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The increasing on-chip parallelism has some substantial implications for HPC applications. Currently, hybrid programming models (typically MPI+OpenMP) are employed for mapping software to the hardware in order to leverage the hardware?s architectural features. In this paper, we present an approach that automatically introduces thread level parallelism into Chombo, a parallel adaptive mesh refinement framework for finite difference type PDE solvers. In Chombo, core algorithms are specified in the ChomboFortran, a macro language extension to F77 that is part of the Chombo framework. This domain-specific language forms an already used target language for an automatic migration of the large number of existing algorithms into a hybrid MPI+OpenMP implementation. It also provides access to the auto-tuning methodology that enables tuning certain aspects of an algorithm to hardware characteristics. Performance measurements are presented for a few of the most relevant kernels with respect to a specific application benchmark using this technique as well as benchmark results for the entire application. The kernel benchmarks show that, using auto-tuning, up to a factor of 11 in performance was gained with 4 threads with respect to the serial reference implementation.

The Salt Disposition Integration (SDI) portfolio of projects provides the infrastructure within existing Liquid Waste facilities to support the startup and long term operation of the Salt Waste Processing Facility (SWPF). Within SDI, the Blend and Feed Project will equip existing waste tanks in the Tank Farms to serve as Blend Tanks where 300,000-800,000 gallons of salt solution will be blended in 1.3 million gallon tanks and qualified for use as feedstock for SWPF. Blending requires the miscible salt solutions from potentially multiple source tanks per batch to be well mixed without disturbing settled sludge solids that may be present in a Blend Tank. Disturbing solids may be problematic both from a feed quality perspective as well as from a process safety perspective where hydrogen release from the sludge is a potential flammability concern. To develop the necessary technical basis for the design and operation of blending equipment, Savannah River National Laboratory (SRNL) completed scaled blending and transfer pump tests and computational fluid dynamics (CFD) modeling. A 94 inch diameter pilot-scale blending tank, including tank internals such as the blending pump, transfer pump, removable cooling coils, and center column, were used in this research. The test tank represents a 1/10.85 …

The specific goal of this work was to understanding the catalytic reactions pathways for the synthesis of vinyl acetate over Pd, Au and PdAu alloys. A combination of both experimental methods (X-ray and Auger spectroscopies, low-energy ion scattering (LEIS), low-energy electron diffraction (LEED) and theory (Density Functional Theory (DFT) calculations and Monte Carlo methods under various different reactions) were used to track the surface chemistry and the influence of alloying. The surface intermediates involved in the various reactions were characterized using reflection-absorption infrared spectroscopy and LEED to identify the nature of the surface species and temperature-programmed desorption (TPD) to follow the decomposition pathways and measure heats of adsorption. These results along with those from density functional theoretical calculations were used determine the kinetics for elementary steps. The results from this work showed that the reaction proceeds via the Samanos mechanism over Pd surfaces whereby the ethylene directly couples with acetate to form an acetoxyethyl intermediate that subsequently undergoes a beta-hydride elimination to form the vinyl acetate monomer. The presence of Au was found to modify the adsorption energies and surface coverages of important surface intermediates including acetate, ethylidyne and ethylene which ultimately influences the critical C-H activation and coupling steps. …

The Resource Description Framework (RDF) is a popular data model for representing linked data sets arising from the web, as well as large scienti#12;c data repositories such as UniProt. RDF data intrinsically represents a labeled and directed multi-graph. SPARQL is a query language for RDF that expresses subgraph pattern-#12;nding queries on this implicit multigraph in a SQL- like syntax. SPARQL queries generate complex intermediate join queries; to compute these joins e#14;ciently, we propose a new strategy based on bitmap indexes. We store the RDF data in column-oriented structures as compressed bitmaps along with two dictionaries. This paper makes three new contributions. (i) We present an e#14;cient parallel strategy for parsing the raw RDF data, building dictionaries of unique entities, and creating compressed bitmap indexes of the data. (ii) We utilize the constructed bitmap indexes to e#14;ciently answer SPARQL queries, simplifying the join evaluations. (iii) To quantify the performance impact of using bitmap indexes, we compare our approach to the state-of-the-art triple-store RDF-3X. We #12;nd that our bitmap index-based approach to answering queries is up to an order of magnitude faster for a variety of SPARQL queries, on gigascale RDF data sets.

Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum …

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Practical disposal of nuclear waste requires high-throughput separation techniques. The most dangerous part of nuclear waste is the fission product, which contains the most active and mobile radioisotopes and produces most of the heat. We suggest that the fission products could be separated as a group from nuclear waste using plasma mass filters. Plasmabased processes are well suited to separating nuclear waste, because mass rather than chemical properties are used for separation. A single plasma stage can replace several stages of chemical separation, producing separate streams of bulk elements, fission products, and actinoids. The plasma mass filters may have lower cost and produce less auxiliary waste than chemical processing plants. Three rotating plasma configurations are considered that act as mass filters: the plasma centrifuge, the Ohkawa filter, and the asymmetric centrifugal trap.

This letter serves as the post-closure inspection letter report for corrective action units on the Nevada National Security Site for calendar year 2011. Copies of completed inspection checklists are included in this report.

To extend their ability to perform accountability and verification measurements of {sup 235}U in a U-Pu oxide matrix, the K-Area Material Storage facility commissioned the development and construction of a Passive/Active {sup 252}Cf Shuffler. A series of {sup 252}Cf, PuO{sub 2}, and U-Pu oxide standards, in addition to a single U{sub 3}O{sub 8} standard, were measured to characterize and calibrate the shuffler. Accompanying these measurements were simulations using MCNP5/MCNPX, aimed at isolating the neutron countrate contributions for each of the isotopes present. Two calibration methods for determining the {sup 235}U content in mixed UPu oxide were then developed, yielding comparable results. The first determines the {sup 235}U mass by estimating the {sup 239}Pu/{sup 235}U ratio-dependent contributions from the primary delayed neutron contributors. The second defines an average linear response based on the {sup 235}U and {sup 239}Pu mass contents. In each case, it was observed that self-shielding due to {sup 235}U mass has a large influence on the observed rates, requiring bounds on the applicable limits of each calibration method.

The recent interest in a hydrogen-based fuel economy has renewed research into metal hydride chemistry. Many of these compounds react readily with water to release hydrogen gas and form a caustic. Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFT) has been used to study the hydrolysis reaction. The LiOH stretch appears at 3670 cm{sup -1}. Raman spectroscopy is a complementary technique that employs monochromatic excitation (laser) allowing access to the low energy region of the vibrational spectrum (<600 cm{sup -1}). Weak scattering and fluorescence typically prevent Raman from being used for many compounds. The role of Li{sub 2}O in the moisture reaction has not been fully studied for LiH. Li{sub 2}O can be observed by Raman while being hidden in the Infrared spectrum.

This report describes experimental results for the selective removal of strontium and cesium from simulated waste solutions using monosodium titanate (MST) and crystalline silicotitanate (CST)-laden filter cartridges. Four types of ion exchange cartridge media (CST and MST designed by both 3M and POROX{reg_sign}) were evaluated. In these proof-of-principle tests effective uptake of both Sr-85 and Cs-137 was observed. However, the experiments were not performed long enough to determine the saturation levels or breakthrough curve for each filter cartridge. POREX{reg_sign} MST cartridges, which by design were based on co-sintering of the active titanates with polyethylene particles, seem to perform as well as the 3M-designed MST cartridges (impregnated filter membrane design) in the uptake of strontium. At low salt simulant conditions (0.29 M Na{sup +}), the instantaneous decontamination factor (D{sub F}) for Sr-85 with the 3M-design MST cartridge measured 26, representing the removal of 96% of the Sr-85. On the other hand, the Sr-85 instantaneous D{sub F} with the POREX{reg_sign} design MST cartridge measured 40 or 98% removal of the Sr-85. Strontium removal with the 3M-design MST and CST cartridges placed in series filter arrangement produced an instantaneous decontamination factor of 41 or 97.6% removal compared to an instantaneous decontamination factor of …

Contours, the connected components of level sets, play an important role in understanding the global structure of a scalar field. In particular their nestingbehavior and topology-often represented in form of a contour tree-have been used extensively for visualization and analysis. However, traditional contour trees onlyencode structural properties like number of contours or the nesting of contours, but little quantitative information such as volume or other statistics. Here we use thesegmentation implied by a contour tree to compute a large number of per-contour (interval) based statistics of both the function defining the contour tree as well asother co-located functions. We introduce a new visual metaphor for contour trees, called topological cacti, that extends the traditional toporrery display of acontour tree to display additional quantitative information as width of the cactus trunk and length of its spikes. We apply the new technique to scalar fields ofvarying dimension and different measures to demonstrate the effectiveness of the approach.

Operational inventory limits for the disposal of solid low-level waste in Slit Trenches 1-7 were established by the Special Analysis (SA) performed by Collard and Hamm (2008). To determine disposal limits for the Slit Trenches, the SA followed the methodology used in the 2008 PA (WSRC, 2008) which assumed that the inventories in each trench were instantaneously placed in 12/1995, which is the date when SLIT1 began operation. The 2008 SA analyzed the impact from placing storm-water runoff covers simultaneously over Slit Trenches 1-7 at 5, 10 and 15 years after the inventory was introduced. To include a measure of conservatism in the limits, the lowest of the limits calculated for any storm-water runoff cover placement time or that calculated in the original 2008 PA was chosen as the operational limit for each radionuclide. Through the availability of funding provided by the American Recovery and Reinvestment Act (ARRA), storm-water runoff covers were placed over Slit Trenches 1-5 in December 2010. SRNL was requested to perform a UDQE for this accelerated action. Table 1 below lists the operational dates for Slit Trenches 1-5 and the time elapsed between when the first waste package was disposed in each Slit Trench and when …

Gribov viewed the axial anomaly as a manifestation of the collective motion of Dirac fermions with arbitrarily high momenta in the vacuum. In the presence of an external magnetic field and a chirality imbalance, this collective motion becomes directly observable in the form of the electric current - this is the chiral magnetic effect (CME). I give an elementary introduction into the physics of CME, and discuss the experimental status and recent developments.

MicroBooNE is a liquid Argon time projection chamber to be built at Fermilab for an accelerator-based neutrino physics experiment and as part of the R&D strategy for a large liquid argon detector at DUSEL. The waveforms of the {approx}9000 sense wires in the chamber are continuously digitized at 2 M samples/s - which results in a large volume of data coming off the TPC. We have developed a lossless data reduction scheme based on Huffman Coding and have tested the scheme on cosmic ray data taken from a small liquid Argon time projection chamber, the BO detector. For sense wire waveforms produced by cosmic ray tracks, the Huffman Coding scheme compresses the data by a factor of approximately 10. The compressed data can be fully recovered back to the original data since the compression is lossless. In addition to accelerator neutrino data, which comes with small duty cycle in sync with the accelerator beam spill, continuous digitized waveforms are to be temporarily stored in the MicroBooNE data-acquisition system for about an hour, long enough for an external alert from possible supernova events. Another scheme, Dynamic Decimation, has been developed to compress further the potential supernova data so that the storage …

We report measurements of the Fermi surface (FS) of the ternary iron-phosphide SrFe{sub 2}P{sub 2} using the de Haas-van Alphen effect. The calculated FS of this compound is very similar to SrFe{sub 2}As{sub 2}, the parent compound of the high temperature superconductors. Our data show that the Fermi surface is composed of two electron and two hole sheets in agreement with bandstructure calculations. Several of the sheets show strong c-axis warping emphasizing the importance of three-dimensionality in the non-magnetic state of the ternary pnictides. We find that the electron and hole pockets have a different topology, implying that this material does not satisfy a ({pi},{pi}) nesting condition.

Almost 40 years ago, Gribov and colleagues at the Leningrad Nuclear Physics Institute developed the ideas that led to the Dokhsitzer-Gribov-Altarelli-Parisi the Baltisky-Fadin-Kuraev-Lipatov equations. These equations describe the evolution of the distributions for quarks and gluon inside a hadron to increased resolution scale of a probe or to smaller values of the fractional momentum of a hadronic constituent. I motivate and discuss the generalization required of these equations needed for high energy processes when the density of constituents is large. This leads to a theory of saturation realized by the Color Glass Condensate

INDEPENDENT VERIFICATION REVIEW AND SURVEY of the Argonne National Laboratory Building 301 Footprint, Argonne Illinois 5061-SR-01-0

We find a correspondence between semiclassical QCD quantized on the light-front and a dual gravity model in anti-de Sitter (AdS) space, thus providing an initial approximation to QCD in its strongly coupled regime. This correspondence - light-front holography - leads to a light-front Hamiltonian and relativistic bound-state wave equations that are functions of an invariant impact variable {zeta} which measures the separation of the quark and gluonic constituents within hadrons at equal lightfront time. The eigenvalues of the resulting light-front Schrodinger and Dirac equations are consistent with the observed light meson and baryon spectrum, and the eigenmodes provide the light-front wavefunctions, the probability amplitudes describing the dynamics of the hadronic constituents. The light-front equations of motion, which are dual to an effective classical gravity theory, possess remarkable algebraic and integrability properties which are dictated by the underlying conformal properties of the theory. We extend the algebraic construction to include a confining potential while preserving the integrability of the mesonic and baryonic bound-state equations.

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The search for broken time reversal symmetry (TRSB) in unconventional superconductors intensified in the past year as more systems have been predicted to possess such a state. Following our pioneering study of TRSB states in Sr{sub 2}RuO{sub 4} using magneto-optic probes, we embarked on a systematic study of several other of these candidate systems. The primary instrument for our studies is the Sagnac magneto-optic interferometer, which we recently developed. This instrument can measure magneto-optic Faraday or Kerr effects with an unprecedented sensitivity of 10 nanoradians at temperatures as low as 100 mK. In this paper we review our recent studies of TRSB in several systems, emphasizing the study of the pseudogap state of high temperature superconductors and the inverse proximity effect in superconductor/ferromagnet proximity structures.

We review recent experimental measurements of the Fermi surface of the iron-pnictide superconductor LaFePO using quantum oscillation techniques. These studies show that the Fermi surface topology is close to that predicted by first principles density functional theory calculations, consisting of quasi-twodimensional electron-like and hole-like sheets. The total volume of the two hole sheets is almost equal to that of the two electron sheets, and the hole and electron Fermi surface sheets are close to a nesting condition. No evidence for the predicted three dimensional pocket arising from the Fe d{sub z}{sup 2} band is found. Measurements of the effective mass suggest a renormalisation of around two, close to the value for the overall band renormalisation found in recent angle resolved photoemission measurements.

We report quantum oscillation measurements that enable the direct observation of the Fermi surface of the low temperature ground state of BaFe{sub 2}As{sub 2}. From these measurements we characterize the low energy excitations, revealing that the Fermi surface is reconstructed in the antiferromagnetic state, but leaving itinerant electrons in its wake. The present measurements are consistent with a conventional band folding picture of the antiferromagnetic ground state, placing important limits on the topology and size of the Fermi surface.