate to the AEC industry. Research limitations/implications The study assessed a single database for the search of related studies. Originality/value The findings of this study serve as an excellent theoretical background for AEC researchers seeking to explore the use of HPC for CMs development in the quest for solving complex problems in the industry.

Advanced Simulation Capability for Environmental Management: Current Status and Future Applications

2013 ◽  
Author(s):  
Mark Freshley ◽  
Paul Dixon ◽  
Paul Black ◽  
Bruce Robinson ◽  
Tom Stockton ◽  
...  
Keyword(s):  
Environmental Management ◽  
Radioactive Waste ◽  
Decision Analysis ◽  
High Performance Computing ◽  
Waste Disposal ◽  
High Performance ◽  
Fate And Transport ◽  
Radioactive Waste Disposal ◽  
The Cost ◽  
Performance Computing

The U.S. Department of Energy (USDOE) Office of Environmental Management (EM), Office of Soil and Groundwater (EM-12), is supporting development of the Advanced Simulation Capability for Environmental Management (ASCEM). ASCEM is a state-of-the-art scientific tool and approach that is currently aimed at understanding and predicting contaminant fate and transport in natural and engineered systems. ASCEM is a modular and open source high-performance computing tool. It will be used to facilitate integrated approaches to modeling and site characterization, and provide robust and standardized assessments of performance and risk for EM cleanup and closure activities. The ASCEM project continues to make significant progress in development of capabilities, with current emphasis on integration of capabilities in FY12. Capability development is occurring for both the Platform and Integrated Toolsets and High-Performance Computing (HPC) multiprocess simulator. The Platform capabilities provide the user interface and tools for end-to-end model development, starting with definition of the conceptual model, management of data for model input, model calibration and uncertainty analysis, and processing of model output, including visualization. The HPC capabilities target increased functionality of process model representations, toolsets for interaction with Platform, and verification and model confidence testing. The integration of the Platform and HPC capabilities were tested and evaluated for EM applications in a set of demonstrations as part of Site Applications Thrust Area activities in 2012. The current maturity of the ASCEM computational and analysis capabilities has afforded the opportunity for collaborative efforts to develop decision analysis tools to support and optimize radioactive waste disposal. Recent advances in computerized decision analysis frameworks provide the perfect opportunity to bring this capability into ASCEM. This will allow radioactive waste disposal to be evaluated based on decision needs, such as disposal, closure, and maintenance. Decision models will be used in ASCEM to identify information/data needs, and model refinements that might be necessary to effectively reduce uncertainty in waste disposal decisions. Decision analysis models start with tools for framing the problem, and continue with modeling both the science side of the problem (for example, inventories, source terms, fate and transport, receptors, risk, etc.), and the cost side of the problem, which could include costs of implementation of any action that is chosen (e.g., for disposal or closure), and the values associated with those actions. The cost side of the decision problem covers economic, environmental and societal costs, which correspond to the three pillars of sustainability (economic, social, and environmental). These tools will facilitate stakeholder driven decision analysis to support optimal sustainable solutions in ASCEM.

scholarly journals Conceptual low-cost on-board high performance computing in CubeSat nanosatellites for pattern recognition in Earth's remote sensing

10.29007/8d25 ◽  
2019 ◽  
Author(s):  
J J Hernández-Gómez ◽  
G A Yañez-Casas ◽  
Alejandro M Torres-Lara ◽  
C Couder-Castañeda ◽  
M G Orozco-del-Castillo ◽  
...  
Keyword(s):  
Remote Sensing ◽  
High Performance Computing ◽  
High Performance ◽  
Low Cost ◽  
Remote Sensing Data ◽  
Artificial Satellites ◽  
Severe Problem ◽  
Sensing Data ◽  
Low Earth Orbits ◽  
Performance Computing

Nowadays, remote sensing data taken from artificial satellites require high space com- munications bandwidths as well as high computational processing burdens due to the vertiginous development and specialisation of on-board payloads specifically designed for remote sensing purposes. Nevertheless, these factors become a severe problem when con- sidering nanosatellites, particularly those based in the CubeSat standard, due to the strong limitations that it imposes in volume, power and mass. Thus, the applications of remote sensing in this class of satellites, widely sought due to their affordable cost and easiness of construction and deployment, are very restricted due to their very limited on-board computer power, notwithstanding their Low Earth Orbits (LEO) which make them ideal for Earth’s remote sensing. In this work we present the feasibility of the integration of an NVIDIA GPU of low mass and power as the on-board computer for 1-3U CubeSats. From the remote sensing point of view, we present nine processing-intensive algorithms very commonly used for the processing of remote sensing data which can be executed on-board on this platform. In this sense, we present the performance of these algorithms on the proposed on-board computer with respect with a typical on-board computer for CubeSats (ARM Cortex-A57 MP Core Processor), showing that they have acceleration factors of average of 14.04× ∼14.72× in average. This study sets the precedent to perform satellite on-board high performance computing so to widen the remote sensing capabilities of CubeSats.

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