Modular average case analysis: Language implementation and extension

Motivated by accurate average-case analysis, MOdular Quantitative Analysis (MOQA) is developed at the Centre for Efficiency Oriented Languages (CEOL). In essence, MOQA allows the programmer to determine the average running time of a broad class of programmes directly from the code in a (semi-)automated way. The MOQA approach has the property of randomness preservation which means that applying any operation to a random structure, results in an output isomorphic to one or more random structures, which is key to systematic timing. Based on original MOQA research, we discuss the design and implementation of a new domain specific scripting language based on randomness preserving operations and random structures. It is designed to facilitate compositional timing by systematically tracking the distributions of inputs and outputs. The notion of a labelled partial order (LPO) is the basic data type in the language. The programmer uses built-in MOQA operations together with restricted control flow statements to design MOQA programs. This MOQA language is formally specified both syntactically and semantically in this thesis. A practical language interpreter implementation is provided and discussed. By analysing new algorithms and data restructuring operations, we demonstrate the wide applicability of the MOQA approach. Also we extend MOQA theory to a number of other domains besides average-case analysis. We show the strong connection between MOQA and parallel computing, reversible computing and data entropy analysis.

Different stimuli, different spatial codes: a visual map and an auditory rate code for oculomotor space in the primate superior colliculus.

Maps are a mainstay of visual, somatosensory, and motor coding in many species. However, auditory maps of space have not been reported in the primate brain. Instead, recent studies have suggested that sound location may be encoded via broadly responsive neurons whose firing rates vary roughly proportionately with sound azimuth. Within frontal space, maps and such rate codes involve different response patterns at the level of individual neurons. Maps consist of neurons exhibiting circumscribed receptive fields, whereas rate codes involve open-ended response patterns that peak in the periphery. This coding format discrepancy therefore poses a potential problem for brain regions responsible for representing both visual and auditory information. Here, we investigated the coding of auditory space in the primate superior colliculus(SC), a structure known to contain visual and oculomotor maps for guiding saccades. We report that, for visual stimuli, neurons showed circumscribed receptive fields consistent with a map, but for auditory stimuli, they had open-ended response patterns consistent with a rate or level-of-activity code for location. The discrepant response patterns were not segregated into different neural populations but occurred in the same neurons. We show that a read-out algorithm in which the site and level of SC activity both contribute to the computation of stimulus location is successful at evaluating the discrepant visual and auditory codes, and can account for subtle but systematic differences in the accuracy of auditory compared to visual saccades. This suggests that a given population of neurons can use different codes to support appropriate multimodal behavior.

A tale of three functions: The self-reported uses of autobiographical memory

Theories hold that autobiographical memory serves several broad functions (directive, self, and social). In the current study, items were derived from the theoretical literature to create the Thinking About Life Experiences (TALE) questionnaire to empirically assess these three functions. Participants (N = 167) completed the TALE. To examine convergent validity, they also rated their overall tendency to think about and to talk about the past and completed the Reminiscence Functions Scale (Webster, 1997). The results lend support to the existence of these theoretical functions, but also offer room for refinements in future thinking about both the breadth and specificity of the functions that autobiographical memory serves.

Automatic parallel code generation for message passing on distributed memory systems

The availability of a very accurate dependence graph for a scalar code is the basis for the automatic generation of an efficient parallel implementation. The strategy for this task which is encapsulated in a comprehensive data partitioning code generation algorithm is described. This algorithm involves the data partition, calculation of assignment ranges for partitioned arrays, addition of a comprehensive set of execution control masks, altering loop limits, addition and optimisation of communications for all data. In this context, the development and implementation of strategies to merge communications wherever possible has proved an important feature in producing efficient parallel implementations for numerical mesh based codes. The code generation strategies described here are embedded within the Computer Aided Parallelisation tools (CAPTools) software as a key part of a toolkit for automating as much as possible of the parallelisation process for mesh based numerical codes. The algorithms used enables parallelisation of real computational mechanics codes with only minor user interaction and without any prior manual customisation of the serial code to suit the parallelisation tool.

Integrating user knowledge with information from parallelisation tools to facilitate the automatic generation of efficient parallel FORTRAN code

User supplied knowledge and interaction is a vital component of a toolkit for producing high quality parallel implementations of scalar FORTRAN numerical code. In this paper we consider the necessary components that such a parallelisation toolkit should possess to provide an effective environment to identify, extract and embed user relevant user knowledge. We also examine to what extent these facilities are available in leading parallelisation tools; in particular we discuss how these issues have been addressed in the development of the user interface of the Computer Aided Parallelisation Tools (CAPTools). The CAPTools environment has been designed to enable user exploration, interaction and insertion of user knowledge to facilitate the automatic generation of very efficient parallel code. A key issue in the user's interaction is control of the volume of information so that the user is focused on only that which is needed. User control over the level and extent of information revealed at any phase is supplied using a wide variety of filters. Another issue is the way in which information is communicated. Dependence analysis and its resulting graphs involve a lot of sophisticated rather abstract concepts unlikely to be familiar to most users of parallelising tools. As such, considerable effort has been made to communicate with the user in terms that they will understand. These features, amongst others, and their use in the parallelisation process are described and their effectiveness discussed.

Automatic code generation of overlapped communications in a parallelisation tool

This paper addresses the exploitation of overlapping communication with calculation within parallel FORTRAN 77 codes for computational fluid dynamics (CFD) and computational structured dynamics (CSD). The obvious objective is to overlap interprocessor communication with calculation on each processor in a distributed memory parallel system and so improve the efficiency of the parallel implementation. A general strategy for converting synchronous to overlapped communication is presented together with tools to enable its automatic implementation in FORTRAN 77 codes. This strategy is then implemented within the parallelisation toolkit, CAPTools, to facilitate the automatic generation of parallel code with overlapped communications. The success of these tools are demonstrated on two codes from the NAS-PAR and PERFECT benchmark suites. In each case, the tools produce parallel code with overlapped communications which is as good as that which could be generated manually. The parallel performance of the codes also improve in line with expectation.

An automatable generic strategy for dynamic load balancing in parallel structured mesh CFD codes

Parallel computing is now widely used in numerical simulation, particularly for application codes based on finite difference and finite element methods. A popular and successful technique employed to parallelize such codes onto large distributed memory systems is to partition the mesh into sub-domains that are then allocated to processors. The code then executes in parallel, using the SPMD methodology, with message passing for inter-processor interactions. In order to improve the parallel efficiency of an imbalanced structured mesh CFD code, a new dynamic load balancing (DLB) strategy has been developed in which the processor partition range limits of just one of the partitioned dimensions uses non-coincidental limits, as opposed to coincidental limits. The ‘local’ partition limit change allows greater flexibility in obtaining a balanced load distribution, as the workload increase, or decrease, on a processor is no longer restricted by the ‘global’ (coincidental) limit change. The automatic implementation of this generic DLB strategy within an existing parallel code is presented in this chapter, along with some preliminary results.

Liquid metal turbulent flow dynamics in a cylindrical container with free surface: experiment and numerical analysis

The liquid metal flow in induction crucible models is known to be unstable, turbulent and difficult to predict in the regime of medium frequencies when the electromagnetic skin-layer is of considerable extent. We present long term turbulent flow measurements by a permanent magnet incorporated potential difference velocity probe in a cylindrical container filled with eutectic melt In-Ga-Sn. The parallel numerical simulation of the long time scale development of the turbulent average flow is presented. The numerical flow model uses an implicit pseudo-spectral code and k-w turbulence model, which was recently developed for the transitional flow modelling. The results compare reasonably to the experiment and demonstrate the time development of the turbulent flow field and the turbulence energy.

Liquid metal turbulent flow dynamics in a cylindrical container with free surface: experiment and numerical analysis

The liquid metal flow in inducation crucible models is known to be higly unstable and turbutlen in the regim e of medium frequecies when the elctronmagnetic skin-layer is of considerable extent. We present long term turbulent flow measurements by a permanent magnet incorporated potential difference veolocity probe in a cylindirical container filled with eutecti mlt In-Ga-SN. The parallel numerical simulation of the long time scale development of the turbulen average flow is presented. The numerical lfow model uses a pseud-spectral code and k-w turbulence model, which was recently developed for the transitional flow modelling. The result compare reasonably to the experiment and demonstrate the time development of the turbulent flow field.

SMARTFIRE: an integrated computational fluid dynamics code and expert system for fire field modelling

SMARTFIRE, an open architecture integrated CFD code and knowledge based system attempts to make fire field modeling accessible to non-experts in Computational Fluid Dynamics (CFD) such as fire fighters, architects and fire safety engineers. This is achieved by embedding expert knowledge into CFD software. This enables the 'black-art' associated with the CFD analysis such as selection of solvers, relaxation parameters, convergence criteria, time steps, grid and boundary condition specification to be guided by expert advice from the software. The user is however given the option of overriding these decisions, thus retaining ultimate control. SMARTFIRE also makes use of recent developments in CFD technology such as unstructured meshes and group solvers in order to make the CFD analysis more efficient. This paper describes the incorporation within SMARTFIRE of the expert fire modeling knowledge required for automatic problem setup and mesh generation as well as the concept and use of group solvers for automatic and manual dynamic control of the CFD code.

The Shared Memory Parallelisation of an Ocean Modelling Code using an Interactive Parallelisation Toolkit

This paper briefly describes an interactive parallelisation toolkit that can be used to generate parallel code suitable for either a distributed memory system (using message passing) or a shared memory system (using OpenMP). This study focuses on how the toolkit is used to parallelise a complex heterogeneous ocean modelling code within a few hours for use on a shared memory parallel system. The generated parallel code is essentially the serial code with OpenMP directives added to express the parallelism. The results show that substantial gains in performance can be achieved over the single thread version with very little effort.

SOFT – generating highly flexible object code from XML specifications

Many code generation tools exist to aid developers in carrying out common mappings, such as from Object to XML or from Object to relational database. Such generated code tends to possess a high binding between the Object code and the target mapping, making integration into a broader application tedious or even impossible. In this paper we suggest XML technologies and the multiple inheritance capabilities of interface based languages such as Java, offer a means to unify such executable specifications, thus building complete, consistent and useful object models declaratively, without sacrificing component flexibility.

Using an interactive parallelisation toolkit to parallelise an ocean modelling code

This paper describes an interactive parallelisation toolkit that can be used to generate parallel code suitable for either a distributed memory system (using message passing) or a shared memory system (using OpenMP). This study focuses on how the toolkit is used to parallelise a complex heterogeneous ocean modelling code within a few hours for use on a shared memory parallel system. The generated parallel code is essentially the serial code with OpenMP directives added to express the parallelism. The results show that substantial gains in performance can be achieved over the single thread version with very little effort.

An environment for OpenMP code parallelization

This chapter discusses the code parallelization environment, where a number of tools that address the main tasks, such as code parallelization, debugging, and optimization are available. The parallelization tools include ParaWise and CAPO, which enable the near automatic parallelization of real world scientific application codes for shared and distributed memory-based parallel systems. The chapter discusses the use of ParaWise and CAPO to transform the original serial code into an equivalent parallel code that contains appropriate OpenMP directives. Additionally, as user involvement can introduce errors, a relative debugging tool (P2d2) is also available and can be used to perform near automatic relative debugging of an OpenMP program that has been parallelized either using the tools or manually. In order for these tools to be effective in parallelizing a range of applications, a high quality fully inter-procedural dependence analysis, as well as user interaction is vital to the generation of efficient parallel code and in the optimization of the backtracking and speculation process used in relative debugging. Results of parallelized NASA codes are discussed and show the benefits of using the environment.