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At least 1,765 records · Page 98

Three-dimensional positioning and structure of chromosomes in a human prophase nucleus

The human genetic material is packaged into 46 chromosomes. The structure of chromosomes is known at the lowest level, where the DNA chain is wrapped around a core of eight histone proteins to form nucleosomes. Around a million of these nucleosomes, each about 11 nm in diameter and 6 nm in thickness, are wrapped up into the complex organelle of the chromosome, whose structure is mostly known at the level of visible light microscopy to form a characteristic cross shape in metaphase. However, the higher-order structure of human chromosomes, between a few tens and hundreds of nanometers, has not been well understood. We show a three-dimensional (3D) image of a human prophase nucleus obtained by serial block-face scanning electron microscopy, with 36 of the complete set of 46 chromosomes captured within it. The acquired image allows us to extract quantitative 3D structural information about the nucleus and the preserved, intact individual chromosomes within it, including their positioning and full spatial morphology at a resolution of around 50 nm in three dimensions. The chromosome positions were found, at least partially, to follow the pattern of chromosome territories previously observed only in interphase. The 3D conformation shows parallel, planar alignment of the chromatids, whose occupied volumes are almost fully accounted for by the DNA and known chromosomal proteins. Here, we also propose a potential new method of identifying human chromosomes in three dimensions, on the basis of the measurements of their 3D morphology.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Scalable Preconditioners for Structure Preserving Discretizations of Maxwell Equations in First Order Form

Here, we report multiple physical time-scales can arise in electromagnetic simulations when dissipative effects are introduced through boundary conditions, when currents follow external time-scales, and when material parameters vary spatially. In such scenarios, the time-scales of interest may be much slower than the fastest time-scales supported by the Maxwell equations, therefore making implicit time integration an efficient approach. The use of implicit temporal discretizations results in linear systems in which fast time-scales, which severely constrain the stability of an explicit method, can manifest as so-called stiff modes. This study proposes a new block preconditioner for structure preserving (also termed physics compatible) discretizations of the Maxwell equations in first order form. The intent of the preconditioner is to enable the efficient solution of multiple-time-scale Maxwell type systems. An additional benefit of the developed preconditioner is that it requires only a traditional multigrid method for its subsolves and compares well against alternative approaches that rely on specialized edge-based multigrid routines that may not be readily available. Lastly, results demonstrate parallel scalability at large electromagnetic wave CFL numbers on a variety of test problems.

97 MATHEMATICS AND COMPUTING↗

ZettaBricks: A Language Compiler and Runtime System for Anyscale Computing

This grant supported the ZettaBricks and OpenTuner projects. ZettaBricks is a new implicitly parallel language and compiler where defining multiple implementations of multiple algorithms to solve a problem is the natural way of programming. ZettaBricks makes algorithmic choice a first class construct of the language. Choices are provided in a way that also allows our compiler to tune at a finer granularity. The ZettaBricks compiler autotunes programs by making both fine-grained as well as algorithmic choices. Choices also include different automatic parallelization techniques, data distributions, algorithmic parameters, transformations, and blocking. Additionally, ZettaBricks introduces novel techniques to autotune algorithms for different convergence criteria. When choosing between various direct and iterative methods, the ZettaBricks compiler is able to tune a program in such a way that delivers near-optimal efficiency for any desired level of accuracy. The compiler has the flexibility of utilizing different convergence criteria for the various components within a single algorithm, providing the user with accuracy choice alongside algorithmic choice. OpenTuner is a generalization of the experience gained in building an autotuner for ZettaBricks. OpenTuner is a new open source framework for building domain-specific multi-objective program autotuners. OpenTuner supports fully-customizable configuration representations, an extensible technique representation to allow for domain-specific techniques, and an easy to use interface for communicating with the program to be autotuned. A key capability inside OpenTuner is the use of ensembles of disparate search techniques simultaneously; techniques that perform well will dynamically be allocated a larger proportion of tests.

97 MATHEMATICS AND COMPUTING↗

GEOS. User Tutorials

GEOS is a massively parallel, multi-physics simulation application utilizing high performance computing (HPC) to address subsurface reservoir stimulation activities with the goal of optimizing current operations and evaluating innovative stimulation methods. GEOS enables coupling of di erent solvers associated with the various physical processes occurring during reservoir stimulation in unique and sophisticated ways, adapted to various geologic settings, materials and stimulation methods. Developed at the Lawrence Livermore National Laboratory (LLNL) as a part of a Laboratory-Directed Research and Development (LDRD) Strategic Initiative (SI) project, GEOS represents the culmination of a multi-year ongoing code development and improvement e ort that has leveraged existing code capabilities and sta expertise to design new computational geosciences software.

58 GEOSCIENCES↗

Modeling Long-Term Changes in Climate, Ice Sheets and Sea Level: Using the Paleo Record to Understand Possibilities for the Future

During the project, we completed the development and testing of the infrastructure for coupled CESM-CISM paleo-simulations. Our development and testing efforts have focused on (1) CISM2, a parallel, scalable code with a suite of higher-order ice-flow solvers, (2) conservative, two-way coupling of CISM and CLM, (3) an efficient spinup method for coupled CESM-CISM simulations, and (4) inclusion of processes important for long, millennial-scale simulations (dynamic topography, orbital acceleration, asynchronous coupling to dynamic vegetation) and their evaluation (isotopes).

58 GEOSCIENCES↗

PCMS: Parallel Coupler For Multimodel Simulations

This paper presents the Parallel Coupler for Multimodel Simulations (PCMS), a new GPU accelerated generalized coupling framework for coupling simulation codes on leadership class supercomputers. PCMS includes distributed control and field mapping methods for up to five dimensions. For field mapping PCMS can utilize discretization and field information to accommodate physics constraints. PCMS is demonstrated with a coupling of the gyrokinetic microturbulence code XGC with a Monte Carlo neutral transport code DEGAS2 and with a 5D distribution function coupling of an energetic particle transport code (GNET) to a gyrokinetic microturbulence code (GTC). Weak scaling is also demonstrated on up to 2,080 GPUs of Frontier with a weak scaling efficiency of 85%.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Microchannel gel electrophoretic separation systems and methods for preparing and using

A micro-analytical platform for performing electrophoresis-based immunoassays was developed by integrating photopolymerized cross-linked polyacrylamide gels within a microfluidic device. The microfluidic immunoassays are performed by gel electrophoretic separation and quantifying analyte concentration based upon conventional polyacrylamide gel electrophoresis (PAGE). To retain biological activity of proteins and maintain intact immune complexes, native PAGE conditions were employed. Both direct (non-competitive) and competitive immunoassay formats are demonstrated in microchips for detecting toxins and biomarkers (cytokines, c-reactive protein) in bodily fluids (serum, saliva, oral fluids). Further, a description of gradient gels fabrication is included, in an effort to describe methods we have developed for further optimization of on-chip PAGE immunoassays. The described chip-based PAGE immunoassay method enables immunoassays that are fast (minutes) and require very small amounts of sample (less than a few microliters). Use of microfabricated chips as a platform enables integration, parallel assays, automation and development of portable devices.

47 OTHER INSTRUMENTATION↗

Microchannel gel electrophoretic separation systems and methods for preparing and using

A micro-analytical platform for performing electrophoresis-based immunoassays was developed by integrating photopolymerized cross-linked polyacrylamide gels within a microfluidic device. The microfluidic immunoassays are performed by gel electrophoretic separation and quantifying analyte concentration based upon conventional polyacrylamide gel electrophoresis (PAGE). To retain biological activity of proteins and maintain intact immune complexes, native PAGE conditions were employed. Both direct (non-competitive) and competitive immunoassay formats are demonstrated in microchips for detecting toxins and biomarkers (cytokines, c-reactive protein) in bodily fluids (serum, saliva, oral fluids). Further, a description of gradient gels fabrication is included, in an effort to describe methods we have developed for further optimization of on-chip PAGE immunoassays. The described chip-based PAGE immunoassay method enables immunoassays that are fast (minutes) and require very small amounts of sample (less than a few microliters). Use of microfabricated chips as a platform enables integration, parallel assays, automation and development of portable devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Collaborative Project: Building improved optimized parameter estimation algorithms to improve methane and nitrogen fluxes in a climate model

Soils in natural and managed ecosystems and wetlands are well known sources of methane, nitrous oxides, and reactive nitrogen gases, but the magnitudes of gas flux to the atmosphere are still poorly constrained. Thus, the reasons for the large increases in atmospheric concentrations of methane and nitrous oxide since the preindustrial time period are not well understood. The low atmospheric concentrations of methane and nitrous oxide, despite being more potent greenhouse gases than carbon dioxide, complicate empirical studies to provide explanations. In addition to climate concerns, the emissions of reactive nitrogen gases from soils are important to the changing nitrogen balance in the earth system, subject to human management, and may change substantially in the future. Thus improved modeling of the emission fluxes of these species from the land surface is important. Currently, there are emission modules for methane and some nitrogen species in the Community Earth System Model’s Community Land Model (CLM-ME/N); however, there are large uncertainties and problems in the simulations, resulting in coarse estimates. In this proposal, we seek to improve these emission modules by combining state-of-the-art process modules for emissions, available data, and new optimization methods. In earth science problems, we often have substantial data and knowledge of processes in disparate systems, and thus we need to combine data and a general process level understanding into a model for projections of future climate that are as accurate as possible. The best methodologies for optimization of parameters in earth system models are still being developed. In this proposal we will develop and apply surrogate algorithms that a) were especially developed for computationally expensive simulations like CLM-ME/N models; b) were (in the earlier surrogate optimization Stochastic RBF) demonstrated to perform very well on computationally expensive complex partial differential equations in earth science with limited numbers of simulations; and, c) will be (as part of the proposed research) significantly improved both by adding asynchronous parallelism, early truncation of unsuccessful simulations, and the improvement of both serial and parallel performance by the use of derivative and sensitivity information from global and local surrogate approximations S(x) . The algorithm development and testing will be focused on the CLM-ME/N model application, but the methods are general and are expected to also perform well on optimization for parameter estimation of other climate models and other classes of continuous multimodal optimization problems arising from complex simulation models. In addition, this proposal will compile available datasets of emissions of methane, nitrous oxides and reactive nitrogen species and develop protocols for site level comparisons with the CLM-ME/N. Once the model parameters are optimized against site level data, the model will be simulated at the global level and compared to atmospheric concentration measurements for the current climate, and future emissions will be estimated using climate change as simulated by the CESM. This proposal combines experts in earth system modeling, optimization, computer science, and process level understanding of soil gas emissions in an interdisciplinary team in order to improve the modeling of methane and nitrogen gas emissions. This proposal thus meets the requirements of the SciDAC RFP, by integrating state-of-the-art computer science and earth system to build an improved earth system model.

54 ENVIRONMENTAL SCIENCES↗

A parallel hub-and-spoke system for large-scale scenario-based optimization under uncertainty

Practical solution of stochastic programming problems generally requires the use of parallel computing resources. Here, we describe the open source package mpi-sppy, in which efficient and scalable parallelization is a central feature. We report computational experiments that demonstrate the ability to solve very large stochastic programming problems - including mixed-integer variants - in minutes of wall clock time, efficiently leveraging significant parallel computing resources. We report results for the largest publicly available instances of stochastic mixed-integer unit commitment problems, solving to provably tight optimality gaps. In addition, we introduce a novel software architecture that facilitates combinations of methods for accelerating convergence that can be combined in plug-and-play manner. Finally, the mpi-sppy package is written in Python, leverages the widely used Pyomo (http://www.pyomo.org) library for modeling mathematical programs, builds on existing MPI implementations to ensure efficiency and scalability, and is available via http://github.com/Pyomo/mpi-sppy.

97 MATHEMATICS AND COMPUTING↗

A Gain Scheduling Wide-Area Damping Controller for the Efficient Integration of Photovoltaic Plant

With photovoltaic generation increasing, the wide-area oscillation has a vital influence on the long-distance power transmission of photovoltaic power. For an efficient integration of photovoltaic generation, a gain scheduling wide-area damping controller (WADC) is designed to guarantee system damping performance under a wide-area signal delay and a changing operating condition, which could be aggravated by the fluctuant and uncertain photovoltaic generation. A linear parameter-varying (LPV) model is proposed to represent all possible operating conditions within varying ranges of the photovoltaic generation and the load. Then, a tensor product (TP) model transformation is applied to transform the LPV model into a TP model. Based on the TP model, a parallel distributed compensation controller (PDC) framework is adopted to design the gain scheduling WADC, which is solved by linear matrix inequalities (LMIs) considering the accommodation to the random interval delay. In addition, a staircase basis function method is proposed to reduce the conservatism of LMIs within the PDC framework. The gain of the proposed WADC will be adjusted according to the operating condition acknowledged through the real-time scheduling and control center, once a wide-area oscillation is detected. Lastly, the performance of the proposed WADC is verified by a 2-area 4-machine system and a 68-bus 16-machine system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Theory and implementation of a very high throughput true random number generator in field programmable gate array

The contribution of this paper is proposing a new entropy extraction mechanism based on sampling phase jitter in ring oscillators to make a high throughput true random number generator in a field programmable gate array (FPGA) practical. Starting from experimental observation and analysis of the entropy source in FPGA, a multi-phase sampling method is exploited to harvest the clock jitter with a maximum entropy and fast sampling speed. This parametrized design is implemented in a Xilinx Artix-7 FPGA, where the carry chains in the FPGA are explored to realize the precise phase shifting. The generator circuit is simple and resource-saving, so that multiple generation channels can run in parallel to scale the output throughput for specific applications. The prototype integrates 64 circuit units in the FPGA to provide a total output throughput of 7.68 Gbps, which meets the requirement of current high-speed quantum key distribution systems. The randomness evaluation, as well as its robustness to ambient temperature, confirms that the new method in a purely digital fashion can provide high-speed high-quality random bit sequences for a variety of embedded applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

WE-EF-BRA-11: Precision Partial-Tumor Irradiation of Dorsal Rodent Mammary Tumors

Purpose: To introduce a pre-clinical treatment technique on a micro-irradiator to treat specific volumes of dorsal mammary tumors in BALB/c mice while sparing lungs and spine. This technique facilitates pre-clinical investigation of tumor response to sub-optimal radiation treatments in which a portion of the tumor is unirradiated, known as a “marginal miss”. In-vitro data suggests that partial tumor radiations trigger a more aggressive phenotype in non-irradiated, regional tumor cells via bystander effects. As the lung tissue is spared, the impact of marginal miss on the development of pulmonary metastasis may be assessed. Methods: End to end test was performed on three BALB/c mice as proof of concept for larger studies. 1Gy was delivered on the micro-irradiator employing previously unexplored lateral parallel-opposed diamond and/or triangle-shaped beams. The margins of the treatment beam were defined using a combination of tumor palpation, barium fiducial markers, and real-time fluoroscopic images. The dose distribution was independently verified with kilovoltage beam Monte Carlo dose calculations with 7% statistical uncertainty and double exposure images. As a final step, the technique was used in a larger pre-clinical study (15Gy, 36 BALB/c mice) and lung metastasis in response to tumor irradiation of 100%, 50% and 0% was quantified. Results: For the Monte-Carlo dose calculations, the dose volume histograms established a maximum dose within the un-irradiated and radiated portions of the mammary tumor of 0.3Gy and 1.5Gy respectively, with a sharp gradient at the boundary. 100% of the lung volume received less than 0.5Gy. This technique proved suitable for a pre-clinical marginal miss study with 50% more lung metastases in partially-radiated mouse models compared to completely. Conclusion: We have developed a novel treatment technique for partial or full irradiation of dorsal mammary tumors incorporating lung sparing.The technique will be useful for exploring the phenomena of aggressive tumor phenotype that may arise from miss-irradiation.

60 APPLIED LIFE SCIENCES↗

Simulation of the full-core pin-model by JMCT Monte Carlo neutron-photon transport code

Since the large numbers of cells over a million, the tallies over a hundred million and the particle histories over ten billion, the simulation of the full-core pin-by-pin model has become a real challenge for the computers and the computational methods. On the other hand, the basic memory of the model has exceeded the limit of a single CPU, so the spatial domain and data decomposition must be considered. JMCT (J Monte Carlo Transport code) has successful fulfilled the simulation of the full-core pin-by-pin model by the domain decomposition and the nested parallel computation. The k{sub eff} and flux of each cell are obtained. (authors)

97 MATHEMATICS AND COMPUTING↗

SU-E-T-303: Spot Scanning Dose Delivery with Rapid Cycling Proton Beams From RCMS

Purpose: A rapid cycling proton beam has several distinct characteristics superior to a slow extraction synchrotron: The beam energy and energy spread, beam intensity and spot size can be varied spot by spot. The feasibility of using a spot scanning beam from a rapidc-ycling-medical-synchrotron (RCMS) at 10 Hz repetition frequency is investigated in this study for its application in proton therapy. Methods: The versatility of the beam is illustrated by two examples in water phantoms: (1) a cylindrical PTV irradiated by a single field and (2) a spherical PTV irradiated by two parallel opposed fields. A uniform dose distribution is to be delivered to the volumes. Geant4 Monte Carlo code is used to validate the dose distributions in each example. Results: Transverse algorithms are developed to produce uniform distributions in each transverseplane in the two examples with a cylindrical and a spherical PTV respectively. Longitudinally, different proton energies are used in successive transverse planes toproduce the SOBP required to cover the PTVs. In general, uniformity of dosedistribution within 3% is obtained for the cylinder and 3.5% for the sphere. The transversealgorithms requires only few hundred beam spots for each plane The algorithms may beapplied to larger volumes by increasing the intensity spot by spot for the same deliverytime of the same dose. The treatment time can be shorter than 1 minute for any fieldconfiguration and tumor shape. Conclusion: The unique beam characteristics of a spot scanning beam from a RCMS at 10 Hz repetitionfrequency are used to design transverse and longitudinal algorithms to produce uniformdistribution for any arbitrary shape and size of targets. The proposed spot scanning beam ismore versatile than existing spot scanning beams in proton therapy with better beamcontrol and lower neutron dose. This work is supported in part by grants from the US Department of Energy under contract; DE-FG02-12ER41800 and the National Science Foundation NSF PHY-1205431.

07 ISOTOPE AND RADIATION SOURCES↗

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗

XPRESS: eXascale PRogramming Environment and System Software

The XPRESS project is the research and development of a complete software architecture for Exascale computing. The four major R&D thrusts include: 1) an Exascale lightweight kernel operating system (LXK), based on the Kitten operating system (OS), to manage billion way hardware parallelism, management of faults and power, management of global virtual name space, and other features of future system architectures; 2) a runtime system (HPX-5), co-designed with LXK, based on the ParalleX execution model that supports dynamic resource management and task scheduling; 3) system interfaces for interoperability between the runtime system and both the OS and the runtime system (RIOS); 4) compilation strategies and systems to translate MPI and OpenMP legacy codes to a form that can be run with performance at least as good as a native code implementation. The software architecture development has been driven by performance evaluation of mini-applications developed at Department of Energy Co-Design Centers as well as ancillary in-house developed applications and benchmarks. Research on the ParalleX execution model has been driven by the development of formal semantics and model checkers for the execution model. The major components of the software architecture are: ParalleX execution model – guiding principles for co-design of components of the system stack with advances in locality management and task prioritization through introspection; HPX runtime system – support of application dynamic adaptive resource management, task scheduling, and introspective control policies; LXK operating system – lightweight kernel operating system for order-constant scalability and low/no noise to manage resources; RIOS – a realm of Exascale system operation unique in the XPRESS project that includes the relationship between the new generation of lightweight kernel operating systems and runtime system software; XPI advanced programming model – intermediate form and low-level (readable) programming interface reflecting the ParalleX model, providing a target for source-to- source high level parallel language translation, and supporting early direct programming experimentation and measurement; Performance models & metrics – providing parameters and their mutual sensitivities to guide co-design and quantify operational behavior; Legacy migration – ensuring seamless transition of legacy codes and programming methods to the future generation of ParalleX-based Exascale systems; . Experiments and evaluation – critical to determining degree of effectiveness and likelihood of ultimate success as well as guiding corrective design changes to achieve DOE objectives; and Applications – collaborations with Co-Design Centers and other mission critical codes. The exemplar implementation of the ParalleX execution model, HPX-5, has been released along with five fully ported applications (LULESH, HPCG, SSSP, WAMR, and DASHMM) and multiple microbenchmarks. Using these applications, the system architecture demonstrated dynamic load balancing through active migration, legacy code migration, and data-driven approaches to for graph-like applications. Crucially for Exascale and billion way parallelism, the needs and patterns of irregular applications in HPX-5 were addressed using local flow control rather than relying on globally synchronized data structures.

97 MATHEMATICS AND COMPUTING↗

PARALLEL PERTURBATION MODEL FOR CYCLE TO CYCLE VARIABILITY PPM4CCV

This code consists of a Fortran 90 implementation of the parallel perturbation model to compute cyclic variability in spark ignition (SI) engines. Cycle-to-cycle variability (CCV) is known to be detrimental to SI engine operation resulting in partial burn and knock, and result in an overall reduction in the reliability of the engine. Numerical prediction of cycle-to-cycle variability (CCV) in SI engines is extremely challenging for two key reasons: (i) high-fidelity methods such as large eddy simulation (LES) are required to accurately capture the in-cylinder turbulent flow field, and (ii) CCV is experienced over long timescales and hence the simulations need to be performed for hundreds of consecutive cycles. In the new technique, the strategy is to perform multiple parallel simulations, each of which encompasses 2-3 cycles, by effectively perturbing the simulation parameters such as the initial and boundary conditions. The PPM4CCV code is a pre-processing code and can be coupled with any engine CFD code. PPM4CCV was coupled with Converge CFD code and a 10-time speedup was demonstrated over the conventional multi-cycle LES in predicting the CCV for a motored engine. Recently, the model is also being applied to fired engines including port fuel injected (PFI) and direct injection spark ignition engines and the preliminary results are very encouraging.

Ameen, Muhsin Mohammed↗