Lars Koesterke

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanitys projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

THE SEGUE STELLAR PARAMETER PIPELINE. I. DESCRIPTION AND COMPARISON OF INDIVIDUAL METHODS

We describe the development and implementation of the Sloan Extension for Galactic Exploration and Understanding (SEGUE) Stellar Parameter Pipeline (SSPP). The SSPP is derived, using multiple techniques, radial velocities, and the fundamental stellar atmospheric parameters (effective temperature, surface gravity, and metallicity) for AFGK-type stars, based on medium-resolution spectroscopy and ugriz photometry obtained during the course of the original Sloan Digital Sky Survey (SDSS-I) and its Galactic extension (SDSS-II/SEGUE). The SSPP also provides spectral classification for a much wider range of stars, including stars with temperatures outside the window where atmospheric parameters can be estimated with the current approaches. This is Paper I in a series of papers on the SSPP; it provides an overview of the SSPP, and tests of its performance using several external data sets. Random and systematic errors are critically examined for the current version of the SSPP, which has been used for the sixth public data release of the SDSS (DR-6).

The SEGUE Stellar Parameter Pipeline. II. Validation with Galactic Globular and Open Clusters

We validate the accuracy and precision of the current SEGUE (Sloan Extension for Galactic Understanding and Exploration) Stellar Parameter Pipeline (SSPP), which determines stellar atmospheric parameters (effective temperature, surface gravity, and metallicity) and radial velocities (RVs), by comparing these estimates for selected members of three globular clusters (M 13, M 15, and M 2) and two open clusters (NGC 2420 and M 67) to the literature values. Spectroscopic and photometric data obtained during the course of the original Sloan Digital Sky Survey (SDSS-I) and its first extension (SDSS-II/SEGUE) are used to determine atmospheric parameter and RV estimates for stars in these clusters. Based on the scatter in the metallicities derived for the members of each cluster, we quantify the typical uncertainty of the SSPP values, σ ([Fe/H]) = 0.13 dex for stars in the range of –0.3 ≤ g – r ≤ 1.3 and 2.0 ≤ log g ≤ 5.0, at least over the metallicity interval spanned by the clusters studied (–2.3 ≤ [Fe/H] ≤ 0). The surface gravities and effective temperatures derived by the SSPP are also compared with those estimated from the comparison of color-magnitude diagrams with stellar evolution models; we find satisfactory agreement (σ(T eff)< 200 K and σ(log g) ≤ 0.4 dex).

THE SEGUE STELLAR PARAMETER PIPELINE. III. COMPARISON WITH HIGH-RESOLUTION SPECTROSCOPY OF SDSS/SEGUE FIELD STARS*

The authors report high-resolution spectroscopy of 125 field stars previously observed as part of the Sloan Digital Sky Survey and its program for Galactic studies, the Sloan Extension for Galactic Understanding and Exploration (SEGUE). These spectra are used to measure radial velocities and to derive atmospheric parameters, which they compare with those reported by the SEGUE Stellar Parameter Pipeline (SSPP). The SSPP obtains estimates of these quantities based on SDSS ugriz photometry and low-resolution (R {approx} 2000) spectroscopy. For F- and G-type stars observed with high signal-to-noise ratios (S/N), they empirically determine the typical random uncertainties in the radial velocities, effective temperatures, surface gravities, and metallicities delivered by the SSPP to be 2.4 km s{sup -1}, 130 K (2.2%), 0.21 dex, and 0.11 dex, respectively, with systematic uncertainties of a similar magnitude in the effective temperatures and metallicities. They estimate random errors for lower S/N spectra based on numerical simulations.

Line-blanketed model atmospheres for WR stars

We describe the treatment of iron group line-blanketing in non-LTE model atmospheres for WR stars. As an example, a blanketed model for the early-type WC star WR 111 is compared to its un-blanketed counter- part. Blanketing aects the ionization structure and the emergent flux distribution of our models. The radiation pressure, as computed within our models, falls short by only a factor of two to provide the mechanical power of the WR wind.

Calibrations of Atmospheric Parameters Obtained from the First Year of SDSS-III APOGEE Observations

The Sloan Digital Sky Survey III (SDSS-III) Apache Point Observatory Galactic Evolution Experiment (APOGEE) is a three-year survey that is collecting 105 high-resolution spectra in the near-IR across multiple Galactic populations. To derive stellar parameters and chemical compositions from this massive data set, the APOGEE Stellar Parameters and Chemical Abundances Pipeline (ASPCAP) has been developed. Here, we describe empirical calibrations of stellar parameters presented in the first SDSS-III APOGEE data release (DR10). These calibrations were enabled by observations of 559 stars in 20 globular and open clusters. The cluster observations were supplemented by observations of stars in NASAs Kepler field that have well determined surface gravities from asteroseismic analysis. We discuss the accuracy and precision of the derived stellar parameters, considering especially effective temperature, surface gravity, and metallicity; we also briefly discuss the derived results for the abundances of the α-elements, carbon, and nitrogen. Overall, we find that ASPCAP achieves reasonably accurate results for temperature and metallicity, but suffers from systematic errors in surface gravity. We derive calibration relations that bring the raw ASPCAP results into better agreement with independently determined stellar parameters. The internal scatter of ASPCAP parameters within clusters suggests that metallicities are measured with a precision better than 0.1 dex, effective temperatures better than 150 K, and surface gravities better than 0.2 dex. The understanding provided by the clusters and Kepler giants on the current accuracy and precision will be invaluable for future improvements of the pipeline.

PerfExpert: An Easy-to-Use Performance Diagnosis Tool for HPC Applications

HPC systems are notorious for operating at a small fraction of their peak performance, and the ongoing migration to multi-core and multi-socket compute nodes further complicates performance optimization. The readily available performance evaluation tools require considerable effort to learn and utilize. Hence, most HPC application writers do not use them. As remedy, we have developed PerfExpert, a tool that combines a simple user interface with a sophisticated analysis engine to detect probable core, socket, and node-level performance bottlenecks in each important procedure and loop of an application. For each bottle-neck, PerfExpert provides a concise performance assessment and suggests steps that can be taken by the programmer to improve performance. These steps include compiler switches and optimization strategies with code examples. We have applied PerfExpert to several HPC production codes on the Ranger supercomputer. In all cases, it correctly identified the critical code sections and provided accurate assessments of their performance.

A SURVEY OF ALKALI LINE ABSORPTION IN EXOPLANETARY ATMOSPHERES

We obtained over 90 hr of spectroscopic observations of four exoplanetary systems with the Hobby‐Eberly Telescope. Observations were taken in transit and out of transit, and we analyzed the differenced spectra—i.e., the transmission spectra—to inspect it for absorption at the wavelengths of the neutral sodium (Nai) doublet at λλ5889,5895 and neutral potassium (Ki )a tλ7698. We used the transmission spectrum at Cai λ6122—which showsstrongstellarabsorptionbutisnotanalkalimetalresonancelinethatweexpecttoshowsignificantabsorption in these atmospheres—as a control line to examine our measurements for systematic errors. We use an empirical Monte Carlo method to quantify these systematic errors. In a reanalysis of the same data set using a reduction and analysis pipeline that was derived independently, we confirm the previously seen Nai absorption in HD 189733b at a level of (−5.26 ± 1.69) × 10 −4 (the average value over a 12 A integration band to be consistent with previous authors). Additionally, we tentatively confirm the Nai absorption seen in HD 209458b (independently by multiple authors) at a level of (−2.63 ± 0.81) × 10 −4 , though the interpretation is less clear. Furthermore, we find Nai absorption of (−3.16 ± 2.06) × 10 −4 at <3σ in HD 149026b; features apparent in the transmission spectrum are consistent with real absorption and indicate this may be a good target for future observations to confirm. No other results (Nai in HD 147506b and Cai and Ki in all four targets) are significant to 3σ, although we observe some features that we argue are primarily artifacts.

New H-Band Stellar Spectral Libraries For The SDSS-III/APOGEE Survey

The Sloan Digital Sky Survey--III (SDSS--III) Apache Point Observatory Galactic Evolution Experiment (APOGEE) has obtained high resolution (R

THE SDSS-III APOGEE SPECTRAL LINE LIST FOR H-BAND SPECTROSCOPY

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