The workshop on High Performance Computing (HPC) Best Practices on File Systems and Archives was the fifth in a series sponsored jointly by the Department Of Energy (DOE) Office of Science and DOE National Nuclear Security Administration. The workshop gathered technical and management experts for operations of HPC file systems and archives from around the world. Attendees identified and discussed best practices in use at their facilities, and documented findings for the DOE and HPC community in this report.

Analysts are overwhelmed with information. They have large archives of historical data, both structured and unstructured, and continuous streams of relevant messages and documents that they need to match to current tasks, digest, and incorporate into their analysis. The purpose of the READ project is to develop technologies to make it easier to catalog, classify, and locate relevant information. We approached this task from multiple angles. First, we tackle the issue of processing large quantities of information in reasonable time. Second, we provide mechanisms that allow users to customize their queries based on latent topics exposed from corpus statistics. Third, we assist users in organizing query results, adding localized expert structure over results. Forth, we use word sense disambiguation techniques to increase the precision of matching user generated keyword lists with terms and concepts in the corpus. Fifth, we enhance co-occurrence statistics with latent topic attribution, to aid entity relationship discovery. Finally we quantitatively analyze the quality of three popular latent modeling techniques to examine under which circumstances each is useful.

One man�s trash is another man�s treasure. Not everything called �waste� is meant for the refuse pile. The mission of the Curation Program is at direct odds with the remediation objectives of the Hanford Site. While others are busily tearing down and burying the Site�s physical structures and their associated contents, the Curation Program seeks to preserve the tangible elements of the Site�s history from these structures for future generations before they flow into the waste stream. Under the provisions of a Programmatic Agreement, Cultural Resources staff initiated a project to identify and collect artifacts and archives that have historic or interpretive value in documenting the role of the Hanford Site throughout the Manhattan Project and Cold War Era. The genesis of Hanford�s modern day Curation Program, its evolution over nearly two decades, issues encountered, and lessons learned along the way � particularly the importance of upper management advocacy, when and how identification efforts should be accomplished, the challenges of working within a radiological setting, and the importance of �first hand� information � are presented.

The workshop aimed to identify outstanding climate change science questions and the observational strategies for addressing them. The scientific focus was clouds, aerosols, and precipitation, and the required ground- and aerial-based observations. The workshop findings will be useful input for setting priorities within the Department of Energy (DOE) and the participating European centers. This joint workshop was envisioned as the first step in enhancing the collaboration among these climate research activities needed to better serve the science community.

The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In April 2010 ESnet and the Office of Biological and Environmental Research, of the DOE Office of Science, organized a workshop to characterize the networking requirements of the science programs funded by BER. The requirements identified at the workshop are summarized and described in more detail in the case studies and the Findings section. A number of common themes emerged from the case studies and workshop discussions. One is that BER science, like many other disciplines, is becoming more and more distributed and collaborative in nature. Another common theme is that data set sizes are exploding. Climate Science in particular is on the verge of needing to manage exabytes of data, and Genomics is on the …

ABSTRACT The International Monitoring System (IMS) consists of up to 80 aerosol and xenon monitoring systems spaced around the world that have collection systems sensitive enough to detect nuclear releases from underground nuclear tests at great distances (CTBT 1996; CTBTO 2011). Although a few of the IMS radionuclide stations are closer together than 1,000 km (such as the stations in Kuwait and Iran), many of them are 2,000 km or more apart. In the absence of a scientific basis for optimizing the duration of atmospheric sampling, historically scientists used a integration times from 24 hours to 14 days for radionuclides (Thomas et al. 1977). This was entirely adequate in the past because the sources of signals were far away and large, meaning that they were smeared over many days by the time they had travelled 10,000 km. The Fukushima event pointed out the unacceptable delay time (72 hours) between the start of sample acquisition and final data being shipped. A scientific basis for selecting a sample duration time is needed. This report considers plume migration of a nondecaying tracer using archived atmospheric data for 2011 in the HYSPLIT (Draxler and Hess 1998; HYSPLIT 2011) transport model. We present two related …

Neutrino interaction events in the MINERvA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERvA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

Several research themes were developed during the course of this project. (1) Low-frequency oceanic varibility; (2) The role of eddies in the Antarctic Circumpolar Current (ACC) region; (3) Deep stratification and the overturning circulation. The key findings were as follows: (1) The stratification below the main thermocline (at about 500m) is determined in the circumpolar region and then communicated to the enclosed portions of the oceans through the overturning circulation. (2) An Atlantic pole-to-pole overturning circulation can be maintained with very small interior mixing as long as surface buoyancy values are shared between the northern North Atlantic and the ACC region.

This month's issue has the following articles: (1) World's Most Intense X-Ray Laser Focuses on Livermore Science - Commentary by William H. Goldstein; (2) Groundbreaking Science with the World's Brightest X Rays - Experiments with x rays of unparalleled brightness and extremely short duration aim to reveal new information about atoms and molecules in motion; (3) From Data to Discovery - Ongoing control system enhancements at the National Ignition Facility bolster the understanding of experimental data and keep the system performing at its peak; (4) The Sun in All Its Splendor - Onboard the Solar Dynamics Observatory, Livermore-developed multilayer mirrors are enabling unprecedented full-disk, high-resolution images of the Sun; and (5) Drilling Deep into Plant Veins - A novel combination of imaging techniques is being used to understand the three-dimensional architecture of plant cell walls.

This project focused on a molecular and biochemical characterization of the protein methyltransferases responsible for methylation of the LS and SS in Rubisco, and the associated functional consequences accompanying these modifications. Our results provided some of the most informative structural and mechanistic understandings of SET domain protein methyltransferases. These results also positioned us to provide the first unambiguous assignment of the kinetic reaction mechanism for SET-domain protein methyltransferases, and to design and engineer an alternative substrate for Rubisco LSMT, enabling substrate specificity and functional significance studies. We demonstrated that the minimal substrate recognized by Rubisco LSMT is free lysine as well as monomethyllysine, an observation corroborated both by structural analyses as well as enzymatic activity and subsequent product distribution analyses. Ternary complexes between Rubisco LSMT and free lysine compared to complexes with monomethyllysine demonstrated that the structural basis for multiple methyl group additions is a consequence of hydrogen-bond driven spatial shifts in the amino group of Lys-14, which maintains the direct in-line geometry necessary for SN2 nucleophilic attack. The structural observations are also consistent with the previous proposal that the multiplicity of methyl group additions takes place through a processive mechanism, with successive methyl group additions to an enzyme protein …

CH2M Hill Plateau Remediation Company (CHPRC) designed, constructed, commissioned, and began operation of the largest groundwater pump and treatment facility in the U.S. Department of Energy's (DOE) nationwide complex. This one-of-a-kind groundwater pump and treatment facility, located at the Hanford Nuclear Reservation Site (Hanford Site) in Washington State, was built in an accelerated manner with American Recovery and Reinvestment Act (ARRA) funds and has attained Leadership in Energy and Environmental Design (LEED) GOLD certification, which makes it the first non-administrative building in the DOE Office of Environmental Management complex to earn such an award. There were many contractual, technical, configuration management, quality, safety, and LEED challenges associated with the design, procurement, construction, and commissioning of this $95 million, 52,000 ft groundwater pump and treatment facility. This paper will present the Project and LEED accomplishments, as well as Lessons Learned by CHPRC when additional ARRA funds were used to accelerate design, procurement, construction, and commissioning of the 200 West Groundwater Pump and Treatment (2W P&T) Facility to meet DOE's mission of treating contaminated groundwater at the Hanford Site with a new facility by June 28, 2012.

Environmental health focus with training conducted as part of the United Negro College Fund Special Programs Corporation/National Library of Medicine HBCU ACCESS Project at Winston-Salem State University, NC on November 10, 2010.

Training update with Environmental a health focus. Training conducted as part of the United Negro College Fund Special Programs Corporation/National Library of Medicine - HBCU ACCESS Project at the University of the District of Columbia, Washington, DC on November 2, 2010.

Training Manual updated for United Negro College Fund Special Programs Corporation/National Library of Medicine - HBCU ACCESS Project for Alcorn State University, Natchez, Mississippi, November 12, 2010

Training conducted as a part of the United Negro College Fund Special Programs/National Library of Medicine -HBCU ACCESS Project at Howard University, Washington, DC on November 20, 2010.

Wide-angle surveys have been an engine for new discoveries throughout the modern history of astronomy, and have been among the most highly cited and scientifically productive observing facilities in recent years. This trend is likely to continue over the next decade, as many of the most important questions in astrophysics are best tackled with massive surveys, often in synergy with each other and in tandem with the more traditional observatories. We argue that these surveys are most productive and have the greatest impact when the data from the surveys are made public in a timely manner. The rise of the 'survey astronomer' is a substantial change in the demographics of our field; one of the most important challenges of the next decade is to find ways to recognize the intellectual contributions of those who work on the infrastructure of surveys (hardware, software, survey planning and operations, and databases/data distribution), and to make career paths to allow them to thrive.

Samples of sludge were collected from the K East fuel storage basin (KE Basin) floor, contiguous pits (Weasel Pit, North Load Out Pit, Dummy Elevator Pit, and Tech View Pit), and fuel storage canisters between 1995 and 2003 for chemical and radionuclide concentration analysis, physical property determination, and chemical process testing work. Because of the value of the sludge in this testing and because of the cost of obtaining additional fresh samples, an ongoing program of sludge preservation has taken place with the goals to track the sludge identities and preserve, as well as possible, the sludge composition by keeping the sludge in sealed jars and maintaining water coverage on the sludge consistent with the controlling Fluor Hanford (FH) Sampling and Analysis plans and FH contracts with the Pacific Northwest National Laboratory (PNNL). This work was originally initiated to provide material for planned hydrothermal treatment testing in accordance with the test plan for the Sludge Treatment Project (STP) corrosion process chemistry follow on testing (Delegard et al. 2007). Although most of the planned hydrothermal testing was canceled in July 2007 (as described in the forward of Delegard et al. 2007), sample consolidation and characterization was continued to identify a set …

Hanford�s Long-Term Stewardship (LTS) Program has evolved from a small, informal process, with minimal support, to a robust program that provides comprehensive transitions from cleanup contractors to long-term stewardship for post-cleanup requirements specified in the associated cleanup decision documents. The LTS Program has the responsibility for almost 100,000 acres of land, along with over 200 waste sites and will soon have six cocooned reactors. Close to 2,600 documents have been identified and tagged for storage in the LTS document library. The program has successfully completed six consecutive transitions over the last two years in support of the U.S. DOE Richland Operations Office�s (DOE-RL) near-term cleanup objectives of significantly reducing the footprint of active cleanup operations for the River Corridor. The program has evolved from one that was initially responsible for defining and measuring Institutional Controls for the Hanford Site, to a comprehensive, post remediation surveillance and maintenance program that begins early in the transition process. In 2013, the first reactor area―the cocooned 105-F Reactor and its surrounding 1,100 acres, called the F Area was transitioned. In another �first,� the program is expected to transition the five remaining cocooned reactors into the program through using a Transition and Turnover Package (TTP). …

Twelve AFIP in-process foil samples, fabricated by either Y-12 or LANL, were shipped from LANL to PNNL for potential characterization using optical and scanning electron microscopy techniques. Of these twelve, nine different conditions were examined to one degree or another using both techniques. For this report a complete description of the results are provided for one archive foil from each source of material, and one unirradiated piece of a foil of each source that was irradiated in the Advanced Test Reactor. Additional data from two other LANL conditions are summarized in very brief form in an appendix. The characterization revealed that all four characterized conditions contained a cold worked microstructure to different degrees. The Y-12 foils exhibited a higher degree of cold working compared to the LANL foils, as evidenced by the highly elongated and obscure U-Mo grain structure present in each foil. The longitudinal orientations for both of the Y-12 foils possesses a highly laminar appearance with such a distorted grain structure that it was very difficult to even offer a range of grain sizes. The U-Mo grain structure of the LANL foils, by comparison, consisted of a more easily discernible grain structure with a mix of equiaxed and …

The Source Physics Experiment (SPE) will involve a series of explosions in various geologic and emplacement conditions to validate numerical simulation methods to predict behavior of seismic wave excitation and propagation for nuclear test monitoring. The first SPE's currently underway involve explosions in the Climax Stock (granitic geology) at the Nevada National Security Site (NNSS). Detailed geologic data and published material properties for the major lithologic units of the NNSS and surrounding region were used to build three-dimensional models for seismic wave propagation simulations. The geologic structure near the SPE shot point is quite varied including granitic, carbonate, tuff and alluvium lithologies. We performed preliminary ground motion simulations for a near-source domain covering 8 km x 8 km at the surface centered on the shot point to investigate various source and propagation effects using WPP, LLNL's anelastic seismic wave finite difference code. Simulations indicate that variations in wave propagation properties of the sub-surface will generate strongly path-dependent response once the energy has left the relatively small granitic geology of the near-surface Climax Stock near the SPE shot point. Rough topography to the north and west of SPE shot point causes additional complexity in the signals including energy on the transverse …

This report explores how error-correction data generated by a Reed-Solomon code may be used as a mechanism to apply changes to an existing installed codebase. Using the Reed-Solomon code to generate error-correction data for a changed or updated codebase will allow the error-correction data to be applied to an existing codebase to both validate and introduce changes or updates from some upstream source to the existing installed codebase.

The U.S. Department of Energy (DOE) has adopted a goal to generate 20% of the nation’s electricity from wind power by 2030. Achieving this “20% Wind Scenario” in 2030 requires acceleration of the current rate of wind project development. Offshore wind resources contribute substantially to the nation’s wind resource, yet to date no offshore wind turbines have been installed in the U.S. Progress developing offshore wind projects has been slowed by technological challenges, uncertainties about impacts to the marine environment, siting and permitting challenges, and viewshed concerns. To address challenges associated with siting and permitting, Pacific Northwest National Laboratory (PNNL) surveyed offshore wind project developers about siting and project development processes, their experience with the environmental permitting process, and the role of coastal and marine spatial planning (CMSP) in development of the offshore wind industry. Based on the responses to survey questions, we identify several priority recommendations to support offshore wind development. Recommendations also include considerations for developing supporting industries in the U.S. and how to use Coastal and Marine Spatial Planning (CMSP) to appropriately consider ocean energy among existing ocean uses. In this report, we summarize findings, discuss the implications, and suggest actions to improve the permitting and siting …

Dampness and mold have been shown in qualitative reviews to be associated with a variety of adverse respiratory health effects, including respiratory tract infections. Several published meta-analyses have provided quantitative summaries for some of these associations, but not for respiratory infections. Demonstrating a causal relationship between dampness-related agents, which are preventable exposures, and respiratory tract infections would suggest important new public health strategies. We report the results of quantitative meta-analyses of published studies that examined the association of dampness or mold in homes with respiratory infections and bronchitis. For primary studies meeting eligibility criteria, we transformed reported odds ratios (ORs) and confidence intervals (CIs) to the log scale. Both fixed and random effects models were applied to the log ORs and their variances. Most studies contained multiple estimated ORs. Models accounted for the correlation between multiple results within the studies analyzed. One set of analyses was performed with all eligible studies, and another set restricted to studies that controlled for age, gender, smoking, and socioeconomic status. Subgroups of studies were assessed to explore heterogeneity. Funnel plots were used to assess publication bias. The resulting summary estimates of ORs from random effects models based on all studies ranged from 1.38 to …

Infrastructures are networks of dynamically interacting systems designed for the flow of information, energy, and materials. Under certain circumstances, disturbances from a targeted attack or natural disasters can cause cascading failures within and between infrastructures that result in significant service losses and long recovery times. Reliable interdependency models that can capture such multi-network cascading do not exist. The research reported here has extended Sandia's infrastructure modeling capabilities by: (1) addressing interdependencies among networks, (2) incorporating adaptive behavioral models into the network models, and (3) providing mechanisms for evaluating vulnerability to targeted attack and unforeseen disruptions. We have applied these capabilities to evaluate the robustness of various systems, and to identify factors that control the scale and duration of disruption. This capability lays the foundation for developing advanced system security solutions that encompass both external shocks and internal dynamics.