A Novel System Oriented Scheduler for Avoiding Haste Problem in Computational Grids

2011 ◽  
Vol 3 (1) ◽  
pp. 21-44
Author(s):  
Ahmed I. Saleh

Scheduling is an important issue that must be handled carefully to realize the “Just login to compute” principle introduced by computational grids. Current grid schedulers suffer from the haste problem, which is the inability to schedule all tasks successfully. Accordingly, some tasks fail to complete execution as they are allocated to unsuitable workers. Others may not start execution as suitable workers are previously allocated to other tasks. This paper introduces the scheduling haste problem and presents a novel high throughput grid scheduler. The proposed scheduler selects the most suitable worker to execute an input grid task. Hence, it minimizes the turnaround time for a set of grid tasks. Moreover, the scheduler is system oriented and avoids the scheduling haste problem. Experimental results show that the proposed scheduler outperforms traditional grid schedulers as it introduces better scheduling efficiency.

Author(s):  
Ahmed I. Saleh

Scheduling is an important issue that must be handled carefully to realize the “Just login to compute” principle introduced by computational grids. Current grid schedulers suffer from the haste problem, which is the inability to schedule all tasks successfully. Accordingly, some tasks fail to complete execution as they are allocated to unsuitable workers. Others may not start execution as suitable workers are previously allocated to other tasks. This paper introduces the scheduling haste problem and presents a novel high throughput grid scheduler. The proposed scheduler selects the most suitable worker to execute an input grid task. Hence, it minimizes the turnaround time for a set of grid tasks. Moreover, the scheduler is system oriented and avoids the scheduling haste problem. Experimental results show that the proposed scheduler outperforms traditional grid schedulers as it introduces better scheduling efficiency.


2018 ◽  
Vol 246 ◽  
pp. 03005
Author(s):  
Fu Xiao ◽  
Li-ming Xiao

This paper proposes a hardware platform for WCDMA baseband data transmission, which consists of USB3.0 interface, general purposes processor (GPP), and software defined radio (SDR) system. In view of the requirements of WCDMA system, the hardware platform consisting of USB3.0 controller, FPGA and DDRII was selected, which finally realized the high throughput rate and low delay transmission of baseband data of WCDMA system. The experimental results show that in this GPP software defined radio system, the interface speed of USB3.0 can reach 200MBps, and the loopback delay time of the system is about 0.7ms, which can meet the requirements of WCDMA system.


2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Patience Chatukuta ◽  
Marie Emma Christine Rey

Abstract Background The study of transient gene expression in cassava plants during virus infection using existing protocols is laborious and may take approximately fifteen weeks due to cassava’s recalcitrance to transformation. The combination of a protoplast system with CRISPR-mediated gene editing promises to shorten the turnaround time from plant tissue culture to high-throughput gene expression screening for candidate genes. Here, we detail a protocol for screening genes associated with the response to South African cassava mosaic virus (SACMV) in cassava protoplasts, with reference to the ubiquitin E3 ligase gene, MeE3L. Methods Cassava protoplasts of model, and SACMV-susceptible and -tolerant genotypes, were transformed with SACMV infectious clones and/or a CRISPR-editing construct targeting the MeE3L using PEG4000-mediated transfection. DNA and RNA were extracted from transformed protoplasts at 24 h post-transfection. Relative SACMV DNA accumulation was determined via qPCR using DpnI-digested total DNA, MeE3L relative expression was determined via reverse transcriptase qPCR, and results were analysed using one-way ANOVA, Tukey’s HSD test and the 2−ΔΔCTstatistical method. The MeE3L exonic region was sequenced on the ABI 3500XL Genetic Analyzer platform; and sequences were analysed for mutations using MAFTT and MEGA-X software. Construction of a phylogenetic tree was done using the Maximum Likelihood method and Jones-Taylor-Thornton (JTT) matrix-based model. Results The differential expression of unedited and mutant MeE3L during SACMV infection of model, susceptible and tolerant cassava protoplasts was determined within 7 weeks after commencement of tissue culture. The study also revealed that SACMV DNA accumulation in cassava protoplasts is genotype-dependent and induces multiple mutations in the tolerant landrace MeE3L homolog. Notably, the susceptible cassava landrace encodes a RINGless MeE3Lwhich is silenced by SACMV-induced mutations. SACMV also induces mutations which silence the MeE3L RING domain in protoplasts from and tolerant cassava landraces. Conclusions This protocol presented here halves the turnaround time for high-throughput screening of genes associated with the host response to SACMV. It provides evidence that a cassava E3 ligase is associated with the response to SACMV and forms a basis for validation of these findings by in planta functional and interaction studies.


2012 ◽  
Vol 95 (4) ◽  
pp. 1089-1096 ◽  
Author(s):  
Robert G Hatfield ◽  
Andrew D Turner

Abstract The bioaccumulation of paralytic shellfish toxins in mussels, oysters, cockles, hard clams, razors, and king scallops is monitored in England, Scotland, and Wales by AOAC Official MethodSM 2005.06 LC-with fluorescence detection (FLD). One of the commonly perceived disadvantages of using this method is the long turnaround time and low throughput in a busy laboratory environment. The chromatographic analysis of each sample typically utilizes a 15 min cycle time to achieve toxin oxidation product separation and column equilibration prior to subsequent analysis. A standard RP C18 analytical column, used successfully in recent years, achieves good separation with a long column lifetime. The analysis of a 40 sample qualitative screening batch takes approximately 18 h, including blanks, standards, and other QC samples. The availability of superficially porous column technology has offered the potential to reduce analysis time while retaining column performance on existing hardware. In this study, AOAC Official Method 2005.06 with LC-FLD was transferred to two different commercially available superficially porous columns, and the method performance characteristics were evaluated. Both columns separated all toxins adequately with cycle times less than half that of the existing method. Linearity for each toxin was acceptable up to two times the European maximum permitted limit of 800 μg di-HCl saxitoxin equivalent/kg flesh. LOD and LOQ values were substantially improved for the majority of toxins, with gonyautoxin 1&4 and neosaxitoxin showing up to a two- and four-fold improvement, respectively, depending on the column used. Quantification results obtained from parallel analysis of contaminated samples were acceptable on both columns. Comparative screen results gave a slight increase in the occurrence of contaminated samples, which was attributed to the improved detection limit for most toxins. Issues with rapidly increasing back pressure, however, were identified with both columns, with a limit of around 500 injections. This compares to the >3000 cycles routinely obtained with the standard RP-C18 HPLC columns currently in use. Overall, the gain achieved with these columns through shorter analysis time and improved analytical sensitivity is potentially of benefit in a high-throughput environment. For the routine high-throughput screening of shellfish samples, however, an improved column lifetime is desirable.


2013 ◽  
Vol 3 (1) ◽  
Author(s):  
Mohammed Amoon

AbstractFault tolerance is an important property in computational grids since the resources are geographically distributed. Job checkpointing is one of the most common utilized techniques for providing fault tolerance in computational grids. The efficiency of checkpointing depends on the choice of the checkpoint interval. Inappropriate checkpointing interval can delay job execution. In this paper, a fault-tolerant scheduling system based on checkpointing technique is presented and evaluated. When scheduling a job, the system uses both average failure time and failure rate of grid resources combined with resources response time to generate scheduling decisions. The system uses the failure rate of the assigned resources to calculate the checkpoint interval for each job. Extensive simulation experiments are conducted to quantify the performance of the proposed system. Experiments have shown that the proposed system can considerably improve throughput, turnaround time, grid load and failure tendency of computational grids.


2006 ◽  
Vol 527-529 ◽  
pp. 159-162 ◽  
Author(s):  
Albert A. Burk ◽  
Michael J. O'Loughlin ◽  
Michael J. Paisley ◽  
Adrian R. Powell ◽  
M.F. Brady ◽  
...  

Experimental results are presented for SiC epitaxial layer growth employing a large-area, up to 8x100-mm, warm-wall planetary SiC-VPE reactor. This high-throughput reactor has been optimized for the growth of uniform 0.01 to 80-micron thick, specular, device-quality SiC epitaxial layers with low background doping concentrations of <1x1014 cm-3 and intentional p- and n-type doping from ~1x1015 cm-3 to >1x1019 cm-3. Intrawafer layer thickness and n-type doping uniformity (σ/mean) of ~2% and ~8% have been achieved to date in the 8x100-mm configuration. The total range of the average intrawafer thickness and doping within a run are approximately ±1% and ±6% respectively.


2015 ◽  
Author(s):  
Greg R Ziegler ◽  
Ryan H Hartsock ◽  
Ivan Baxter

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.


2020 ◽  
Author(s):  
Nancy Matic ◽  
Tanya Lawson ◽  
Gordon Ritchie ◽  
Aleksandra Stefanovic ◽  
Victor Leung ◽  
...  

Introduction: With surging global demand for increased SARS-CoV-2 testing capacity, clinical laboratories seek automated, high-throughput molecular solutions, particularly for specimen types which do not rely upon supply of specialized collection devices or viral transport media (VTM). Saliva was evaluated as a diagnostic specimen for SARS-CoV-2 using the cobas SARS-CoV-2 Test on the cobas 6800 instrument. Methods: Saliva specimens submitted from various patient populations under investigation for COVID-19 from March-July 2020 were processed in the laboratory with sterile phosphate-buffered saline in a 1:2 dilution and vortexed with glass beads. The processed saliva samples were tested using a commercial assay for detection of the SARS-CoV-2 E gene (LightMix) in comparison to the cobas SARS-CoV-2 Test. Results: 22/64 (34.4%) of the saliva samples were positive for SARS-CoV-2. Positive and negative concordance between the LightMix and cobas assays were 100%. There was no cross-contamination of samples observed on the cobas 6800. The overall invalid rate for saliva on the cobas 6800 (1/128, 0.78%) was similar to the baseline invalid rate observed for nasopharyngeal swabs/VTM and plasma samples. Conclusions: Saliva is a feasible specimen type for SARS-CoV-2 testing on the cobas 6800, with potential to improve turnaround time and enhance testing capacity.


2021 ◽  
Author(s):  
Zita Hubler ◽  
Xiao Song ◽  
Cameron Norris ◽  
Mehul Jani ◽  
David Alouani ◽  
...  

ABSTRACTObjectivesEmerging SARS-CoV-2 variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure.MethodsWe use a tiered high-throughput SARS-CoV-2 screening program to characterizes variants in a supra-regional health system over 76 days. Combining targeted qPCR and selective sequencing, we screen positive SARS-CoV-2 samples from all hospitals within our health care system for genotyping dominant and emerging variants.ResultsThe median turnaround for genotyping was two days using the high-throughput qPCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower CT value, lower age at infection, and increased vaccine breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach.ConclusionsThese findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combing qPCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.Key messagesA tiered approach that uses qPCR-based screening to identify dominant variants and sequencing for unique variants maximizes throughput, turnaround time, and information gleaned from each sample.In our population, the Delta variant became dominant in less than a month and is associated with lower CT, lower age at infection, and increased breakthrough cases.We identified low-level variants, including the variant of interest B.1.621 and a Delta variant with an E484K mutation in our population using existing hospital infrastructure.


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