Efficient HTTP based I/O on very large datasets for high performance computing with the libdavix library

Remote data access for data analysis in high performance computing is commonly done with specialized data access protocols and storage systems. These protocols are highly optimized for high throughput on very large datasets, multi-streams, high availability, low latency and efficient parallel I/O. The purpose of this paper is to describe how we have adapted a generic protocol, the Hyper Text Transport Protocol (HTTP) to make it a competitive alternative for high performance I/O and data analysis applications in a global computing grid: the Worldwide LHC Computing Grid. In this work, we first analyze the design differences between the HTTP protocol and the most common high performance I/O protocols, pointing out the main performance weaknesses of HTTP. Then, we describe in detail how we solved these issues. Our solutions have been implemented in a toolkit called davix, available through several recent Linux distributions. Finally, we describe the results of our benchmarks where we compare the performance of davix against a HPC specific protocol for a data analysis use case.Comment: Presented at: Very large Data Bases (VLDB) 2014, Hangzho

Increase of ribavirin dose improves sustained virological response in HCV-genotype 1 patients with a partial response to peg-interferon and ribavirin

Background and aim. In patients with chronic hepatitis C receiving Peg interferon/ribavirin (PEG-IFN/RBV) who do not achieve ≥ 2log-reduction in HCV-RNA at week 12 (null responders, NR) and in those with ≥ 2log-decrease but detectable at week 24 (partial responders, PR) the probability to achieve the sustained virological response (SVR) is almost null. The aim of this study was to investigate the efficacy of individualized schedule of progressively increased RBV doses in the setting of PEG-IFN/RBV treatment. Material and methods. PR or NR to PEG-IFN/RBV instead of discontinuing treatment were enrolled to receive increasing doses of RBV until a target theoretical concentration ([tRBV]) of ≥ 15 μmol/L (by pharmacokinetic formula based on glomerular filtration rate). HCV-RNA was assessed every 4 weeks and, if detectable, RBV dose was gradually increased until negativization. Twelve weeks later, patients with detectable HCV-RNA discontinued therapy while those with undetectable HCV-RNA continued for further 48 weeks. Results. Twenty genotype-1 patients (8 NR and 12 PR) were enrolled. After 12 weeks 9 (45%) were still HCV-RNA positive and were discontinued, while remaining 11 had undetectable HCV-RNA. One stopped treatment for side effects. Ten completed treatment. Five (all PR) achieved SVR. Side effects incidence was similar to that observed during PEG-IFN/RBV. Conclusions. In conclusion, RBV high doses, according to individualized schedule, increase SVR in PR on a similar extent to that of triple therapy but without increase of side effects. Such treatment should be considered in PR with no access or intolerant to protease inhibitors (PI)

Establishing Applicability of SSDs to LHC Tier-2 Hardware Configuration

Solid State Disk technologies are increasingly replacing high-speed hard disks as the storage technology in high-random-I/O environments. There are several potentially I/O bound services within the typical LHC Tier-2 - in the back-end, with the trend towards many-core architectures continuing, worker nodes running many single-threaded jobs and storage nodes delivering many simultaneous files can both exhibit I/O limited efficiency. We estimate the effectiveness of affordable SSDs in the context of worker nodes, on a large Tier-2 production setup using both low level tools and real LHC I/O intensive data analysis jobs comparing and contrasting with high performance spinning disk based solutions. We consider the applicability of each solution in the context of its price/performance metrics, with an eye on the pragmatic issues facing Tier-2 provision and upgradesComment: 6 pages, 1 figure, 4 tables. Conference proceedings for CHEP201

Aging Studies for the Large Honeycomb Drift Tube System of the Outer Tracker of HERA-B

The HERA-B Outer Tracker consists of drift tubes folded from polycarbonate foil and is operated with Ar/CF4/CO2 as drift gas. The detector has to stand radiation levels which are similar to LHC conditions. The first prototypes exposed to radiation in HERA-B suffered severe radiation damage due to the development of self-sustaining currents (Malter effect). In a subsequent extended R&D program major changes to the original concept for the drift tubes (surface conductivity, drift gas, production materials) have been developed and validated for use in harsh radiation environments. In the test program various aging effects (like Malter currents, gain loss due to anode aging and etching of the anode gold surface) have been observed and cures by tuning of operation parameters have been developed.Comment: 14 pages, 6 figures, to be published in the Proceedings of the International Workshop On Aging Phenomena In Gaseous Detectors, 2-5 Oct 2001, Hamburg, German

The Outer Tracker Detector of the HERA-B Experiment. Part II: Front-End Electronics

The HERA-B Outer Tracker is a large detector with 112674 drift chamber channels. It is exposed to a particle flux of up to 2x10^5/cm^2/s thus coping with conditions similar to those expected for the LHC experiments. The front-end readout system, based on the ASD-8 chip and a customized TDC chip, is designed to fulfil the requirements on low noise, high sensitivity, rate tolerance, and high integration density. The TDC system is based on an ASIC which digitizes the time in bins of about 0.5 ns within a total of 256 bins. The chip also comprises a pipeline to store data from 128 events which is required for a deadtime-free trigger and data acquisition system. We report on the development, installation, and commissioning of the front-end electronics, including the grounding and noise suppression schemes, and discuss its performance in the HERA-B experiment

The Outer Tracker Detector of the HERA-B Experiment Part I: Detector

The HERA-B Outer Tracker is a large system of planar drift chambers with about 113000 read-out channels. Its inner part has been designed to be exposed to a particle flux of up to 2.10^5 cm^-2 s^-1, thus coping with conditions similar to those expected for future hadron collider experiments. 13 superlayers, each consisting of two individual chambers, have been assembled and installed in the experiment. The stereo layers inside each chamber are composed of honeycomb drift tube modules with 5 and 10 mm diameter cells. Chamber aging is prevented by coating the cathode foils with thin layers of copper and gold, together with a proper drift gas choice. Longitudinal wire segmentation is used to limit the occupancy in the most irradiated detector regions to about 20 %. The production of 978 modules was distributed among six different laboratories and took 15 months. For all materials in the fiducial region of the detector good compromises of stability versus thickness were found. A closed-loop gas system supplies the Ar/CF4/CO2 gas mixture to all chambers. The successful operation of the HERA-B Outer Tracker shows that a large tracker can be efficiently built and safely operated under huge radiation load at a hadron collider.Comment: 28 pages, 14 figure

Utility of neutrophil-to-lymphocyte ratio to identify long-term survivors among HCC patients treated with sorafenib

Sorafenib is the first multikinase inhibitor demonstrating a survival benefit for patients suffering from advanced hepatocellular carcinoma (HCC). However, 1 issue remains open: what is the factor able to predict which patients will be long survivors?In the present study, we harnessed the potential of conditional survival, aiming at estimating the probability that a patient receiving sorafenib survives for more than 3 years.The present multicentric study was conducted on a cohort of 438 HCC patients. The primary end point was conditional overall survival. Kaplan-Meier survival analysis was used to calculate conditional overall survival probabilities at 3 years.The 3-year conditional survival of patients without disease progression highlights that NLR and ECOG are the factors that most accurately predict the probability of long survival. The 3-year conditional survival of patients with disease progression showed a medium effect size for HCV status, alpha-fetoprotein and NLR at all time-points. Macro-vascular portal vein invasion, extra hepatic disease, and BCLC we have a large effect size at 6 months and a medium effect size at 12 and 24 months.Our findings support the use of baseline NLR for the identification of patients with a higher probability of long-survival. NLR should be used as a stratification factor in the forthcoming clinical trials on the drugs for the advanced HCC now in pipeline

Open and Hidden Charm Production in 920 GeV Proton-Nucleus Collisions

The HERA-B collaboration has studied the production of charmonium and open charm states in collisions of 920 GeV protons with wire targets of different materials. The acceptance of the HERA-B spectrometer covers negative values of xF up to xF=-0.3 and a broad range in transverse momentum from 0.0 to 4.8 GeV/c. The studies presented in this paper include J/psi differential distributions and the suppression of J/psi production in nuclear media. Furthermore, production cross sections and cross section ratios for open charm mesons are discussed.Comment: 5 pages, 9 figures, to be published in the proceedings of the 6th International Conference on Hyperons, Charm & Beauty Hadrons (BEACH04), Chicago, IL, June 27 - July 3, 200

Inclusive V0V^0 Production Cross Sections from 920 GeV Fixed Target Proton-Nucleus Collisions

Inclusive differential cross sections $d\sigma_{pA}/dx_F$ and $d\sigma_{pA}/dp_t^2$ for the production of \kzeros, \lambdazero, and \antilambda particles are measured at HERA in proton-induced reactions on C, Al, Ti, and W targets. The incident beam energy is 920 GeV, corresponding to $\sqrt {s} = 41.6$ GeV in the proton-nucleon system. The ratios of differential cross sections \rklpa and \rllpa are measured to be $6.2\pm 0.5$ and $0.66\pm 0.07$, respectively, for \xf $\approx-0.06$. No significant dependence upon the target material is observed. Within errors, the slopes of the transverse momentum distributions $d\sigma_{pA}/dp_t^2$ also show no significant dependence upon the target material. The dependence of the extrapolated total cross sections $\sigma_{pA}$ on the atomic mass $A$ of the target material is discussed, and the deduced cross sections per nucleon $\sigma_{pN}$ are compared with results obtained at other energies.Comment: 17 pages, 7 figures, 5 table

Search for the Flavor-Changing Neutral Current Decay D0→μ+μ−D^0 \to \mu^+\mu^- with the HERA-B Detector

We report on a search for the flavor-changing neutral current decay $D^0 \to \mu^+\mu^-$ using $50 \times 10^6$ events recorded with a dimuon trigger in interactions of 920 GeV protons with nuclei by the HERA-B experiment. We find no evidence for such decays and set a 90% confidence level upper limit on the branching fraction $Br(D^0 \to \mu^+\mu^-) <2.0 \times 10^{-6}$.Comment: 17 pages, 4 figures (of which 1 double), paper to be submitted to Physics Letters