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

A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity

L1 is a ubiquitous interspersed repeated sequence in mammals that achieved its high copy number by autonomous retrotransposition. Individual L1 elements within a genome differ in sequence and retrotransposition activity. Retrotransposition requires two L1-encoded proteins, ORF1p and ORF2p. Chimeric elements were used to map a 15-fold difference in retrotransposition efficiency between two L1 variants from the mouse genome, TFC and TFspa, to a single amino acid substitution in ORF1p, D159H. The steady-state levels of L1 RNA and protein do not differ significantly between these two elements, yet new insertions are detected earlier and at higher frequency in TFC, indicating that it converts expressed L1 intermediates more effectively into new insertions. The two ORF1 proteins were purified and their nucleic acid binding and chaperone activities were examined in vitro. Although the RNA and DNA oligonucleotide binding affinities of these two ORF1 proteins were largely indistinguishable, D159 was significantly more effective as a nucleic acid chaperone than H159. These findings support a requirement for ORF1p nucleic acid chaperone activity at a late step during L1 retrotransposition, extend the region of ORF1p that is known to be critical for its functional interactions with nucleic acids, and enhance understanding of nucleic acid chaperone activity

Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388

Light Isotope Abundances in Solar Energetic Particles measured by the Space Instrument NINA

This article reports nine Solar Energetic Particle events detected by the instrument NINA between October 1998 and April 1999. NINA is a silicon-based particle detector mounted on-board the Russian satellite Resurs-01-N4, which has flown at an altitude of about 800 km in polar inclination since July 1998. For every solar event the power-law He4 spectrum across the energy interval 10--50 MeV/n was reconstructed, and spectral indexes, gamma, from 1.8 to 6.8 extracted. Data of He3 and He4 were used to determine the He3/He4 ratio, that for some SEP events indicated an enrichment in He3. For the 1998 November 7 event the ratio reached a maximum value of 0.33+- 0.06, with spectral indexes of gamma = 2.5 +- 0.6 and gamma = 3.7 +- 0.3 for He3 and He4, respectively. The He3/He4 ratio averaged over the remaining events was 0.011 +- 0.004. For all events the deuterium-to-proton ratio was determined. The average value over all events was (3.9+-1.4) 10^{-5} across the energy interval 9--12 MeV/n. For one event (1998 November 24) this ratio yielded approximately 10 times higher than normal coronal values. Upper limits on the H3/H1 counting ratio for all events were determined. For the 1998 November 14 SEP event the high flux of heavy particles detected made it possible to reconstruct the carbon and oxygen flux.Comment: 42 pages, 14 figures, submitted to Journal of Geophysical Researc

THE SPACE TELESCOPE NINA: RESULTS OF A BEAM TEST CALIBRATION

Abstract In June 1998 the telescope NINA will be launched in space on board of the Russian satellite Resource-01 n.4. The main scientific objective of the mission is the study of the anomalous, galactic and solar components of the cosmic rays in the energy interval 10–200 MeV/n. The core of the instrument is a silicon detector whose performances have been tested with a particle beam at the GSI Laboratory in Germany in 1997; we report here on the results obtained during the beam calibration

The small satellite NINA-MITA to study galactic and solar cosmic rays in low-altitude polar orbit

Abstract The satellite MITA, carrying on board the scientific payload NINA-2, was launched on July the 15th, 2000 from the cosmodrome of Plesetsk (Russia) with a Cosmos-3M rocket. The satellite and the payload are currently operating within nominal parameters. NINA-2 is the first scientific payload for the technological flight of the Italian small satellite MITA. The detector used in this mission is identical to the one already flying on the Russian satellite Resurs-O1 n.4 in a 840-km sun-synchronous orbit, but makes use of the extensive computer and telemetry capabilities of MITA bus to improve the active data acquisition time. NINA physics objectives are to study cosmic nuclei from hydrogen to iron in the energy range between 10 MeV/n and 1 GeV/n during the years 2000–2003, that is the solar maximum period. The device is capable of charge identification up to iron with isotope sensitivity up to oxigen. The 87.3 degrees, 460 km altitude polar orbit allows investigations of cosmic rays of solar and galactic origin, so to study long and short term solar transient phenomena, and the study of the trapped radiation at higher geomagnetic cutoff

An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications

The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generated an atlas of the rate of copy number changes (CNCs) in all the gene families of ten animal genomes. We grouped the gene families with similar CNC dynamics into rate pattern groups (RPGs) and annotated their function using a novel bottom-up approach. By comparing CNC rate patterns, we showed that most of the species-specific CNC rates groups are formed by gene duplication rather than gene loss, and most of the changes in rates of CNCs may be the result of adaptive evolution. We also found that the functions of many RPGs match their biological significance well. Our work confirmed the role of gene duplication in generating novel phenotypes, and the results can serve as a guide for researchers to connect the phenotypic features to certain gene duplications