Congestion Game Scheduling Implementation for High-Throughput Virtual Drug Screening Using BOINC-Based Desktop Grid

Nikitina, Natalia; Ivashko, Evgeny; Tchernykh, Andrei

doi:10.1007/978-3-319-62932-2_46

Cited by 6 publications

(3 citation statements)

References 27 publications

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“…The work [39] proposes a task scheduling algorithm to address this challenge. The space of molecules is divided into blocks according to the chemical properties of molecules.…”

Section: Domain-imposed Criteria For Task Schedulingmentioning

confidence: 99%

Task Scheduling in Desktop Grids: Open Problems

2017

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Abstract:We survey the areas of Desktop Grid task scheduling that seem to be insu ciently studied so far and are promising for e ciency, reliability, and quality of Desktop Grid computing. These topics include optimal task grouping, "needle in a haystack" paradigm, gametheoretical scheduling, domain-imposed approaches, special optimization of the nal stage of the batch computation, and Enterprise Desktop Grids.

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“…The work [39] proposes a task scheduling algorithm to address this challenge. The space of molecules is divided into blocks according to the chemical properties of molecules.…”

Section: Domain-imposed Criteria For Task Schedulingmentioning

confidence: 99%

Task Scheduling in Desktop Grids: Open Problems

2017

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“…Researchers have explored how existing distributed computing paradigms and algorithms can be adapted to VC. Examples include evolutionary algorithms[46] [47], virtual drug discovery[48], MPI-style distributed parallel programming[49], Map-Reduce computing[50], data analytics[51], machine learning[52] [53][54], gene sequence alignment[55], climate modeling[56], and distributed sensor networks[57]. Desell et al describe a system that combines VC and participatory "citizen science"[58].Silva et al proposed extending BOINC to allow job submission by volunteers[59].…”

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confidence: 99%

BOINC: A Platform for Volunteer Computing

Anderson

2019

J Grid Computing

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Volunteer computing" is the use of consumer digital devices for high-throughput scientific computing. It can provide large computing capacity at low cost, but presents challenges due to device heterogeneity, unreliability, and churn. BOINC, a widely-used open-source middleware system for volunteer computing, addresses these challenges. We describe its features, architecture, and implementation.Volunteer computing (VC) is the use of consumer digital devices, such as desktop and laptop computers, tablets, and smartphones, for high-throughput scientific computing. Device owners participate in VC by installing a program that downloads and executes jobs from servers operated by science projects. There are currently about 30 VC projects in many scientific areas and at many institutions. The research enabled by VC has resulted in numerous papers in Nature, Science, PNAS, Physical Review, Proteins, PloS Biology, Bioinformatics, J. of Mol. Biol., J. Chem. Phys, and other top journals [1].About 700,000 devices are actively participating in VC projects. These devices have about 4 million CPU cores and 560,000 GPUs, and collectively provide an average throughput of 93 PetaFLOPS. The devices are primarily modern, high-end computers: they average 16.5 CPU GigaFLOPS and 11.4 GB of RAM, and most have a GPU capable of general-purpose computing using OpenCL or CUDA.In terms of power consumption, data-center nodes are more efficient (i.e. have greater FLOPS/watt) than many consumer devices. However, to compare net energy usage, two other factors must be considered. First, data centers use air conditioning to remove the heat generated by hardware; consumer devices generally do not. Second, in cool climates, the heat generated by consumer devices contributes to ambient heating, so the net energy cost of computing may be zero. Thus it's not clear whether VC is globally more or less energy efficient than data-center computing. In any case, this does not affect VC's cost to the scientist, since the energy is paid for by volunteers.VC is best suited to high-throughput computing (HTC): workloads consisting of large groups or streams of jobs where the goal is high rate of job completion, rather than low job turnaround time. VC is less suited to workloads that have extreme memory or storage requirements, or for which the ratio of network communication (i.e. input and output file size) to computing is extremely high.VC differs from other forms of HTC, such as grids and clouds, in several ways: The computers are anonymous and untrusted.  The computers are heterogeneous in many hardware and software dimensions; for example, of desktops and laptops participating in VC, 85% are Windows, 7% are Macs, and 7% are Linux. Job turnaround times are uncertain because of sporadic host availability.  There is significant "device churn", i.e. arrival and disappearance of computers. Creating the resource pool requires volunteer recruitment and retention, and the client software must be easy for consumers to install and run. The scale of VC is larger: ...

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“…In order to solve embarassingly parallel problems, desktop grids are usually employed [6]. Alternatively, enterprise desktop grids [12,24] (as well as other types of desktop grids) could be employed to solve them. However, in the present study another type of desktop grid computing -volunteer computing [1] -was used.…”

Section: Introductionmentioning

confidence: 99%

Using Volunteer Computing to Study Some Features of Diagonal Latin Squares

et al. 2017

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Abstract:In this research, the study concerns around several features of diagonal Latin squares (DLSs) of small order. Authors of the study suggest an algorithm for computing minimal and maximal numbers of transversals of DLSs. According to this algorithm, all DLSs of a particular order are generated, and for each square all its transversals and diagonal transversals are constructed. The algorithm was implemented and applied to DLSs of order at most 7 on a personal computer. The experiment for order 8 was performed in the volunteer computing project Gerasim@home. In addition, the problem of nding pairs of orthogonal DLSs of order 10 was considered and reduced to Boolean satis ability problem. The obtained problem turned out to be very hard, therefore it was decomposed into a family of subproblems. In order to solve the problem, the volunteer computing project SAT@home was used. As a result, several dozen pairs of described kind were found.

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Congestion Game Scheduling Implementation for High-Throughput Virtual Drug Screening Using BOINC-Based Desktop Grid

Cited by 6 publications

References 27 publications

Task Scheduling in Desktop Grids: Open Problems

Task Scheduling in Desktop Grids: Open Problems

BOINC: A Platform for Volunteer Computing

Using Volunteer Computing to Study Some Features of Diagonal Latin Squares

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