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At least 1,315 records · Page 73

Storage for Advanced Scientific Use-Cases and Beyond

The dCache project provides open-source storage software deployed internationally to satisfy ever more demanding scientific storage requirements. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, through wide access and easy integration with existing systems. In this paper, we describe some of the recent features that facilitate the use of storage to maximise the gain from stored data, including quality-of-service management, heterogeneous systems - both through integrated tertiary storage support and geographical locality - the parallel NFS (pNFS) extension, and innovative delegated authorisation schemes.

43 PARTICLE ACCELERATORS↗

Modeling Changes in Measured Conductance of Thin Boron Carbide Semiconducting Films Under Irradiation

Semiconducting, p-type, amorphous partially dehydrogenated boron carbide films (a-B 10 C 2+x :H y ) were deposited utilizing plasma enhanced chemical vapor deposition (PECVD) onto n-type silicon thus creating a heterojunction diode. A model was developed for the conductance of the device as a function of perturbation frequency (f) that incorporates changes of the electrical properties for both the a-B 10 C 2+x :H y film and the silicon substrate when irradiated. The virgin model has 3 independent variables (R1, C1, R3), and 1 dependent variable (f). These samples were then irradiated with 200 keV He + ions, and the conductance model was matched to the measured data. It was found that initial irradiation (0.1 displacements per atom (dpa) equivalent) resulted in a decrease in the parallel junction resistance parameter from 6032 Ω to 2705 Ω. Further irradiation drastically increased the parallel junction resistance parameter to 39000 Ω (0.2 dpa equivalent), 77440 Ω (0.3 dpa equivalent), and 190000 Ω (0.5 dpa equivalent). It is believed that the initial irradiation causes type inversion of the silicon substrate changing the original junction from a p-n to a p-p+ with a much lower barrier height leading to a lower junction resistance component between the a-B 10 C 2+x :H y and irradiated silicon. In addition, it was found that after irradiation, a second parallel resistor and capacitor component is required for the model, introducing 2 additional independent variables (R2, C2). This is interpreted as the junction between the irradiated and virgin silicon near ion end of range.

36 MATERIALS SCIENCE↗

Response of the Dielectric Parameters of (110)SrTiO{sub 3} Films to the Formation of Ferroelectric Domains in Their Volume

Three-layer SrRuO{sub 3}/SrTiO{sub 3}/SrRuO{sub 3} heterostructures were grown by laser evaporation on (110)LaAlO{sub 3} substrates. Photolithography and ion etching are used to form plane-parallel film capacitors, in which a layer of strontium titanate is placed between two film electrodes of strontium ruthenate. Data on the structure and orientation of the intermediate SrTiO{sub 3} layer in the grown heterostructures were obtained. The variation of the dielectric constant and dielectric loss of the SrTiO{sub 3} intermediate layer upon varying the temperature and intensity of an external electric field was studied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computational and empirical studies predict Mycobacterium tuberculosis -specific T cells as a biomarker for infection outcome

Identifying biomarkers for tuberculosis (TB) is an ongoing challenge in developing immunological correlates of infection outcome and protection. Biomarker discovery is also necessary for aiding design and testing of new treatments and vaccines. To effectively predict biomarkers for infection progression in any disease, including TB, large amounts of experimental data are required to reach statistical power and make accurate predictions. We took a two-pronged approach using both experimental and computational modeling to address this problem. We first collected 200 blood samples over a 2-year period from 28 non-human primates (NHP) infected with a low dose of Mycobacterium tuberculosis . We identified T cells and the cytokines that they were producing (single and multiple) from each sample along with monkey status and infection progression data. Machine learning techniques were used to interrogate the experimental NHP datasets without identifying any potential TB biomarker. In parallel, we used our extensive novel NHP datasets to build and calibrate a multi-organ computational model that combines what is occurring at the site of infection (e.g., lung) at a single granuloma scale with blood level readouts that can be tracked in monkeys and humans. We then generated a large in silico repository of in silico granulomas coupled to lymph node and blood dynamics and developed an in silico tool to scale granuloma level results to a full host scale to identify what best predicts Mycobacterium tuberculosis (Mtb) infection outcomes. The analysis of in silico blood measures identifies Mtb -specific frequencies of effector T cell phenotypes at various time points post infection as promising indicators of infection outcome. As a result, we emphasize that pairing wetlab and computational approaches holds great promise to accelerate TB biomarker discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Concentrations and Sources of Airborne Particles in a Neonatal Intensive Care Unit

Premature infants in neonatal intensive care units (NICUs) have underdeveloped immune systems, making them susceptible to adverse health consequences from air pollutant exposure. Little is known about the sources of indoor airborne particles that contribute to the exposure of premature infants in the NICU environment. In this study, we monitored the spatial and temporal variations of airborne particulate matter concentrations along with other indoor environmental parameters and human occupancy. The experiments were conducted over one year in a private-style NICU. The NICU was served by a central heating, ventilation and air-conditioning (HVAC) system equipped with an economizer and a high-efficiency particle filtration system. The following parameters were measured continuously during weekdays with 1-min resolution: particles larger than 0.3 μm resolved into 6 size groups, CO 2 level, dry-bulb temperature and relative humidity, and presence or absence of occupants. Altogether, over sixteen periods of a few weeks each, measurements were conducted in rooms occupied with premature infants. In parallel, a second monitoring station was operated in a nearby hallway or at the local nurses’ station. The monitoring data suggest a strong link between indoor particle concentrations and human occupancy. Detected particle peaks from occupancy were clearly discernible among larger particles and imperceptible for submicron (0.3–1 μm) particles. The mean indoor particle mass concentrations averaged across the size range 0.3–10 μm during occupied periods was 1.9 μg/m 3 , approximately 2.5 times the concentration during unoccupied periods (0.8 μg/m 3 ). Contributions of within-room emissions to total PM10 mass in the baby rooms averaged 37–81%. Near-room indoor emissions and outdoor sources contributed 18–59% and 1–5%, respectively. Airborne particle levels in the size range 1–10 μm showed strong dependence on human activities, indicating the importance of indoor-generated particles for infant’s exposure to airborne particulate matter in the NICU.

60 APPLIED LIFE SCIENCES↗

Rendering and Compositing Infrastructure Improvements to VisIt for Insitu Rendering

Compared to posthoc rendering, insitu rendering often generates larger numbers of images, as a result rendering performance and scalability are critical in the insitu setting. In this work we present improvements to VisIt's rendering and compositing infrastructure that deliver increased performance and scalability in both posthoc and insitu settings. We added the capability for alpha blend compositing and use it with ordered compositing when datasets have disjoint block domain decomposition to optimize the rendering of transparent geometry. We also made improvements that increase overall efficiency by reducing communication and data movement and have addressed a number of performance issues. We structured our code to take advantage of SIMD parallelization and use threads to overlap communication and compositing. We tested our improvements on a 20 core workstation using 8 cores to render geometry generated from a $256^3$ cosmology dataset and on a Cray XC31 using 512 cores to render geometry generated from a $2000^2 \times 800$ plasma dataset. Our results show that ordered compositing provides a speed up of up to $4 \times$ over the current sort first strategy. The other improvements resulted in modest speed up with one notable exception where we achieve up to $40 \times$ speed up of rendering and compositing of opaque geometry when both opaque and transparent geometry are rendered together. We also investigated the use of depth peeling, but found that the implementation provided by VTK is substantially slower,both with and without GPU acceleration, than a local camera order sort.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual Revision 3.7

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

97 MATHEMATICS AND COMPUTING↗

PIPER: Performance Insight for Programmers and Exascale Runtimes: Guiding the Development of the Exascale Software Stack

The PIPER project set out to develop methodologies and software for measurement, analysis, attribution, and presentation of performance data for extreme-scale systems. Goals of the project were to support analysis of massive multi-scale parallelism, heterogeneous architectures, multi-faceted performance concerns, and to support both post-mortem performance analysis to identify program features that contribute to problematic performance and on-line performance analysis to drive adaptation. This final report summarizes the research and development activity at Rice University as part of the PIPER project. Producing a complete suite of performance tools for exascale platforms during the course of this project was impossible since both hardware and software for exascale systems is still a moving target. For that reason, the project focused broadly on the development of new techniques for measurement and analysis of performance on modern parallel architectures, enhancements to HPCToolkit’s software infrastructure to support our research goals or use on sophisticated applications, engaging developers of multithreaded runtimes to explore how support for tools should be integrated into their designs, engaging operating system developers with feature requests for enhanced monitoring support, engaging vendors with requests that they add hardware measure- ment capabilities and software interfaces needed by tools as they design new components of HPC platforms including processors, accelerators and networks, and finally collaborations with partners interested in using HPCToolkit to analyze and tune scalable parallel applications.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual Revision 3.8

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual (Rev. 3.11)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual (Revision 3.15)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

PETSc/TAO Users Manual: Revision 3.18

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than packages such as MATLAB or a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or lldb, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗

PETSc/TAO Users Manual (Rev. 3.20)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

Wellbore Fracture Imaging Using Inflow Detection Measurements

One of the most striking measurements taken during DOE’s EGS Collab project at the 4850-foot depth location was the so-called ‘sewer cam’, which enabled direct visualization of the flow of water into the production well through fractures during the stimulation. The ability to see directly which fractures were flowing and (roughly) how much was a breakthrough in understanding the topology of the created fracture network. Achieving this kind of fracture flow imaging at FORGE would be more challenging because of the 225°C temperature, but equally or even more valuable if it could be achieved. In 2017, a joint project between Sandia and Stanford developed a downhole tool concept to measure the enthalpy of multiphase fluid entering a geothermal well from individual fractures (Gao et al., 2017). For the FORGE project, measuring enthalpy is of less interest because the fluid is expected to be single-phase liquid water. However, the foundation of the device was the measurement of chloride ion concentration, which could form the basis for a direct measurement of inflow from fractures. During the 2017 project, this novel chloride sensing system was implemented into a laboratory test instrument, and we confirmed the capability of the system to measure the ion concentration of fluid entering a model wellbore through a small entry port. The wellbore was a 6-inch diameter model well, and the port was approximately 0.08 inch (2mm) in diameter. The device could measure the chloride concentration accurately even when the well was flowing in a bubbly flow. Given its accuracy, the tool should be able to identify locations of water entering the wellbore even if the ion concentration differs only slightly from that of the water in the well. It is likely that different fractures may flow slightly different chloride concentrations, which would make it feasible to detect individual fractures as well as to estimate the volume of their flow. Ultimately, we could also recognize different fractures flowing back significantly different ion concentrations after fracturing in the FORGE wells. This could be realized by adding different ions in the fracturing fluids in different fractures created at different stages of stimulation (and modifying the tool to include different ion specificity). Sandia’s tool was shown during the study to have the capability to withstand the 225°C temperature, and the electrochemical sensing elements were tested in the laboratory to 225°C at 1500 psia for 24 hours. An early implementation of the fully integrated downhole electrochemical tool, including high-temperature electronics, robust housing, and wireline truck interface, had previously been constructed and tested successfully at Sandia; thus, hardware development tasks focused on advancing the technology readiness level (TRL) of this promising technology for FORGE deployment, rather than on developing a new scientific basis for its operation. The data collection electronics in this tool allowed for several other sensors (pressure, temperature, flow spinner) to be implemented in parallel as well. The research was a new collaboration between Stanford and Sandia to modify and refine the tool for FORGE deployment, to make the downhole measurements, and to characterize the evolving fractures.

15 GEOTHERMAL ENERGY↗

Efficacy of the Cell Perturbation Method in Large-Eddy Simulations of Boundary Layer Flow over Complex Terrain

A challenge to simulating turbulent flow in multiscale atmospheric applications is the efficient generation of resolved turbulence motions over an area of interest. One approach is to apply small perturbations to flow variables near the inflow planes of turbulence-resolving simulation domains nested within larger mesoscale domains. While this approach has been examined in numerous idealized and simple terrain cases, its efficacy in complex terrain environments has not yet been fully explored. Here, we examine the benefits of the stochastic cell perturbation method (CPM) over real complex terrain using data from the 2017 Perdigão field campaign, conducted in an approximately 2-km wide valley situated between two nearly parallel ridges. Following a typical configuration for multiscale simulation using nested domains within the Weather Research and Forecasting (WRF) model to downscale from the mesoscale to a large-eddy simulation (LES), we apply the CPM on a domain with horizontal grid spacing of 150 m. At this resolution, spurious coherent structures are often observed under unstable atmospheric conditions with moderate mean wind speeds. Results from such an intermediate resolution grid are often nested down for finer, more detailed LES, where these spurious structures adversely affect the development of turbulence on the subsequent finer grid nest. We therefore examine the impacts of the CPM on the representation of turbulence within the nested LES domain under moderate mean flow conditions in three different stability regimes: weakly convective, strongly convective, and weakly stable. In addition, two different resolutions of the underlying terrain are used to explore the role of the complex topography itself in generating turbulent structures. We demonstrate that the CPM improves the representation of turbulence within the LES domain, relative to the use of high-resolution complex terrain alone. During the convective conditions, the CPM improves the rate at which smaller-scales of turbulence form, while also accelerating the attenuation of the spurious numerically generated roll structures near the inflow boundary. During stable conditions, the coarse mesh spacing of the intermediate LES domain used herein was insufficient to maintain resolved turbulence using CPM as the flow develops downstream, highlighting the need for yet higher resolution under even weakly stable conditions, and the importance of accurate representation of flow on intermediate LES grids.

17 WIND ENERGY↗

End-System Aware Peak Link Utilization Transport for Big Data Transfer over Dedicated Connections

High-performance networks provisioning 10/40-Gbps dedicated channels have been rapidly developed andincreasingly deployed to support big data transfers on the order of terabytes or petabytes in large-scale network-intensiveapplications. However, end users have not seen corresponding increase in application throughput mainly because traditional end-to-end transport methods are not optimized for such connections. New congestion or flow control mechanisms are desirable to meet the challenges brought to transport protocol design by dedicated connections. The advent and proliferation of multi-core processors make it now possible to improve application throughput by providing multiple processing and network resources to a single data transfer. Based on the existing PLUT method, we proposed a new dynamic buffer management scheme and an automatic parallelism tuning mechanism to achieve the maximal bottleneck rate. The performance superiority of PLUT is justified by the experimental results collected over a local 10Gbps dedicated connection.

Rao, Nageswara↗