An Extensible Timing Infrastructure for Adaptive Large-scale Applications

Real-time access to accurate and reliable timing information is necessary to profile scientific applications, and crucial as simulations become increasingly complex, adaptive, and large-scale. The Cactus Framework provides flexible and extensible capabilities for timing information through a well designed infrastructure and timing API. Applications built with Cactus automatically gain access to built-in timers, such as gettimeofday and getrusage, system-specific hardware clocks, and high-level interfaces such as PAPI. We describe the Cactus timer interface, its motivation, and its implementation. We then demonstrate how this timing information can be used by an example scientific application to profile itself, and to dynamically adapt itself to a changing environment at run time

From Tensor Equations to Numerical Code -- Computer Algebra Tools for Numerical Relativity

In this paper we present our recent work in developing a computer-algebra tool for systems of partial differential equations (PDEs), termed "Kranc". Our work is motivated by the problem of finding solutions of the Einstein equations through numerical simulations. Kranc consists of Mathematica based computer-algebra packages, that facilitate the task of dealing with symbolic tensorial calculations and realize the conversion of systems of partial differential evolution equations into parallelized C or Fortran code.Comment: LaTeX llncs style, 9 pages, 1 figure, to appaer in the proceedings of "SYNASC 2004 - 6th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing", Timisoara, Romania, September 26-30 200

From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization is based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.Comment: 18 pages, 4 figures, accepted for publication in Scientific Programmin

AstroGrid-D: Grid Technology for Astronomical Science

We present status and results of AstroGrid-D, a joint effort of astrophysicists and computer scientists to employ grid technology for scientific applications. AstroGrid-D provides access to a network of distributed machines with a set of commands as well as software interfaces. It allows simple use of computer and storage facilities and to schedule or monitor compute tasks and data management. It is based on the Globus Toolkit middleware (GT4). Chapter 1 describes the context which led to the demand for advanced software solutions in Astrophysics, and we state the goals of the project. We then present characteristic astrophysical applications that have been implemented on AstroGrid-D in chapter 2. We describe simulations of different complexity, compute-intensive calculations running on multiple sites, and advanced applications for specific scientific purposes, such as a connection to robotic telescopes. We can show from these examples how grid execution improves e.g. the scientific workflow. Chapter 3 explains the software tools and services that we adapted or newly developed. Section 3.1 is focused on the administrative aspects of the infrastructure, to manage users and monitor activity. Section 3.2 characterises the central components of our architecture: The AstroGrid-D information service to collect and store metadata, a file management system, the data management system, and a job manager for automatic submission of compute tasks. We summarise the successfully established infrastructure in chapter 4, concluding with our future plans to establish AstroGrid-D as a platform of modern e-Astronomy.Comment: 14 pages, 12 figures Subjects: data analysis, image processing, robotic telescopes, simulations, grid. Accepted for publication in New Astronom

A Massive Data Parallel Computational Framework for Petascale/Exascale Hybrid Computer Systems

Heterogeneous systems are becoming more common on High Performance Computing (HPC) systems. Even using tools like CUDA and OpenCL it is a non-trivial task to obtain optimal performance on the GPU. Approaches to simplifying this task include Merge (a library based framework for heterogeneous multi-core systems), Zippy (a framework for parallel execution of codes on multiple GPUs), BSGP (a new programming language for general purpose computation on the GPU) and CUDA-lite (an enhancement to CUDA that transforms code based on annotations). In addition, efforts are underway to improve compiler tools for automatic parallelization and optimization of affine loop nests for GPUs and for automatic translation of OpenMP parallelized codes to CUDA. In this paper we present an alternative approach: a new computational framework for the development of massively data parallel scientific codes applications suitable for use on such petascale/exascale hybrid systems built upon the highly scalable Cactus framework. As the first non-trivial demonstration of its usefulness, we successfully developed a new 3D CFD code that achieves improved performance.Comment: Parallel Computing 2011 (ParCo2011), 30 August -- 2 September 2011, Ghent, Belgiu

Numerical Relativity As A Tool For Computational Astrophysics

The astrophysics of compact objects, which requires Einstein's theory of general relativity for understanding phenomena such as black holes and neutron stars, is attracting increasing attention. In general relativity, gravity is governed by an extremely complex set of coupled, nonlinear, hyperbolic-elliptic partial differential equations. The largest parallel supercomputers are finally approaching the speed and memory required to solve the complete set of Einstein's equations for the first time since they were written over 80 years ago, allowing one to attempt full 3D simulations of such exciting events as colliding black holes and neutron stars. In this paper we review the computational effort in this direction, and discuss a new 3D multi-purpose parallel code called ``Cactus'' for general relativistic astrophysics. Directions for further work are indicated where appropriate.Comment: Review for JCA