Augmented Reality for Urban Simulation Visualization

Visualizations of large simulations are not only computationally intensive but also difficult for the viewer to interpret, due to the huge amount of data to be processed. The case of urban wind flow simulations proves the benefits of mobile Augmented Reality visualizations, both in terms of selection of data relevant to the user and facilitated and comprehensible access to simulation results

Multi-Target Vectorization with MTPS C++ Generic Library

International audienceThis article introduces a C++ template library dedicated at vectorizing algorithms for different target architectures: Multi-Target Parallel Skeleton (MTPS). Skeletons describing the data structures and algorithms are provided and allow MTPS to generate a code with optimized memory access patterns for the choosen architecture. MTPS currently supports x86-64 multicore CPUs and CUDA enabled GPUs. On these architectures, performances close to hardware limits are observed

Center for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasma

The UCLA work on this grant was to design and help implement an object-oriented version of the GTC code, which is written in Fortran90. The GTC code is the main global gyrokinetic code used in this project, and over the years multiple, incompatible versions have evolved. The reason for this effort is to allow multiple authors to work together on GTC and to simplify future enhancements to GTC. The effort was designed to proceed incrementally. Initially, an upper layer of classes (derived types and methods) was implemented which called the original GTC code 'under the hood.' The derived types pointed to data in the original GTC code, and the methods called the original GTC subroutines. The original GTC code was modified only very slightly. This allowed one to define (and refine) a set of classes which described the important features of the GTC code in a new, more abstract way, with a minimum of implementation. Furthermore, classes could be added one at a time, and at the end of the each day, the code continued to work correctly. This work was done in close collaboration with Y. Nishimura from UC Irvine and Stefan Ethier from PPPL. Ten classes were ultimately defined and implemented: gyrokinetic and drift kinetic particles, scalar and vector fields, a mesh, jacobian, FLR, equilibrium, interpolation, and particles species descriptors. In the second state of this development, some of the scaffolding was removed. The constructors in the class objects now allocated the data and the array data in the original GTC code was removed. This isolated the components and now allowed multiple instantiations of the objects to be created, in particular, multiple ion species. Again, the work was done incrementally, one class at a time, so that the code was always working properly. This work was done in close collaboration with Y. Nishimura and W. Zhang from UC Irvine and Stefan Ethier from PPPL. The third stage of this work was to integrate the capabilities of the various versions of the GTC code into one flexible and extensible version. To do this, we developed a methodology to implement Design Patterns in Fortran90. Design Patterns are abstract solutions to generic programming problems, which allow one to handle increased complexity. This work was done in collaboration with Henry Gardner, a computer scientist (and former plasma physicist) from the Australian National University. As an example, the Strategy Pattern is being used in GTC to support multiple solvers. This new code is currently being used in the study of energetic particles. A document describing the evolution of the GTC code to this new object-oriented version is available to users of GTC

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

ComPASS: a tool for distributed parallel finite volume discretizations on general unstructured polyhedral meshes

International audienceThe objective of the ComPASS project is to develop a parallel multiphase Darcy flow simulator adapted to general unstructured polyhedral meshes (in a general sense with possibly non planar faces) and to the parallelization of advanced finite volume discretizations with various choices of the degrees of freedom such as cell centres, vertices, or face centres. The main targeted applications are the simulation of CO2 geological storage, nuclear waste repository and reservoir simulations. The CEMRACS 2012 summer school devoted to high performance computing has been an ideal framework to start this collaborative project. This paper describes what has been achieved during the four weeks of the CEMRACS project which has been focusing on the implementation of basic features of the code such as the distributed unstructured polyhedral mesh, the synchronization of the degrees of freedom, and the connection to scientific libraries including the partitioner METIS, the visualization tool PARAVIEW, and the parallel linear solver library PETSc. The parallel efficiency of this first version of the ComPASS code has been validated on a toy parabolic problem using the Vertex Approximate Gradient finite volume spacial discretization with both cell and vertex degrees of freedom, combined with an Euler implicit time integration

Benchmarking in a rotating annulus: a comparative experimental and numerical study of baroclinic wave dynamics

The differentially heated rotating annulus is a widely studied tabletop-size laboratory model of the general mid-latitude atmospheric circulation. The two most relevant factors of cyclogenesis, namely rotation and meridional temperature gradient are quite well captured in this simple arrangement. The radial temperature difference in the cylindrical tank and its rotation rate can be set so that the isothermal surfaces in the bulk tilt, leading to the formation of baroclinic waves. The signatures of these waves at the free water surface have been analyzed via infrared thermography in a wide range of rotation rates (keeping the radial temperature difference constant) and under different initial conditions. In parallel to the laboratory experiments, five groups of the MetStr\"om collaboration have conducted numerical simulations in the same parameter regime using different approaches and solvers, and applying different initial conditions and perturbations. The experimentally and numerically obtained baroclinic wave patterns have been evaluated and compared in terms of their dominant wave modes, spatio-temporal variance properties and drift rates. Thus certain ``benchmarks'' have been created that can later be used as test cases for atmospheric numerical model validation

Coordination language for distributed clean

The distributed evaluation of functional programs and the communication between computational nodes require high-level process description and coordination mechanism. This paper presents the D-Clean high-level functional language, which supports the distributed computation of Clean functions over a cluster. The lazy functional programming language Clean is extended by new language elements in order to achieve parallel features. The distributed computations of functions are expressed in the form of process-networks. D-Clean introduces language primitives to control the dataflow in a distributed process-network. A process scheme defines a partial computation graph, where the nodes are functions to be evaluated and the edges are communication channels. The computational nodes are implemented as statically typed Clean programs. The schemes are parameterized by functions, types and data for defining process networks. D-Clean is compiled to an intermediate level language called D-Box. The D-Clean generic constructs are instantiated into D-Box expressions. D-Box is designed for the description of the computational nodes. D-Box expressions hide implementation details and enable direct control over the process-network. The asynchronous communication is based on language-independent middleware services. The present paper provides the syntax and the informal semantics of both coordination languages. To illustrate the definition of a distributed functional computational pattern using the D-Clean language a farm skeleton running example is presented