Optimized Broadcast for Deep Learning Workloads on Dense-GPU InfiniBand Clusters: MPI or NCCL?

Dense Multi-GPU systems have recently gained a lot of attention in the HPC arena. Traditionally, MPI runtimes have been primarily designed for clusters with a large number of nodes. However, with the advent of MPI+CUDA applications and CUDA-Aware MPI runtimes like MVAPICH2 and OpenMPI, it has become important to address efficient communication schemes for such dense Multi-GPU nodes. This coupled with new application workloads brought forward by Deep Learning frameworks like Caffe and Microsoft CNTK pose additional design constraints due to very large message communication of GPU buffers during the training phase. In this context, special-purpose libraries like NVIDIA NCCL have been proposed for GPU-based collective communication on dense GPU systems. In this paper, we propose a pipelined chain (ring) design for the MPI_Bcast collective operation along with an enhanced collective tuning framework in MVAPICH2-GDR that enables efficient intra-/inter-node multi-GPU communication. We present an in-depth performance landscape for the proposed MPI_Bcast schemes along with a comparative analysis of NVIDIA NCCL Broadcast and NCCL-based MPI_Bcast. The proposed designs for MVAPICH2-GDR enable up to 14X and 16.6X improvement, compared to NCCL-based solutions, for intra- and inter-node broadcast latency, respectively. In addition, the proposed designs provide up to 7% improvement over NCCL-based solutions for data parallel training of the VGG network on 128 GPUs using Microsoft CNTK.Comment: 8 pages, 3 figure

How to assess the acceptance of an electronic health record system?

Being able to access a patient’s clinical data in due time is critical to any medical setting. Clinical data is very diverse both in content and in terms of which system produces it. The Electronic Health Record (EHR) aggregates a patient’s clinical data and makes it available across different systems. Considering that user’s resistance is a critical factor in system implementation failure, the understanding of user behavior remains a relevant object of investigation. The purpose of this paper is to outline how we can assess the technology acceptance of an EHR using the Technology Acceptance Model 3 (TAM3) and the Delphi methodology. An assessment model is proposed in which findings are based on the results of a questionnaire answered by health professionals whose activities are supported by the EHR technology. In the case study simulated in this paper, the results obtained showed an average of 3 points and modes of 4 and 5, which translates to a good level of acceptance.The work has been supported by FCT – Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/2019.The work has been supported by FCT – Fundação para a Ciência e Tecnologia within the Project Scope DSAIPA/DS/0084/2018

Formulation of Sodium Alginate Nanospheres Containing Amphotericin B for the Treatment of Systemic Candidiasis

Purpose: The aim of this work was to formulate sodium alginate nanospheres of amphotericin B by controlled gellification method and to evaluate the role of the nanospheres as a “passive carrier” in targeted antifungal therapy. Methods: Sodium alginate nanospheres of amphotericin B were prepared by controlled gellification method, and the particle size analysis was carried out by scanning electron microscopy. The carrier capacity of sodium alginate was evaluated in terms of drug to polymer ratio. In vitro release study was carried out on all drug loaded nanospheres by the dialysis method. Release kinetics of drug from different drug loaded nanospheres was also determined. The in vivo antifungal efficacy of nanospheres bound drug vis-à-vis the free drug was evaluated in candidiasis- induced mice models. Results: Preparation of nanospheres through controlled gellification method yielded particles with a size range of 419.6 ± 0.28 nm. Studies on drug to polymer ratio showed a linear relationship between concentration of drug and drug loading capacity. In vitro release kinetic study revealed that the release of drug from the nanospheres followed Fickian diffusion. In vivo studies showed that the nanosphere-bound drug produced a higher antifungal efficacy than the free drug. Conclusion: The formulated sodium alginate nanospheres containing amphotericin B was found to have better antifungal activity when compared to the free drug and also yielded sustained in vitro release. Keywords: Nanospheres, sodium alginate, amphotericin B, controlled gellification method, in vitro & in vivo release > Tropical Journal of Pharmaceutical Research Vol. 6 (1) 2007: pp. 653-65

Does complimentary information from multispectral imaging improve face presentation attack detection?

Presentation Attack Detection (PAD) has been extensively studied, particularly in the visible spectrum. With the advancement of sensing technology beyond the visible range, multispectral imaging has gained significant attention in this direction. We present PAD based on multispectral images constructed for eight different presentation artifacts resulted from three different artifact species. In this work, we introduce Face Presentation Attack Multispectral (FPAMS) database to demonstrate the significance of employing multispectral imaging. The goal of this work is to study complementary information that can be combined in two different ways (image fusion and score fusion) from multispectral imaging to improve the face PAD. The experimental evaluation results present an extensive qualitative analysis of 61650 sample multispectral images collected for bonafide and artifacts. The PAD based on the score fusion and image fusion method presents superior performance, demonstrating the significance of employing multispectral imaging to detect presentation artifacts.Comment: Accepted in International IEEE Applied Sensing Conference (IEEE APSCON) 202

Progression of Coronary Artery Calcium and Incident Heart Failure: The Multi-Ethnic Study of Atherosclerosis.

BackgroundAlthough the association between coronary artery calcium (CAC) and future heart failure (HF) has been shown previously, the value of CAC progression in the prediction of HF has not been investigated. In this study, we investigated the association of CAC progression with subclinical left ventricular (LV) dysfunction and incident HF in the Multi-Ethnic Study of Atherosclerosis.Methods and resultsThe Multi-Ethnic Study of Atherosclerosis is a population-based study consisting of 6814 men and women aged 45 to 84, free of overt cardiovascular disease at enrollment, who were recruited from 4 ethnicities. We included 5644 Multi-Ethnic Study of Atherosclerosis participants who had baseline and follow-up cardiac computed tomography and were free of HF and coronary heart disease before the second cardiac computed tomography. Mean (±SD) age was 61.7±10.2 years and 47.2% were male. The Cox proportional hazard models and multivariable linear regression models were deployed to determine the association of CAC progression with incident HF and subclinical LV dysfunction, respectively. Over a median follow-up of 9.6 (interquartile range: 8.8-10.6) years, 182 participants developed incident HF. CAC progression of 10 units per year was associated with 3% of increased risk of HF independent of overt coronary heart disease (P=0.008). In 2818 participants with available cardiac magnetic resonance images, CAC progression was associated with increased LV end diastolic volume (β=0.16; P=0.03) and LV end systolic volume (β=0.12; P=0.006) after excluding participants with any coronary heart disease.ConclusionsCAC progression was associated with incident HF and modestly increased LV end diastolic volume and LV end systolic volume at follow-up exam independent of overt coronary heart disease

Regional Transmission and Reassortment of 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) Viruses in Bulgarian Poultry 2017/18

Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 highly-pathogenic avian influenza (HPAI) viruses. In this study we used genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the northeastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from di�erent European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates a complete lack of reassortment in all segments but the matrix protein gene (MP), which presents as multiple smaller clusters associated with di�erent European 2.3.4.4b viruses. Ancestral reconstruction of host states of the hemagglutinin (HA) gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence, we suggest the surveillance of domestic ducks as they are an epidemiologically relevant species for subclinical infection. Monitoring the spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks. The 2.3.4.4b lineage which caused the largest recorded poultry epidemic in Europe continues to circulate, and the risk of further transmission by wild birds during migration remains

Small-worlds: How and why

We investigate small-world networks from the point of view of their origin. While the characteristics of small-world networks are now fairly well understood, there is as yet no work on what drives the emergence of such a network architecture. In situations such as neural or transportation networks, where a physical distance between the nodes of the network exists, we study whether the small-world topology arises as a consequence of a tradeoff between maximal connectivity and minimal wiring. Using simulated annealing, we study the properties of a randomly rewired network as the relative tradeoff between wiring and connectivity is varied. When the network seeks to minimize wiring, a regular graph results. At the other extreme, when connectivity is maximized, a near random network is obtained. In the intermediate regime, a small-world network is formed. However, unlike the model of Watts and Strogatz (Nature {\bf 393}, 440 (1998)), we find an alternate route to small-world behaviour through the formation of hubs, small clusters where one vertex is connected to a large number of neighbours.Comment: 20 pages, latex, 9 figure

Annual Risk of Tuberculosis infection in Chennai City

Aim: To study the proportion of children infected with Mycobacterium Tuberculosis in Chennai city. Methodology: A cluster sampling methodology was adopted to select an estimated sample size of 7000 children from five corporation zones selected systematically from ten zones of the city. A total of 7098 children aged 1-9 years were subjected to Mantoux and test read; 1897 (27%) from slum area and 5201 (73%) from non-slum area. Results: The prevalence of infection among children without BCG scar was estimated to be 10.5 % (ARTI of 2.0%) and was similar to that among children irrespective of scar status. The prevalence of infection was higher among children in slum areas (11.1%; ARTI 2.1%) compared to non-slum areas (8.9%; ARTI 1.7%); but the difference was not statistically different. Conclusion: The tuberculosis situation in Chennai as measured by risk of infection was higher in urban city area than rural areas and comparable to that found in other cities as reported from earlier studies. This information can be used as baseline information for monitoring the epidemiological trends in Chennai city in future