Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud

Methods developed at the Texas Advanced Computing Center (TACC) are described and demonstrated for automating the construction of an elastic, virtual cluster emulating the Stampede2 high performance computing (HPC) system. The cluster can be built and/or scaled in a matter of minutes on the Jetstream self-service cloud system and shares many properties of the original Stampede2, including: i) common identity management, ii) access to the same file systems, iii) equivalent software application stack and module system, iv) similar job scheduling interface via Slurm. We measure time-to-solution for a number of common scientific applications on our virtual cluster against equivalent runs on Stampede2 and develop an application profile where performance is similar or otherwise acceptable. For such applications, the virtual cluster provides an effective form of "cloud bursting" with the potential to significantly improve overall turnaround time, particularly when Stampede2 is experiencing long queue wait times. In addition, the virtual cluster can be used for test and debug without directly impacting Stampede2. We conclude with a discussion of how science gateways can leverage the TACC Jobs API web service to incorporate this cloud bursting technique transparently to the end user.Comment: 6 pages, 0 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Discard survival in Trammel net and Danish seine

European plaice (Pleuronectes platessa) is a key species for Danish commercial and recreational fishing. A discard ban in the reformed European Union’s Common Fisheries Policy includes the possibility of exempting from the landing obligation “species for which scientific evidence demonstrates high survival rates”. Although smaller coastal fishing vessels make up a substantial part of the commercial Danish fishing fleet, discard survival in plaice from these vessels is not well studied. To address this issue, a study on discard survival in plaice from trammel net and Danish Seine was established as a cooperation between Aalborg University, Copenhagen University and Foreningen for Skånsomt Kystfiskeri. Methodology was developed to collect, assess and observe discard survival in plaice from trammel net and Danish Seine. Experiments were conducted in 2017 and 2018 from three commercial coastal fishing vessels. Livewells were designed to house captured individuals for up to 11 days for observation of short-term survival rate. Catch-damage-index (CDI) and Reflex Action Mortality Predictor (RAMP) were used to assess fish condition immediately after capture and at the end of the observation periods. Results showed 100% survival rate in plaice from trammel net and 87% survival rate in plaice from Danish Seine. For the majority of fish assessed after capture, reflex impairments were absent and injuries were primarily minor bruises, fin fraying, and net marks. Assessments of injuries and reflex impairments after observation showed the condition of the fish generally did not worsen during the observation periods. The project is financed by the European Fisheries Fund and the Ministry of Environment and Food of Denmark

Nebraska Agricultural Water Management Demonstration Network (NAWMDN): Integrating Research and Extension/Outreach

Maximizing the net benefits of irrigated plant production through appropriately designed agricultural water management programs is of growing importance in Nebraska, and other western and Midwestern states, because many areas are involved in management and policy changes to conserve irrigation water. In Nebraska, farmers are being challenged to practice conservation methods and use water resources more efficiently while meeting plant water requirements and maintaining high yields. Another challenge Nebraska experiences in it\u27s approximately 3.5‐million‐ha irrigated lands is limited adoption of newer technologies/tools to help farmers better manage irrigation, conserve water and energy, and increase plant water use efficiency. In 2005, the Nebraska Agricultural Water Management Demonstration Network (NAWMDN or Network) was formed from an interdisciplinary team of partners including the Natural Resources Districts (NRD); USDA‐NRCS; farmers from south central, northeast, west central, and western Nebraska; crop consultants; and University of Nebraska‐Lincoln faculty. The main goal of the Network is to enable the transfer of high quality research‐based information to Nebraskans through a series of demonstration projects established in farmers\u27 fields and implement newer tools and technologies to address and enhance plant water use efficiency, water conservation, and reduce energy consumption for irrigation. The demonstration projects are supported by the scientifically‐based field research and evaluation projects conducted at the University of Nebraska‐Lincoln, South Central Agricultural Laboratory located near Clay Center, Nebraska. The Network was formed with only 15 farmers as collaborators in only one of the 23 NRDs in 2005. As of late 2009, the number of active collaborators has increased to over 300 in 12 NRDs and 35 of 93 counties. The Network is impacting both water and energy conservation due to farmers adopting information and newer technologies for irrigation management. The NAWMDN is helping participants to improve irrigation management and efficiency by monitoring plant growth stages and development, soil moisture, and crop evapotranspiration. As a result, they are reducing irrigation water application amounts and associated energy savings is leading to greater profitability to participating farmers. This article describes the goals and objectives of the Network, technical and educational components, operational functions, and procedures used in the NAWMDN. The quantitative impacts in terms of water and energy conservation are reported

NEBRASKA AGRICULTURAL WATER MANAGEMENT DEMONSTRATION NETWORK (NAWMDN): INTEGRATING RESEARCH AND EXTENSION/OUTREACH

Maximizing the net benefits of irrigated plant production through appropriately designed agricultural water management programs is of growing importance in Nebraska, and other western and Midwestern states, because many areas are involved in management and policy changes to conserve irrigation water. In Nebraska, farmers are being challenged to practice conservation methods and use water resources more efficiently while meeting plant water requirements and maintaining high yields. Another challenge Nebraska experiences in it\u27s approximately 3.5‐million‐ha irrigated lands is limited adoption of newer technologies/tools to help farmers better manage irrigation, conserve water and energy, and increase plant water use efficiency. In 2005, the Nebraska Agricultural Water Management Demonstration Network (NAWMDN or Network) was formed from an interdisciplinary team of partners including the Natural Resources Districts (NRD); USDA‐NRCS; farmers from south central, northeast, west central, and western Nebraska; crop consultants; and University of Nebraska‐Lincoln faculty. The main goal of the Network is to enable the transfer of high quality research‐based information to Nebraskans through a series of demonstration projects established in farmers\u27 fields and implement newer tools and technologies to address and enhance plant water use efficiency, water conservation, and reduce energy consumption for irrigation. The demonstration projects are supported by the scientifically‐based field research and evaluation projects conducted at the University of Nebraska‐Lincoln, South Central Agricultural Laboratory located near Clay Center, Nebraska. The Network was formed with only 15 farmers as collaborators in only one of the 23 NRDs in 2005. As of late 2009, the number of active collaborators has increased to over 300 in 12 NRDs and 35 of 93 counties. The Network is impacting both water and energy conservation due to farmers adopting information and newer technologies for irrigation management. The NAWMDN is helping participants to improve irrigation management and efficiency by monitoring plant growth stages and development, soil moisture, and crop evapotranspiration. As a result, they are reducing irrigation water application amounts and associated energy savings is leading to greater profitability to participating farmers. This article describes the goals and objectives of the Network, technical and educational components, operational functions, and procedures used in the NAWMDN. The quantitative impacts in terms of water and energy conservation are reported

Semi-empirical relationships to assess the seismic performance of slopes from an updated version of the Italian seismic database

Funder: Dipartimento della Protezione Civile, Presidenza del Consiglio dei Ministri; doi: http://dx.doi.org/10.13039/100012783; Grant(s): ReLUIS research project - Working Pachage 16: Geotechnical Engineering - Task Group 2: Slope stabilityAbstractSeismic performance of slopes can be assessed through displacement-based procedures where earthquake-induced displacements are usually computed following Newmark-type calculations. These can be adopted to perform a parametric integration of earthquake records to evaluate permanent displacements for different slope characteristics and seismic input properties. Several semi-empirical relationships can be obtained for different purposes: obtaining site-specific displacement hazard curves following a fully-probabilistic approach, to assess the seismic risk associated with the slope; providing semi-empirical models within a deterministic framework, where the seismic-induced permanent displacement is compared with threshold values related to different levels of seismic performance; calibrating the seismic coefficient to be used in pseudo-static calculations, where a safety factor against limit conditions is computed. In this paper, semi-empirical relationships are obtained as a result of a parametric integration of an updated version of the Italian strong-motion database, that, in turn, is described and compared to older versions of the database and to well-known ground motion prediction equations. Permanent displacement is expressed as a function of either ground motion parameters, for a given yield seismic coefficient of the slope, or of both ground motion parameters and the seismic coefficient. The first are meant to be used as a tool to develop site-specific displacement hazard curves, while the last can be used to evaluate earthquake-induced slope displacements, as well as to calibrate the seismic coefficient to be used in a pseudo-static analysis. Influence of the vertical component of seismic motion on these semi-empirical relationships is also assessed.</jats:p

(Im)material Culture : Towards an Archaeology of Cybercrime

Cybercrime is ubiquitous. People now inhabit a digital environment comprising permanent risk, exponential threats, and multiple virtual/physical harms, forming a global community of malefactors and the criminally exploited. The purpose of this paper is two-fold. First, through an archaeological lens, to characterize the new materiality of cybercrime (including its artefacts and architecture alongside digital/virtual manifestations). And second, to explore the potential for new perspectives on cybercrime borne out of this archaeological approach. In short: what is the archaeology of cybercrime and can new understandings emerge from an archaeological perspective? In undertaking this research we also challenge the long-held presumption that non-physical traces cannot be studied archaeologically. It is our contention that they can

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

<p>Abstract</p> <p>Background</p> <p>The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.</p> <p>Results</p> <p>One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (<it>p </it>≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including <it>WNT10B </it>and <it>DKK2 </it>in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- <it>BAX </it>and <it>BMPR1B </it>were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (<it>p </it>≤ 0.1 or <it>p </it>≤ 0.05).</p> <p>Conclusions</p> <p>Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of <it>BAX </it>and <it>BMPR1B </it>gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.</p