A generalized wavelet-packet based technique for decomposing signals into coherent and non-cohere... more A generalized wavelet-packet based technique for decomposing signals into coherent and non-coherent parts is presented. As a first test, the algorithm is applied to the vorticity field of numerical simulations of weakly decaying two-dimensional turbulence. The coherent vortex structures that emerge in the flow evolution are systematically filtered from the solution. Once extracted, a number of vortex properties are computed and their time evolution is compared with the theoretical predictions of Carnevale et al. (Carnevale et al., Phys. Rev. Lett. 66, 2735, (1991).) Our results compare well with a previous attempt to verify the scaling theory (J. Weiss and J. C. McWilliams, Phys. Fluids A. 5 , 608, (1993).), in which the vortices are extracted from the same data using a complex pattern recognition algorithm (J. C. McWilliams, J. Fluid Mech. 219, 361 (1990).) based exclusively on apriori knowledge of the properties of the vortex structures. The similarity of the results is encouragin...
A code called UNÌC is currently under development at Argonne National Laboratory (ANL). The aim o... more A code called UNÌC is currently under development at Argonne National Laboratory (ANL). The aim of the code is to provide a neutronic solver with the same geometrical flexibility of Monte Carlo codes and without the approximations (homogenization and energy condensation) associated with the common multi-step approach currently used. Moreover, UNÌC will offer the capability of multi-resolution in phase space. At the moment, two methodologies are implemented: a second order spherical harmonics (P N) form of the transport equation and the first order method of characteristics. To improve overall performance (per-processor and scalability to thousands of processors) and reduce memory requirements, we are developing some specialized implementations of key PETSc preconditioners and matrix objects.
SHARP (Simulation-based High-efficiency Advanced Reactor Prototyping) is a modern suite of codes ... more SHARP (Simulation-based High-efficiency Advanced Reactor Prototyping) is a modern suite of codes to simulate the key components of a fast reactor core. The SHARP toolkit is organized as a collection of modules, each representing the key components of the physics to be modeled – neutron transport, thermal hydraulics, fuel/structure behavior – together with pre and post-processing for geometry definition, mesh generation, visualization, user interface, etc. The physics models are designed to make minimal possible use of lumped parameter models, homogenization, and empirical correlations in favor of more direct solution of the fundamental governing equations, when sufficient computing resources are available. Thus, one of the key design goals is to effectively leverage leadership class computing resources – viz. BG/P and Cray Supercomputers that are on the current trajectory to delivering sustained petaflops performance. Further, the nature of the physical problem to be investigated wi...
Type Ia supernovae are thought to be the result of a thermonuclear explosion in a white dwarf tha... more Type Ia supernovae are thought to be the result of a thermonuclear explosion in a white dwarf that is approaching the Chandrasekhar mass limit. The properties of the supernova explosion, including its energy, depends significantly on the way in which the thermonuclear runaway begins. Where in the white dwarf ignition takes place, and how many ignition points there are, are
... Jared C. Roach 1 , Andrew F. Siegel 1, 2 , Ger van den Engh 1 , Barbara Trask 1 and Leroy Hoo... more ... Jared C. Roach 1 , Andrew F. Siegel 1, 2 , Ger van den Engh 1 , Barbara Trask 1 and Leroy Hood 1: The authors are in the Department of Molecular Biotechnology, University of ... We evaluate four BAC selection strategies: mapping, random BAC, limited seeding and parking. ...
Proceedings of IGARSS '94 - 1994 IEEE International Geoscience and Remote Sensing Symposium, 1994
Abstract: During July and August of 1993, a low grazing angle (LOGAN) radar experiment was conduc... more Abstract: During July and August of 1993, a low grazing angle (LOGAN) radar experiment was conducted from the Chesapeake Light Tower which is located on the continental shelf approximately 24 km east of Cape Henry, Virginia. High resolution (0.15 m) and calibrated radar ...
We present tools and methods for checking the consistency of gene and metabolic networks models. ... more We present tools and methods for checking the consistency of gene and metabolic networks models. Qualitative informations on interaction signs and on variations of concentration are collected and used in models of signicant size. Öis approach is based on a mathematical foundation whose hypotheses delimit the applicability.
ABSTRACT There has been considerable interest in recent years in collisionless reconnection dynam... more ABSTRACT There has been considerable interest in recent years in collisionless reconnection dynamics governed by the generalized Ohm's law in which electron inertia provides the mechanism for breaking field lines. It has been suggested in several theoretical studies that the nonlinear reconnection dynamics, to leading order, is independent of the mechanism that breaks field lines (that is, electron inertia). We test this suggestion carefully using the new Magnetic Reconnection Code (MRC) developed at the Center for Magnetic Reconnection Studies. The MRC is a new massively parallel code with Adaptive Mesh Refinement (AMR) that integrates the equations of Hall MHD. The use of AMR enables unprecedented levels of resolution of the current and vorticity layers and uncovers interesting secondary dynamics not seen in previous studies. We apply the MRC to the study of two problems, one involving free reconnection caused by a spontaneous and fast collisionless instability, the other involving forced reconnection induced by boundary perturbations on a stable plasma. In the case of free reconnection, over the range of parameters covered by our simulations, it is shown that the nonlinear reconnection rate is near-explosive, and furthermore, that the nonlinear magnetic island width is an invariant function of a dimensionless variable which is the product of the linear growth rate and time. Now, since the linear growth rate is a function of the ion sound radius as well as the electron skin depth, we conclude that the nonlinear reconnection rate is not independent of electron inertia. In the case of forced reconnection, after a slow growth phase, the dynamics exhibits an impulsive growth in the amplitude of the thin current sheet, and a subsequent current disruption mediated by secondary instabilities. These results, in which electron inertia provides the mechanism for breaking field lines, are contrasted with resistive Hall MHD simulations in which resistivity provides the mechanism for breaking field lines.
Dataset storage, exchange, and access play a critical role in scientific applications. For such p... more Dataset storage, exchange, and access play a critical role in scientific applications. For such purposes netCDF serves as a portable, efficient file format and programming interface, which is popular in numerous scientific application domains. However, the original interface does not provide an efficient mechanism for parallel data storage and access. In this work, we present a new parallel interface for
The objective of this project was to test new coupling algorithms and enable efficient and; scala... more The objective of this project was to test new coupling algorithms and enable efficient and; scalable multi-physics simulations of advanced nuclear reactors, with considerations regarding; the implementation of such algorithms in massively parallel environments. Numerical tests were; carried out to verify the proposed approach and the examples included some reactor transients.; The project was directly related to the Sodium Fast
ABSTRACT Monte Carlo (MC) neutral particle transport codes are considered the gold-standard for n... more ABSTRACT Monte Carlo (MC) neutral particle transport codes are considered the gold-standard for nuclear simulations, but they cannot be robustly applied to high-fidelity nuclear reactor analysis without accommodating several terabytes of materials and tally data. While this is not a large amount of aggregate data for a typical high performance computer, MC methods are only embarrassingly parallel when the key data structures are replicated for each processing element, an approach which is likely infeasible on future machines. The present work explores the use of spatial domain decomposition to make full-scale nuclear reactor simulations tractable with Monte Carlo methods, presenting a simple implementation in a production-scale code. Good performance is achieved for mesh-tallies of up to 2.39TB distributed across 512 compute nodes while running a full-core reactor benchmark on the Mira Blue Gene/Q supercomputer at the Argonne National Laboratory. In addition, the effects of load imbalances are explored with an updated performance model that is empirically validated against observed timing results. Several load balancing techniques are also implemented to demonstrate that imbalances can be largely mitigated, including a new and efficient way to distribute extra compute resources across coarse domain meshes.
2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE), 2013
ABSTRACT The FLASH code has evolved into a modular and extensible scientific simulation software ... more ABSTRACT The FLASH code has evolved into a modular and extensible scientific simulation software system over the decade of its existence. During this time it has been cumulatively used by over a thousand researchers in several scientific communities (i.e. astrophysics, cosmology, high-energy density physics, turbulence, fluid-structure interactions) to obtain results for research. The code started its life as an amalgamation of two already existing software packages and sections of other codes developed independently by various participating members of the team for other purposes. In the evolution process it has undergone four major revisions, three of which involved a significant architectural advancement. A corresponding evolution of the software process and policies for maintenance occurred simultaneously. The code is currently in its 4.x release with a substantial user community. Recently there has been an upsurge in the contributions by external users; some provide significant new capability. This paper outlines the software development and evolution processes that have contributed to the success of the FLASH code.
Metastatic cancer to the pancreas accounts for less than 2% of all pancreatic malignancies. In co... more Metastatic cancer to the pancreas accounts for less than 2% of all pancreatic malignancies. In contrast to other metastatic tumors, renal cell carcinoma (RCC) has a propensity to metastasize as a solitary pancreatic lesion. While symptomatic patients may present with obstructive jaundice, abdominal pain, or gastrointestinal bleeding, the diagnosis of metastatic pancreatic involvement is often made in asymptomatic patients, during follow-up evaluation in the aftermath of an initial diagnosis of renal cell carcinoma. Microcystic serous cystadenoma of the pancreas is an uncommon pancreatic exocrine neoplasm that morphologically resembles conventional (clear cell) RCC, in so far as both tumors are characterized by neoplastic cells with clear cytoplasm, relatively uniform nuclei and scant associated tumor stroma. Herein, we report 2 immunohistochemically confirmed cases of unsuspected metastatic RCC to the pancreas, with the metastatic tumor in each case confined to a preexisting microcystic serous cystadenoma of the pancreas.
A generalized wavelet-packet based technique for decomposing signals into coherent and non-cohere... more A generalized wavelet-packet based technique for decomposing signals into coherent and non-coherent parts is presented. As a first test, the algorithm is applied to the vorticity field of numerical simulations of weakly decaying two-dimensional turbulence. The coherent vortex structures that emerge in the flow evolution are systematically filtered from the solution. Once extracted, a number of vortex properties are computed and their time evolution is compared with the theoretical predictions of Carnevale et al. (Carnevale et al., Phys. Rev. Lett. 66, 2735, (1991).) Our results compare well with a previous attempt to verify the scaling theory (J. Weiss and J. C. McWilliams, Phys. Fluids A. 5 , 608, (1993).), in which the vortices are extracted from the same data using a complex pattern recognition algorithm (J. C. McWilliams, J. Fluid Mech. 219, 361 (1990).) based exclusively on apriori knowledge of the properties of the vortex structures. The similarity of the results is encouragin...
A code called UNÌC is currently under development at Argonne National Laboratory (ANL). The aim o... more A code called UNÌC is currently under development at Argonne National Laboratory (ANL). The aim of the code is to provide a neutronic solver with the same geometrical flexibility of Monte Carlo codes and without the approximations (homogenization and energy condensation) associated with the common multi-step approach currently used. Moreover, UNÌC will offer the capability of multi-resolution in phase space. At the moment, two methodologies are implemented: a second order spherical harmonics (P N) form of the transport equation and the first order method of characteristics. To improve overall performance (per-processor and scalability to thousands of processors) and reduce memory requirements, we are developing some specialized implementations of key PETSc preconditioners and matrix objects.
SHARP (Simulation-based High-efficiency Advanced Reactor Prototyping) is a modern suite of codes ... more SHARP (Simulation-based High-efficiency Advanced Reactor Prototyping) is a modern suite of codes to simulate the key components of a fast reactor core. The SHARP toolkit is organized as a collection of modules, each representing the key components of the physics to be modeled – neutron transport, thermal hydraulics, fuel/structure behavior – together with pre and post-processing for geometry definition, mesh generation, visualization, user interface, etc. The physics models are designed to make minimal possible use of lumped parameter models, homogenization, and empirical correlations in favor of more direct solution of the fundamental governing equations, when sufficient computing resources are available. Thus, one of the key design goals is to effectively leverage leadership class computing resources – viz. BG/P and Cray Supercomputers that are on the current trajectory to delivering sustained petaflops performance. Further, the nature of the physical problem to be investigated wi...
Type Ia supernovae are thought to be the result of a thermonuclear explosion in a white dwarf tha... more Type Ia supernovae are thought to be the result of a thermonuclear explosion in a white dwarf that is approaching the Chandrasekhar mass limit. The properties of the supernova explosion, including its energy, depends significantly on the way in which the thermonuclear runaway begins. Where in the white dwarf ignition takes place, and how many ignition points there are, are
... Jared C. Roach 1 , Andrew F. Siegel 1, 2 , Ger van den Engh 1 , Barbara Trask 1 and Leroy Hoo... more ... Jared C. Roach 1 , Andrew F. Siegel 1, 2 , Ger van den Engh 1 , Barbara Trask 1 and Leroy Hood 1: The authors are in the Department of Molecular Biotechnology, University of ... We evaluate four BAC selection strategies: mapping, random BAC, limited seeding and parking. ...
Proceedings of IGARSS '94 - 1994 IEEE International Geoscience and Remote Sensing Symposium, 1994
Abstract: During July and August of 1993, a low grazing angle (LOGAN) radar experiment was conduc... more Abstract: During July and August of 1993, a low grazing angle (LOGAN) radar experiment was conducted from the Chesapeake Light Tower which is located on the continental shelf approximately 24 km east of Cape Henry, Virginia. High resolution (0.15 m) and calibrated radar ...
We present tools and methods for checking the consistency of gene and metabolic networks models. ... more We present tools and methods for checking the consistency of gene and metabolic networks models. Qualitative informations on interaction signs and on variations of concentration are collected and used in models of signicant size. Öis approach is based on a mathematical foundation whose hypotheses delimit the applicability.
ABSTRACT There has been considerable interest in recent years in collisionless reconnection dynam... more ABSTRACT There has been considerable interest in recent years in collisionless reconnection dynamics governed by the generalized Ohm's law in which electron inertia provides the mechanism for breaking field lines. It has been suggested in several theoretical studies that the nonlinear reconnection dynamics, to leading order, is independent of the mechanism that breaks field lines (that is, electron inertia). We test this suggestion carefully using the new Magnetic Reconnection Code (MRC) developed at the Center for Magnetic Reconnection Studies. The MRC is a new massively parallel code with Adaptive Mesh Refinement (AMR) that integrates the equations of Hall MHD. The use of AMR enables unprecedented levels of resolution of the current and vorticity layers and uncovers interesting secondary dynamics not seen in previous studies. We apply the MRC to the study of two problems, one involving free reconnection caused by a spontaneous and fast collisionless instability, the other involving forced reconnection induced by boundary perturbations on a stable plasma. In the case of free reconnection, over the range of parameters covered by our simulations, it is shown that the nonlinear reconnection rate is near-explosive, and furthermore, that the nonlinear magnetic island width is an invariant function of a dimensionless variable which is the product of the linear growth rate and time. Now, since the linear growth rate is a function of the ion sound radius as well as the electron skin depth, we conclude that the nonlinear reconnection rate is not independent of electron inertia. In the case of forced reconnection, after a slow growth phase, the dynamics exhibits an impulsive growth in the amplitude of the thin current sheet, and a subsequent current disruption mediated by secondary instabilities. These results, in which electron inertia provides the mechanism for breaking field lines, are contrasted with resistive Hall MHD simulations in which resistivity provides the mechanism for breaking field lines.
Dataset storage, exchange, and access play a critical role in scientific applications. For such p... more Dataset storage, exchange, and access play a critical role in scientific applications. For such purposes netCDF serves as a portable, efficient file format and programming interface, which is popular in numerous scientific application domains. However, the original interface does not provide an efficient mechanism for parallel data storage and access. In this work, we present a new parallel interface for
The objective of this project was to test new coupling algorithms and enable efficient and; scala... more The objective of this project was to test new coupling algorithms and enable efficient and; scalable multi-physics simulations of advanced nuclear reactors, with considerations regarding; the implementation of such algorithms in massively parallel environments. Numerical tests were; carried out to verify the proposed approach and the examples included some reactor transients.; The project was directly related to the Sodium Fast
ABSTRACT Monte Carlo (MC) neutral particle transport codes are considered the gold-standard for n... more ABSTRACT Monte Carlo (MC) neutral particle transport codes are considered the gold-standard for nuclear simulations, but they cannot be robustly applied to high-fidelity nuclear reactor analysis without accommodating several terabytes of materials and tally data. While this is not a large amount of aggregate data for a typical high performance computer, MC methods are only embarrassingly parallel when the key data structures are replicated for each processing element, an approach which is likely infeasible on future machines. The present work explores the use of spatial domain decomposition to make full-scale nuclear reactor simulations tractable with Monte Carlo methods, presenting a simple implementation in a production-scale code. Good performance is achieved for mesh-tallies of up to 2.39TB distributed across 512 compute nodes while running a full-core reactor benchmark on the Mira Blue Gene/Q supercomputer at the Argonne National Laboratory. In addition, the effects of load imbalances are explored with an updated performance model that is empirically validated against observed timing results. Several load balancing techniques are also implemented to demonstrate that imbalances can be largely mitigated, including a new and efficient way to distribute extra compute resources across coarse domain meshes.
2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE), 2013
ABSTRACT The FLASH code has evolved into a modular and extensible scientific simulation software ... more ABSTRACT The FLASH code has evolved into a modular and extensible scientific simulation software system over the decade of its existence. During this time it has been cumulatively used by over a thousand researchers in several scientific communities (i.e. astrophysics, cosmology, high-energy density physics, turbulence, fluid-structure interactions) to obtain results for research. The code started its life as an amalgamation of two already existing software packages and sections of other codes developed independently by various participating members of the team for other purposes. In the evolution process it has undergone four major revisions, three of which involved a significant architectural advancement. A corresponding evolution of the software process and policies for maintenance occurred simultaneously. The code is currently in its 4.x release with a substantial user community. Recently there has been an upsurge in the contributions by external users; some provide significant new capability. This paper outlines the software development and evolution processes that have contributed to the success of the FLASH code.
Metastatic cancer to the pancreas accounts for less than 2% of all pancreatic malignancies. In co... more Metastatic cancer to the pancreas accounts for less than 2% of all pancreatic malignancies. In contrast to other metastatic tumors, renal cell carcinoma (RCC) has a propensity to metastasize as a solitary pancreatic lesion. While symptomatic patients may present with obstructive jaundice, abdominal pain, or gastrointestinal bleeding, the diagnosis of metastatic pancreatic involvement is often made in asymptomatic patients, during follow-up evaluation in the aftermath of an initial diagnosis of renal cell carcinoma. Microcystic serous cystadenoma of the pancreas is an uncommon pancreatic exocrine neoplasm that morphologically resembles conventional (clear cell) RCC, in so far as both tumors are characterized by neoplastic cells with clear cytoplasm, relatively uniform nuclei and scant associated tumor stroma. Herein, we report 2 immunohistochemically confirmed cases of unsuspected metastatic RCC to the pancreas, with the metastatic tumor in each case confined to a preexisting microcystic serous cystadenoma of the pancreas.
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Papers by Andrew Siegel