GenBase: A Complex Analytics Genomics Benchmark

This paper introduces a new benchmark, designed to test database management system (DBMS) performance on a mix of data management tasks (joins, filters, etc.) and complex analytics (regression, singular value decomposition, etc.) Such mixed workloads are prevalent in a number of application areas, including most science workloads and web analytics. As a specific use case, we have chosen genomics data for our benchmark, and have constructed a collection of typical tasks in this area. In addition to being representative of a mixed data management and analytics workload, this benchmark is also meant to scale to large dataset sizes and multiple nodes across a cluster. Besides presenting this benchmark, we have run it on a variety of storage systems including traditional row stores, newer column stores, Hadoop, and an array DBMS. We present performance numbers on all systems on single and multiple nodes, and show that performance differs by orders of magnitude between the various solutions. In addition, we demonstrate that most platforms have scalability issues. We also test offloading the analytics onto a coprocessor. The intent of this benchmark is to focus research interest in this area; to this end, all of our data, data generators, and scripts are available on our web site

Galactos: Computing the Anisotropic 3-Point Correlation Function for 2 Billion Galaxies

The nature of dark energy and the complete theory of gravity are two central questions currently facing cosmology. A vital tool for addressing them is the 3-point correlation function (3PCF), which probes deviations from a spatially random distribution of galaxies. However, the 3PCF's formidable computational expense has prevented its application to astronomical surveys comprising millions to billions of galaxies. We present Galactos, a high-performance implementation of a novel, O(N^2) algorithm that uses a load-balanced k-d tree and spherical harmonic expansions to compute the anisotropic 3PCF. Our implementation is optimized for the Intel Xeon Phi architecture, exploiting SIMD parallelism, instruction and thread concurrency, and significant L1 and L2 cache reuse, reaching 39% of peak performance on a single node. Galactos scales to the full Cori system, achieving 9.8PF (peak) and 5.06PF (sustained) across 9636 nodes, making the 3PCF easily computable for all galaxies in the observable universe.Comment: 11 pages, 7 figures, accepted to SuperComputing 201

Exploiting NVM in Large-scale Graph Analytics

Data center applications like graph analytics require servers with ever larger memory capacities. DRAM scaling, how- ever, is not able to match the increasing demands for ca- pacity. Emerging byte-addressable, non-volatile memory technologies (NVM) offer a more scalable alternative, with memory that is directly addressable to software, but at a higher latency and lower bandwidth. Using an NVM hardware emulator, we study the suitabil- ity of NVM in meeting the memory demands of four state of the art graph analytics frameworks, namely Graphlab, Galois, X-Stream and Graphmat. We evaluate their perfor- mance with popular algorithms (Pagerank, BFS, Triangle Counting and Collaborative filtering) by allocating mem- ory exclusive from DRAM (DRAM-only) or emulated NVM (NVM-only). While all of these applications are sensitive to higher latency or lower bandwidth of NVM, resulting in perfor- mance degradation of up to 4X with NVM-only (compared to DRAM-only), we show that the performance impact is somewhat mitigated in the frameworks that exploit CPU memory-level parallelism and hardware prefetchers. Further, we demonstrate that, in a hybrid memory system with NVM and DRAM, intelligent placement of application data based on their relative importance may help offset the overheads of the NVM-only solution in a cost-effective man- ner (i.e., using only a small amount of DRAM). Specifically, we show that, depending on the algorithm, Graphmat can achieve close to DRAM-only performance (within 1.2X) by placing only 6.7% to 31.5% of its total memory footprint in DRA

Management of Multi Drug Resistance Tuberculosis in the Field: Tuberculosis Research Centre Experience

Setting: Multi-drug TB resistant (resistant to isoniazid and rifampicin) patients identified from a rural and urban area. Objective: To study the feasibility of managing MDR TB patients under field conditions where DOTS programme has been implemented Methods: MDR TB Patients identified among patients treated under DOTS in the rural area and from cases referred by the NGO when MDR TB was suspected form the study population. Culture and drug susceptibility testing were done at Tuberculosis Research Centre (TRC). Treatment regimen was decided on individual basis. After a period of initial hospitalization, treatment was continued in the respective peripheral health facility or with the NGO after identifying a DOT provider in the field. Patients attended TRC at monthly intervals for clinical, sociological and bacteriological evaluations. Drugs for the month were pre-packed and handed over to the respective center. Results: A total of 66 MDR TB patients (46 from the rural and 20 from the NGO) started on treatment form the study population and among them 20 (30%) were resistant to one or more second line drugs (Eto, Ofx, Km) including a case of “XDR TB”. Less than half the patients stayed in the hospital for more than 10 days. The treatment was provided partially under supervision. Providing injection was identified to be a major problem. Response to treatment could be correctly predicted based on the 6-month smear results in 40 of 42 regular patients. Successful treatment outcome was observed only in 37% of cases with a high default of 24%. Adverse reactions necessitating modification of treatment was required only for three patients. Implications Despite having reliable DST and drug logistics, the main challenge was to maintain patients on such prolonged treatment by identifying a provider closer to the patient who can also give injection, have social skills and manage of minor adverse reactions

Sputum conversion at the end of intensive phase of Category-1 regimen in the treatment of pulmonary tuberculosis patients with diabetes mellitus or HIV infection: An analysis of risk factors

Background & objectives: New smear-positive pulmonary tuberculosis (PTB) patients in the Revised National Tuberculosis Control Programme (RNTCP) are treated with a 6-month short-course chemotherapy (SCC) regimen irrespective of co-morbid conditions. We undertook this retrospective analysis to compare sputum conversion rates (smear, culture) at the end of intensive phase (IP) of Category-1 regimen among patients admitted to concurrent controlled clinical trials: pulmonary tuberculosis alone (PTB) or with type 2 diabetes mellitus (DM-TB) or HIV infection (HIV-TB), and to identify the risk factors influencing sputum conversion. Methods: In this retrospective analysis sputum conversion rates at the end of intensive phase (IP) in three concurrent studies undertaken among PTB, DM-TB and HIV-TB patients, during 1998 – 2002 at the Tuberculosis Research Centre (TRC), Chennai, were compared. Sputum smears were examined by fluorescent microscopy. HIV infected patients did not receive anti-retroviral treatment (ART). Patients with DM were treated with oral hypoglycaemic drugs or insulin (sc). Results: The study population included 98, 92 and 88 patients in the PTB, DM-TB and HIV-TB studies. At the end of IP the smear conversion (58, 61, and 62%) and culture conversion (86, 88 and 92%) rates were similar in the three groups respectively. The variables associated with lack of sputum smear or culture conversion were age >45 yr, higher pre-treatment smear and culture grading, and extent of the radiographic involvement. Interpretation & conclusions: Our findings confirm that the current policy of the control programme to treat all pulmonary TB patients with or with out co-morbid conditions with Category-I regimen appears to be appropriate

Scaling up studies on PEMFC using a modified serpentine flow field incorporating porous sponge inserts to observe water molecules

This is the final version. Available from MDPI via the DOI in this record. Flooding of the cathode flow channel is a major hindrance in achieving maximum performance from Proton Exchange Membrane Fuel Cells (PEMFC) during the scaling up process. Water accumulated between the interface region of Gas Diffusion Layer (GDL) and rib of the cathode flow field can be removed by the use of Porous Sponge Inserts (PSI) on the ribs. In the present work, the experimental investigations are carried out on PEMFC for the various reaction areas, namely 25, 50 and 100 cm2. Stoichiometry value of 2 is maintained for all experiments to avoid variations in power density obtained due to differences in fuel utilization. The experiments include two flow fields, namely Serpentine Flow Field (SFF) and Modified Serpentine with Staggered provisions of 4 mm PSI (4mm x 2mm x 2mm) Flow Field (MSSFF). The peak power densities obtained on MSSFF are 0.420 W/cm2, 0.298 W/cm2 and 0.232 W/cm2 compared to SFF which yields 0.242 W/cm2, 0.213 W/cm2 and 0.171 W/cm2 for reaction areas of 25, 50 and 100 cm2 respectively. Further, the reliability of experimental results is verified for SFF and MSSFF on 25 cm2 PEMFC by using Electrochemical Impedance Spectroscopy (EIS). The use of 4 mm PSI is found to improve the performance of PEMFC through the better water management.All India Council for Technical EducationDepartment of Science and Technology, New Delh