Portability, predictability and performance for parallel computing: BSP in practice

We report on practical experience using the Oxford BSP Library to parallelize a large electromagnetic code, the British Aerospace finite-difference time-domain code EMMA T:FD3D. The Oxford BS Library is one of the first realizations of the Bulk Synchronous Parallel computational model to be targeted at numerically intensive scientific (typically Fortran) computing. The BAe EMMA code is one of the first large-scale applications to be parallelized using this library, and it is an important demonstration of the cost effectiveness of the BSP approach. We illustrate how BSP cost-modelling techniques can be used to predict and optimize performance for single-source programs across different parallel platforms. We provide predicted and observed performance figures for an industrial-strength, single-source parallel code for a variety of real parallel architectures: shared memory multiprocessors, workstation clusters and massively parallel platforms.

CAPLib - A 'thin layer' message passing library to support computational mechanics codes on distributed memory parallel systems

The Computer Aided Parallelisation Tools (CAPTools) [Ierotheou, C, Johnson SP, Cross M, Leggett PF, Computer aided parallelisation tools (CAPTools)-conceptual overview and performance on the parallelisation of structured mesh codes, Parallel Computing, 1996;22:163±195] is a set of interactive tools aimed to provide automatic parallelisation of serial FORTRAN Computational Mechanics (CM) programs. CAPTools analyses the user's serial code and then through stages of array partitioning, mask and communication calculation, generates parallel SPMD (Single Program Multiple Data) messages passing FORTRAN. The parallel code generated by CAPTools contains calls to a collection of routines that form the CAPTools communications Library (CAPLib). The library provides a portable layer and user friendly abstraction over the underlying parallel environment. CAPLib contains optimised message passing routines for data exchange between parallel processes and other utility routines for parallel execution control, initialisation and debugging. By compiling and linking with different implementations of the library, the user is able to run on many different parallel environments. Even with today's parallel systems the concept of a single version of a parallel application code is more of an aspiration than a reality. However for CM codes the data partitioning SPMD paradigm requires a relatively small set of message-passing communication calls. This set can be implemented as an intermediate `thin layer' library of message-passing calls that enables the parallel code (especially that generated automatically by a parallelisation tool such as CAPTools) to be as generic as possible. CAPLib is just such a `thin layer' message passing library that supports parallel CM codes, by mapping generic calls onto machine specific libraries (such as CRAY SHMEM) and portable general purpose libraries (such as PVM an MPI). This paper describe CAPLib together with its three perceived advantages over other routes: - as a high level abstraction, it is both easy to understand (especially when generated automatically by tools) and to implement by hand, for the CM community (who are not generally parallel computing specialists); - the one parallel version of the application code is truly generic and portable; - the parallel application can readily utilise whatever message passing libraries on a given machine yield optimum performance.

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.

Parallel mesh partitioning on distributed memory systems

The problem of deriving parallel mesh partitioning algorithms for mapping unstructured meshes to parallel computers is discussed in this chapter. In itself this raises a paradox - we seek to find a high quality partition of the mesh, but to compute it in parallel we require a partition of the mesh. In fact, we overcome this difficulty by deriving an optimisation strategy which can find a high quality partition even if the quality of the initial partition is very poor and then use a crude distribution scheme for the initial partition. The basis of this strategy is to use a multilevel approach combined with local refinement algorithms. Three such refinement algorithms are outlined and some example results presented which show that they can produce very high global quality partitions, very rapidly. The results are also compared with a similar multilevel serial partitioner and shown to be almost identical in quality. Finally we consider the impact of the initial partition on the results and demonstrate that the final partition quality is, modulo a certain amount of noise, independent of the initial partition.

Spank performance tour [at National Review of Live Art 2008]

Spank is a duet about two women’s journeys as they play out different roles. One woman recalls stinging anecdotes marked by intimacy, jealousy, fear and fantasy from her childhood in the 70s suburbs – round the corner from where Mike Leigh would film Life Is Sweet. Her Double (projected on screen) reads from a newspaper about an event that punctured the local community, creating an enduring cultural scar, her voice lacking emotion. Both women must eventually face one another and ask, who is deceiving whom? The consequences of guilt and shame and the unstable shift from private memory to public consequence is inevitable and deadly.[ABSTRACT BY THE AUTHOR]

Effect of chronic angiotensin converting enzyme inhibition on spatial memory and anxiety-like behavours in rats

Angiotensin converting enzyme inhibitors (ACEis) are widely used anti-hypertensive agents that are also reported to have positive effects on mood and cognition. The present study examined the influence of the ACEi, perindopril, on cognitive performance and anxiety measures in rats. Two groups of rats were treated orally for one week with the ACEi, perindopril, at doses of 0.1 and 1.0mg/kg/day. Learning was assessed by the reference memory task in the water maze, comparing treated to control rats. Over five training days both perindopril-treated groups learnt the location of the submerged platform in the water maze task significantly faster than control rats. A 60s probe trial on day 6 showed that the 1.0mg/kg/day group spent significantly longer time in the training quadrant than control rats. This improved performance in the swim maze task was not due to the effect of perindopril on motor activity or the anxiety levels of the rats as perindopril-treated and control animals behaved similarly in activity boxes and on the elevated+maze. These results confirm the anecdotal human studies that ACEis have a positive influence on cognition and provide possibilities for ACEis to be developed into therapies for memory loss.

An orally available compound prevents deficits in memory caused by the Alzheimer amyloid-B oligomers.

Despite progress in defining a pathogenic role for amyloid beta protein (Abeta) in Alzheimer's disease, orally bioavailable compounds that prevent its effects on hippocampal synaptic plasticity and cognitive function have not yet emerged. A particularly attractive therapeutic strategy is to selectively neutralize small, soluble Abeta oligomers that have recently been shown to mediate synaptic dysfunction. METHODS: Using electrophysiological, biochemical, and behavioral assays, we studied how scyllo-inositol (AZD-103; molecular weight, 180) neutralizes the acutely toxic effects of Abeta on synaptic function and memory recall. RESULTS: Scyllo-inositol, but not its stereoisomer, chiro-inositol, dose-dependently rescued long-term potentiation in mouse hippocampus from the inhibitory effects of soluble oligomers of cell-derived human Abeta. Cerebroventricular injection into rats of the soluble Abeta oligomers interfered with learned performance on a complex lever-pressing task, but administration of scyllo-inositol via the drinking water fully prevented oligomer-induced errors. INTERPRETATION: A small, orally available natural product penetrates into the brain in vivo to rescue the memory impairment produced by soluble Abeta oligomers through a mechanism that restores hippocampal synaptic plasticity.

Gender influences the detection of spatial working memory deficits in bipolar disorder.

Objective: Despite evidence that gender may influence neurocognitive functioning, few studies have examined its effects in bipolar disorder (BD) a priori. The aim of this study was to examine how gender influences executive-type functions, which are potentially useful as endophenotypes for BD. Methods: The performance of 26 euthymic patients(12 males, 14 females) with DSM-IV BD (20 BD type I and six BD type II) was compared to that of 26 controls (12 males, 14 females) on tests of executive function. Controls were matched to patients on an individual basis for sex, age and premorbid IQ. Tests assessed spatial working memory (SWM), planning, attentional set-shifting and verbal fluency. Results: Overall, patients showed deficits in SWM strategy (p < 0.001) and made more SWM errors relative to controls (p < 0.001). These deficits were more apparent in male-only comparisons (both p < 0.001) than in female-only comparisons (both p < 0.05). When examined in isolation, male controls were significantly better at performing the SWM task than female controls (both p < 0.05). This pattern was not observed in the patient cohort: male patients had poorer strategy scores than female patients (p < 0.05), but made a similar number of SWM errors. Conclusions: These findings provide evidence that gender can influence the detection of SWM deficits in the euthymic phase of BD, as the sex-related disequilibrium in SWM identified in healthy controls was disrupted in BD. © 2008 The Authors Journal compilation © 2008 Blackwell Munksgaard.

The Association Between Childhood Trauma and Memory Functioning in Schizophrenia

Objective: Both neurocognitive impairments and a history of childhood abuse are highly prevalent in patients with schizophrenia. Childhood trauma has been associated with memory impairment as well as hippocampal volume reduction in adult survivors. The aim of the following study was to examine the contribution of childhood adversity to verbal memory functioning in people with schizophrenia. Methods: Eighty-five outpatients with a Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) diagnosis of chronic schizophrenia were separated into 2 groups on the basis of self-reports of childhood trauma. Performance on measures of episodic narrative memory, list learning, and working memory was then compared using multivariate analysis of covariance. Results: Thirty-eight (45%) participants reported moderate to severe levels of childhood adversity, while 47 (55%) reported no or low levels of childhood adversity. After controlling for premorbid IQ and current depressive symptoms, the childhood trauma group had significantly poorer working memory and episodic narrative memory. However, list learning was similar between groups. Conclusion: Childhood trauma is an important variable that can contribute to specific ongoing memory impairments in schizophrenia.

Apolipoprotein epsilon4 and neuropsychological performance in Alzheimer's disease and vascular dementia

The apolipoprotein (APOE) epsilon4 allele is a genetic risk factor for the development of Alzheimer's disease (AD). It has also been associated with vascular dementia (VaD) in some but not all studies. Previous studies have examined the role of APOE in predicting performance on cognitive tests in both demented and non-demented populations. In cognitively intact individuals, statistically significant group differences between APOE epsilon4 carriers and non-carriers have been demonstrated for several cognitive domains. In AD studies of the impact of APOE epsilon4 on cognition have been conflicting while no previous study has assessed cognition and impact of APOE epsilon4 in VaD. In this study we investigated the impact of APOE epsilon4 on performance in neuropsychological tests including information processing speed in patients with mild-moderate AD and VaD. We incorporated both computerized and pen and paper tests to ensure a sensitive method of assessing cognition. 109 patients participated in the study (VaD=41, AD=68). Neurocognitive performance of 44 epsilon4 present AD patients was compared to 24 epsilon4absent patients and performance of 23 epsilon4 present VaD patients was compared to 18 epsilon4 absent patients. There was evidence that APOE epsilon4 conferred a risk of poorer cognitive functioning in both patient groups. In the AD group presence of epsilon4 conferred a negative impact on some measures of speed of information processing and immediate recall while in the VaD group epsilon4 present patients had evidence of poorer accuracy on tasks such as choice reaction time and spatial working memory. In AD and VaD groups epsilon4 present patients showed impairment in selective attention. These findings provide further support of the negative impact of the epsilon4 allele in cognition.

Sensory systems and spatial memory in the fruit bat Rousettus aegyptiacus

The megachiropteran fruit bat Rousettus aegyptiacus is able to orient and navigate using both vision and echolocation. These two sensory systems have different environmental constraints however, echolocation being relatively short range when compared with vision. Despite this difference, an experiment testing their memory of a perch location demonstrates that once the location of a perch is learned R. aegyptiacus is not influenced by the movement of local landmark cues in the vicinity of the perch under either light or dark conditions. Thus despite the differing constraints of vision and echolocation, this suggests a place is remembered as a location in space and not by associations with landmarks in the vicinity. A decrease in initial performance when the task was repeated in the dark suggested the possibility that a memory of a location learned using vision does not generalize to echolocation.

Working Memory and Postural Control: Adult Age Differences in Potential for Improvement, Task Priority, and Dual Tasking

We investigate dynamic posture control and working memory (NBack) retest practice in young and older adults, focusing on older adults' potential for improvement in the component tasks but more importantly in dual-task performance. Participants performed the 2 tasks in 11 sessions under single- and dual-task conditions. Posture improvement was observed with retest practice for both groups. Increase in cognitive load after initial practice led to greater dual-task costs in both tasks in older adults and higher costs in memory in young adults. With continued practice, costs were reduced by both groups; however, the 2 groups focused improvement on different tasks: Older adults focused on posture but young adults on cognition. These results emphasize older adults' potential for improvement in dual-task performance and their flexibility to utilize the practice gains in posture to optimize cognitive performance.

Position control of shape memory alloy actuators using self tuning fuzzy PID controller

Shape Memory Alloy (SMA) actuators, which have the ability to return to a predetermined shape when heated, have many potential applications such as aeronautics, surgical tools, robotics and so on. Although the conventional PID controller can be used with slow response systems, there has been limited success in precise motion control of SMA actuators, since the systems are disturbed by unknown factors beside their inherent nonlinear hysteresis and changes in the surrounding environment of the systems. This paper presents a new development of a SMA position control system by using a self-tuning fuzzy PID controller. This control algorithm is used by tuning the parameters of the PID controller thereby integrating fuzzy inference and producing a fuzzy adaptive PID controller, which can then be used to improve the control performance of nonlinear systems. The experimental results of position control of SMA actuators using conventional and self-tuning fuzzy PID controllers are both included in this paper.

Internal model control for shape memory alloy actuators using fuzzy based Preisach model

This paper investigates a possible application of Preisach model to control shape memory alloy (SMA) actuators using an internal model control strategy. The developed strategy consists in including the Preisach hysteresis model of SMA actuator and the inverse Preisach model within the control structure. In this work, an extrema input hystory and a fuzzy inference is utilized to replace the classical Preisach model. This allows to reduce a large amount of experimental parameters and computation time of the classical Preisach model. To demonstrate the effectiveness of the proposed controller in improving control performance and hysteresis compensation of SMA actuators, experimental results from real time control are presented.