Service-Learning Faculty Assessment: Report of Results, 2018

In Spring 2018, the VCU Service-Learning Office sponsored an evaluation process that gathered feedback from faculty members who teach service-learning classes. The goal was to deepen understanding of the barriers faced by VCU’s service-learning faculty instructors and to solicit feedback about key strategies for overcoming these barriers. An independent research consultant conducted the evaluation in two phases: an online anonymous survey and a 30-minute phone interview. Eighty service-learning instructors completed the online survey, and a stratified sample of 18 instructors completed the telephone interviews. Findings indicated that both the online survey respondents and phone interview participants experienced similar supports and barriers to teaching their service-learning classes. Key findings and recommendations are outlined in the full report

Energy-efficiency evaluation of Intel KNL for HPC workloads

Energy consumption is increasingly becoming a limiting factor to the design of faster large-scale parallel systems, and development of energy-efficient and energy-aware applications is today a relevant issue for HPC code-developer communities. In this work we focus on energy performance of the Knights Landing (KNL) Xeon Phi, the latest many-core architecture processor introduced by Intel into the HPC market. We take into account the 64-core Xeon Phi 7230, and analyze its energy performance using both the on-chip MCDRAM and the regular DDR4 system memory as main storage for the application data-domain. As a benchmark application we use a Lattice Boltzmann code heavily optimized for this architecture and implemented using different memory data layouts to store its lattice. We assessthen the energy consumption using different memory data-layouts, kind of memory (DDR4 or MCDRAM) and number of threads per core

FER: A Benchmark for the Roofline Analysis of FPGA Based HPC Accelerators

Nowadays, the use of hardware accelerators to boost the performance of HPC applications is a consolidated practice, and among others, GPUs are by far the most widespread. More recently, some data centers have successfully deployed also FPGA accelerated systems, especially to boost machine learning inference algorithms. Given the growing use of machine learning methods in various computational fields, and the increasing interest towards reconfigurable architectures, we may expect that in the near future FPGA based accelerators will be more common in HPC systems, and that they could be exploited also to accelerate general purpose HPC workloads. In view of this, tools able to benchmark FPGAs in the context of HPC are necessary for code developers to estimate the performance of applications, as well as for computer architects to model that of systems at scale. To fulfill these needs, we have developed FER (FPGA Empirical Roofline), a benchmarking tool able to empirically measure the computing performance of FPGA based accelerators, as well as the bandwidth of their on-chip and off-chip memories. FER measurements enable to draw Roofline plots for FPGAs, allowing for performance comparisons with other processors, such as CPUs and GPUs, and to estimate at the same time the performance upper-bounds that applications could achieve on a target device. In this paper we describe the theoretical model on which FER relies, its implementation details, and the results measured on Xilinx Alveo accelerator cards

Using accelerators to speed up scientific and engineering codes: perspectives and problems

Accelerators are quickly emerging as the leading technology to further boost computing performances; their main feature is a massively parallel on-chip architecture. NVIDIA and AMD GPUs and the Intel Xeon-Phi are examples of accelerators available today. Accelerators are power-efficient and deliver up to one order of magnitude more peak performance than traditional CPUs. However, existing codes for traditional CPUs require substantial changes to run efficiently on accelerators, including rewriting with specific programming languages. In this contribution we present our experience in porting large codes to NVIDIA GPU and Intel Xeon-Phi accelerators. Our reference application is a CFD code based on the Lattice Boltzmann (LB) method. The regular structure of LB algorithms makes them suitable for processor architectures with a large degree of parallelism. However, the challenge of exploiting a large fraction of the theoretically available performance is not easy to met. We consider a state-of-the-art two-dimensional LB model based on 37 populations (a D2Q37 model), that accurately reproduces the thermo-hydrodynamics of a 2D-fluid obeying the equation-of-state of a perfect gas. We describe in details how we implement and optimize our LB code for Xeon-Phi and GPUs, and then analyze performances on single- and multi-accelerator systems. We finally compare results with those available on recent traditional multi-core CPUs

In vitro and in vivo selection of potentially probiotic lactobacilli from Nocellara del Belice table olives

Table olives are increasingly recognized as a vehicle as well as a source of probiotic bacteria, especially those fermented with traditional procedures based on the activity of indigenous microbial consortia, originating from local environments. In the present study, we report characterization at the species level of 49 Lactic Acid Bacteria (LAB) strains deriving from Nocellara del Belice table olives fermented with the Spanish or Castelvetrano methods, recently isolated in our previous work. Ribosomal 16S DNA analysis allowed identification of 4 Enterococcus gallinarum, 3 E. casseliflavus, 14 Leuconostoc mesenteroides, 19 Lactobacillus pentosus, 7 L. coryniformis, and 2 L. oligofermentans. The L. pentosus and L. coryniformis strains were subjected to further screening to evaluate their probiotic potential, using a combination of in vitro and in vivo approaches. The majority of them showed high survival rates under in vitro simulated gastro-intestinal conditions, and positive antimicrobial activity against Salmonella enterica serovar Typhimurium, Listeria monocytogenes and enterotoxigenic Escherichia coli (ETEC) pathogens. Evaluation of antibiotic resistance to ampicillin, tetracycline, chloramphenicol, or erythromycin was also performed for all selected strains. Three L. coryniformis strains were selected as very good performers in the initial in vitro testing screens, they were antibiotic susceptible, as well as capable of inhibiting pathogen growth in vitro. Parallel screening employing the simplified model organism Caenorhabditis elegans, fed the Lactobacillus strains as a food source, revealed that one L. pentosus and one L. coryniformis strains significantly induced prolongevity effects and protection from pathogen-mediated infection. Moreover, both strains displayed adhesion to human intestinal epithelial Caco-2 cells and were able to outcompete foodborne pathogens for cell adhesion. Overall, these results are suggestive of beneficial features for novel LAB strains, which renders them promising candidates as starters for the manufacturing of fermented table olives with probiotic added value

Matched filters for coalescing binaries detection on massively parallel computers

We discuss some computational problems associated to matched filtering of experimental signals from gravitational wave interferometric detectors in a parallel-processing environment. We then specialize our discussion to the use of the APEmille and apeNEXT processors for this task. Finally, we accurately estimate the performance of an APEmille system on a computational load appropriate for the LIGO and VIRGO experiments, and extrapolate our results to apeNEXT.Comment: 19 pages, 6 figure

An exploratory study of information sources and key findings on UK cocaine-related deaths.

Cocaine-related deaths have increased since the early 1990s in Europe, including the UK. Being multi-factorial, they are difficult to define, detect and record. The European Monitoring Centre for Drugs and Drug Addiction commissioned research to: describe trends reported to Special Mortality Registries and General Mortality Registers; provide demographic and drug-use characteristic information of cases; and establish how deaths are identified and classified. A questionnaire was developed and piloted amongst all European Monitoring Centre for Drugs and Drug Addiction Focal Point experts/Special Mortality Registries: 19 (63%) responded; nine countries provided aggregated data. UK General Mortality Registers use cause of death and toxicology to identify cocaine-related deaths. Categorisation is based on International Classification of Diseases codes. Special Mortality Registries use toxicology, autopsy, evidence and cause of death. The cocaine metabolites commonly screened for are: benzoylecgonine, ecgonine methyl ester, cocaethylene and ecgonine. The 2000s saw a generally accelerating upward trend in cases, followed by a decline in 2009. The UK recorded 2700-2900 deaths during 1998-2012. UK Special Mortality Registry data (2005-2009) indicate: 25-44 year-olds account for 74% of deaths; mean age=34 (range 15-81) years; 84% male. Cocaine overdoses account for two-thirds of cases; cocaine alone being mentioned/implicated in 23% in the UK. Opioids are involved in most (58%) cocaine overdose cases

A combined proteomics, metabolomics and in vivo analysis approach for the characterization of probiotics in large-scale production

The manufacturing processes of commercial probiotic strains may be affected in different ways in the attempt to optimize yield, costs, functionality, or stability, influencing gene expression, protein patterns, or metabolic output. Aim of this work is to compare different samples of a high concentration (450 billion bacteria) multispecies (8 strains) formulation produced at two different manufacturing sites, United States of America (US) and Italy (IT), by applying a combination of functional proteomics, metabolomics, and in vivo analyses. Several protein-profile differences were detected between IT-and US-made products, with Lactobacillus paracasei, Streptococcus thermophilus, and Bifidobacteria being the main affected probiotics/microorganisms. Performing proton nuclear magnetic spectroscopy (1H-NMR), some discrepancies in amino acid, lactate, betaine and sucrose concentrations were also reported between the two products. Finally, we investigated the health-promoting and antiaging effects of both products in the model organism Caenorhabditis elegans. The integration of omics platforms with in vivo analysis has emerged as a powerful tool to assess manufacturing procedures

Effects of the ionizing radiation disinfection treatment on historical leather

Microorganisms often cause significant damage on historical objects. The archive or library materials as well as textile or leather artifacts suffer serious attacks that need appropriate care treatments. Several biocide processes have been implemented but often their application does not preserve the material of the good. The objective of this work is the disinfection through ionizing radiation of leather wallpaper from the museum building Palazzo Chigi in Ariccia (Rome, Italy). The controlled sterilization treatments were carried out using X-ray beams to eliminate the microorganisms present on the leather and maintaining unchanged the properties of the constituent material. Some fragments of decorated leather wallpaper, dating back to the 1700s, were irradiated with X-rays up to 5,000 Gy. The amount of microorganisms was evaluated by microbiological analysis before and after X-ray irradiation treatments to identify the dose that inhibits the bacterial load. It will be shown how the results obtained by the application of different chemical-physical techniques (Scanning Electron Microscopy, Fourier Transform Infrared spectroscopy and Light Transmission Analysis) have helped in the evaluation of the impact of the X-rays on leather chemical and physical integrity