一种基于PVM的并行BP神经网络

通过分析单计算机的BP神经网络学习和执行算法,提出了使用PVM构造多计算机的并行神经网络。该并行神经网络的实现灵活应用于高可靠性和大规模数据的分析和处理中。同时,该BP神经网络的并行设计与实现,可广泛应用于其他神经网络模型的并行计算机实现。

基于PVM的博弈树的网络并行搜索

通过分析博弈理论和α-β剪枝搜索过程,提出了使用PVM构造并行搜索网络。设计和实现了基于PVM的博弈树并行搜索过程。在博弈树搜索中通过构造的并行搜索网络和使用分而治之的策略把搜索过程分布在多个计算机上同时进行,在叶计算机结点的搜索中,通过α-β剪枝技术,剪枝了大量的搜索结点。全局并行搜索和局部剪枝技术的使用,加快了搜索的速度,解决了使用单计算机搜索速度和时间不可行的问题。该博弈并行搜索模型,适用于一般的博弈树搜索问题。

基于PVM的启发式搜索的并行计算模型设计

通过分析人工智能中的A和A*启发式搜索,提出了通过PVM工具包,设计和实现A和A*启发式搜索的并行计算模型。在启发搜索过程中同时进行评估函数计算,使计算的速度加快。解决了在搜索解空间庞大,评估函数计算复杂的情况下,使用单计算机计算速度慢的问题。该文实现了基于PVM的启发式搜索过程,该模型可应用于一般性启发式搜索问题的并行计算模型。

基于移动代理的网格计算系统体系结构研究

本文针对物理链路可靠性低、容错性要求高、实体异构程度高的基础设施网格化需求，在系统分析当前主流的网格体系结构的基础上，研究了移动代理（PVM）系统的特性，根据移动代理的特点，提出了基于移动代理的四层网格计算模型MAGC(Mobile Agent Based Grid Computing)，描述了MAGC模型的层次结构，给出了MAGC模型的一个设计方案，分析了MAGC模型的特点，最后介绍了在Aglet平台下实现的原型系统。本文取得的成果主要包括： 第二章提出了基于移动代理的四层网格计算模型(MAGC)，说明了模型中每个层次的功能和层次之间的依赖关系。MAGC模型基于代码迁移，可以解决网络环境恶劣的条件下，网格系统的运行与部署问题。设计了MAGC模型的两个重要基础结构：作业机制和消息机制。设计了移动代理平台抽象层，使网格系统独立于具体的移动代理平台，从而具有一定的可移植性。 第三章在MAGC模型的基础上，进一步给出了MAGC模型的一个实现方案，阐述了MAGC模型中四个子层的功能和组件划分，对每层所包含的组件和组件实现的功能进行了描述，说明了系统的启动方式。 第四章基于MAGC模型构建了一个原型系统，原型系统以IBM开发的Aglets移动代理软件包为基础，实现了作业机制、消息机制和MAGC模型中的移动代理平台抽象层、系统服务层、API层、应用作业层四个子层。

Computer aided parallelisation tools (CAPTools) — conceptual overview and performance on the parallelisation of structured mesh codes

Computer Aided Parallelisation Tools (CAPTools) is a toolkit designed to automate as much as possible of the process of parallelising scalar FORTRAN 77 codes. The toolkit combines a very powerful dependence analysis together with user supplied knowledge to build an extremely comprehensive and accurate dependence graph. The initial version has been targeted at structured mesh computational mechanics codes (eg. heat transfer, Computational Fluid Dynamics (CFD)) and the associated simple mesh decomposition paradigm is utilised in the automatic code partition, execution control mask generation and communication call insertion. In this, the first of a series of papers [1–3] the authors discuss the parallelisations of a number of case study codes showing how the various component tools may be used to develop a highly efficient parallel implementation in a few hours or days. The details of the parallelisation of the TEAMKE1 CFD code are described together with the results of three other numerical codes. The resulting parallel implementations are then tested on workstation clusters using PVM and an i860-based parallel system showing efficiencies well over 80%.

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.

Interaction of malaria parasites with host late endocytic and autophagic pathways is essential for Plasmodium liver stage development

RESUMO: A Malária é causada por parasitas do género Plasmodium, sendo a doença parasitária mais fatal para o ser humano. Apesar de, durante o século passado, o desenvolvimento económico e a implementação de diversas medidas de controlo, tenham permitido erradicar a doença em muitos países, a Malária continua a ser um problema de saúde grave, em particular nos países em desenvolvimento. A Malária é transmitida através da picada de uma fêmea de mosquito do género Anopheles. Durante a picada, os esporozoítos são injetados na pele do hospedeiro, seguindo-se a fase hepática e obrigatória do ciclo de vida. No fígado, os esporozoítos infetam os hepatócitos onde se replicam, dentro de um vacúolo parasitário (VP) e de uma forma imunitária silenciosa, em centenas de merozoitos. Estas novas formas do parasita são as responsáveis por infetar os eritrócitos, iniciando a fase sanguínea da doença, onde se os primeiros sintomas se manifestam, tais como a característica febre cíclica. A fase hepática da doença é a menos estudada e compreendida. Mais ainda, as interações entre o VP e os organelos da células hospedeira estão ainda pouco caracterizados. Assim, neste estudo, as interações entre os organelos endocíticos e autofágicos da célula hospedeira e o VP foram dissecados, observando-se que os anfisomas, que são organelos resultantes da intersecção do dois processos de tráfego intracelular, interagem com o parasita. Descobrimos que a autofagia tem também uma importante função imunitária durante a fase hepática inicial, ao passo, que durante o desenvolvimento do parasita, já numa fase mais tardia, o parasita depende da interação com os endossomas tardios e anfisomas para crescer. Vesiculas de BSA, EGF e LC3, foram, também, observadas dentro do VP, sugerindo que os parasitas são capazes de internalizar material endocítico e autofágico do hospedeiro. Mais ainda, mostramos que esta interação depende da cinase PIKfyve, responsável pela conversão do fosfoinositidio-3-fosfato no fosfoinositidio-3,5-bifosfato, uma vez que inibindo esta cinase o parasita não é capaz de crescer normalmente. Finalmente, mostramos que a proteína TRPML1, uma proteína efetora do fosfoinositidio-3,5-bifosfato, e envolvida no processo de fusão das membranas dos organelos endocíticos e autofágicos, também é necessária para o crescimento do parasita. Desta forma, o nosso estudo sugere que a membrana do VP funde com vesiculas endocíticas e autofágicas tardias, de uma forma dependente do fositidio-3,5-bifosfato e do seu effetor TRPML1, permitindo a troca de material com a célula hospedeira. Concluindo, os nossos resultados evidenciam que o processo autofágico que ocorre na célula hospedeira tem um papel duplo durante a fase hepática da malaria. Enquanto numa fase inicial os hepatócitos usam o processo autofágico como forma de defesa contra o parasita, já durante a fase de replicação o VP funde com vesiculas autofágicas e endocíticas de forma a obter os nutrientes necessários ao seu desenvolvimento.--------- ABSTRACT: Malaria, which is caused by parasites of the genus Plasmodium, is the most deadly parasitic infection in humans. Although economic development and the implementation of control measures during the last century have erradicated the disease from many areas of the world, it remains a serious human health issue, particularly in developing countries. Malaria is transmitted by female mosquitoes of the genus Anopheles. During the mosquito blood meal, Plasmodium spp. sporozoites are injected into the skin dermis of the vertebrate host, followed by an obligatory liver stage. Upon entering the liver, Plasmodium parasites infect hepatocytes and silently replicate inside a host cell-derived parasitophorous vacuole (PV) into thousands of merozoites. These new parasite forms can infect red blood cells initiating the the blood stage of the disease which shows the characteristic febrile malaria episodes. The liver stage is the least characterized step of the malaria infection. Moreover, the interactions between the Plasmodium spp. PV and the host cell trafficking pathways are poorly understood. We dissected the interaction between Plasmodium parasites and the host cell endocytic and autophagic pathways and we found that both pathways intersect and interconnect in the close vicinity of the parasite PV, where amphisomes are formed and accumulate. Interestingly, we observed a clearance function for autophagy in hepatocytes infected with Plasmodium berghei parasites at early infection times, whereas during late liver stage development late endosomes and amphisomes are required for parasite growth. Moreover, we found the presence of internalized BSA, EGF and LC3 inside parasite vacuoles, suggesting that the parasites uptake endocytic and autophagic cargo. Furthermore, we showed that the interaction between the PV and host traffic pathways is dependent on the kinase PIKfyve, which converts the phosphoinositide PI(3)P into PI(3,5)P2, since PIKfyve inhibition caused a reduction in parasite growth. Finally, we showed that the PI(3,5)P2 effector protein TRPML1, which is involved in late endocytic and autophagic membrane fusion, is also required for parasite development. Thus, our studies suggest that the parasite parasitophorous vacuole membrane (PVM) is able to fuse with late endocytic and autophagic vesicles in a PI(3,5)P2- and TRPML1-dependent manner, allowing the exchange of material between the host cell and the parasites, necessary for the rapid development of the latter that is seen during the liver stage of infection. In conclusion, we present evidence supporting a specific and essential dual role of host autophagy during the course of Plasmodium liver infection. Whereas in the initial hours of infection the host cell uses autophagy as a cell survival mechanism to fight the infection, during the replicative phase the PV fuses with host autophagic and endocytic vesicles to obtain nutrients required for parasite growth.

Observations on the Publicity and Usage of Parallel Programming Systems and Languages: A Survey Approach

In this publication, we report on an online survey that was carried out among parallel programmers. More than 250 people worldwide have submitted answers to our questions, and their responses are analyzed here. Although not statistically sound, the data we provide give useful insights about which parallel programming systems and languages are known and in actual use. For instance, the collected data indicate that for our survey group MPI and (to a lesser extent) C are the most widely used parallel programming system and language, respectively.

GENESIS: an efficient, transparent and easy to use cluster operating system

Present operating systems are not built to support parallel computing––they do not provide services to manage parallelism, i.e., to globally manage parallel processes and computational resources. The cluster operating environments that are used to assist the execution of parallel applications do not provide support for both programming paradigms, message passing (MP) or distributed shared memory (DSM)––they are mainly offered as separate components implemented at the user level as library and independent server processes. Due to poor operating systems users must deal with clusters as a set of independent computers rather than to see this cluster as a single powerful computer. A single system image (SSI) of the cluster is not offered to users. There is a need for an operating system for clusters. We claim and demonstrate in this paper that it is possible to develop a cluster operating system that is able to efficiently manage parallelism; use cluster resources efficiently; support MP in the form of standard MP and PVM, and DSM; offer SSI; and make it easy to use. We show that to achieve these aims this operating system should inherit many features of a distributed operating system and provide new services which address the needs of parallel processes, cluster's resources, and application developers. In order to substantiate the claim the first version of a cluster operating system managing parallelism and offering SSI, called GENESIS, has been developed.

Management of SPMD based parallel processing on clusters of workstations

Current attempts to manage parallel applications on Clusters of Workstations (COWs) have either generally followed the parallel execution environment approach or been extensions to existing network operating systems, both of which do not provide complete or satisfactory solutions. The efficient and transparent management of parallelism within the COW environment requires enhanced methods of process instantiation, mapping of parallel process to workstations, maintenance of process relationships, process communication facilities, and process coordination mechanisms. The aim of this research is to synthesise, design, develop and experimentally study a system capable of efficiently and transparently managing SPMD parallelism on a COW. This system should both improve the performance of SPMD based parallel programs and relieve the programmer from the involvement into parallelism management in order to allow them to concentrate on application programming. It is also the aim of this research to show that such a system, to achieve these objectives, is best achieved by adding new special services and exploiting the existing services of a client/server and microkernel based distributed operating system. To achieve these goals the research methods of the experimental computer science should be employed. In order to specify the scope of this project, this work investigated the issues related to parallel processing on COWs and surveyed a number of relevant systems including PVM, NOW and MOSIX. It was shown that although the MOSIX system provide a number of good services related to parallelism management, none of the system forms a complete solution. The problems identified with these systems include: instantiation services that are not suited to parallel processing; duplication of services between the parallelism management environment and the operating system; and poor levels of transparency. A high performance and transparent system capable of managing the execution of SPMD parallel applications was synthesised and the specific services of process instantiation, process mapping and process interaction detailed. The process instantiation service designed here provides the capability to instantiate parallel processes using either creation or duplication methods and also supports multiple and group based instantiation which is specifically design for SPMD parallel processing. The process mapping service provides the combination of process allocation and dynamic load balancing to ensure the load of a COW remains balanced not only at the time a parallel program is initialised but also during the execution of the program. The process interaction service guarantees to maintain transparently process relationships, communications and coordination services between parallel processes regardless of their location within the COW. The combination of these services provides an original architecture and organisation of a system that is capable of fully managing the execution of SPMD parallel applications on a COW. A logical design of a parallelism management system was developed derived from the synthesised system and was shown that it should ideally be based on a distributed operating system employing the client server model. The client/server based distributed operating system provides the level of transparency, modularity and flexibility necessary for a complete parallelism management system. The services identified in the synthesised system have been mapped to a set of server processes including: Process Instantiation Server providing advanced multiple and group based process creation and duplication; Process Mapping Server combining load collection, process allocation and dynamic load balancing services; and Process Interaction Server providing transparent interprocess communication and coordination. A Process Migration Server was also identified as vital to support both the instantiation and mapping servers. The RHODOS client/server and microkernel based distributed operating system was selected to carry out research into the detailed design and to be used for the implementation this parallelism management system. RHODOS was enhanced to provide the required servers and resulted in the development of the REX Manager, Global Scheduler and Process Migration Manager to provide the services of process instantiation, mapping and migration, respectively. The process interaction services were already provided within RHODOS and only required some extensions to the existing Process Manager and IPC Managers. Through a variety of experiments it was shown that when this system was used to support the execution of SPMD parallel applications the overall execution times were improved, especially when multiple and group based instantiation services are employed. The RHODOS PMS was also shown to greatly reduce the programming burden experienced by users when writing SPMD parallel applications by providing a small set of powerful primitives specially designed to support parallel processing. The system was also shown to be applicable and has been used in a variety of other research areas such as Distributed Shared Memory, Parallelising Compilers and assisting the port of PVM to the RHODOS system. The RHODOS Parallelism Management System (PMS) provides a unique and creative solution to the problem of transparently and efficiently controlling the execution of SPMD parallel applications on COWs. Combining advanced services such as multiple and group based process creation and duplication; combined process allocation and dynamic load balancing; and complete COW wide transparency produces a totally new system that addresses many of the problems not addressed in other systems.

Parallel matrix inversion techniques

In this paper, we present techniques for inverting sparse, symmetric and positive definite matrices on parallel and distributed computers. We propose two algorithms, one for SIMD implementation and the other for MIMD implementation. These algorithms are modified versions of Gaussian elimination and they take into account the sparseness of the matrix. Our algorithms perform better than the general parallel Gaussian elimination algorithm. In order to demonstrate the usefulness of our technique, we implemented the snake problem using our sparse matrix algorithm. Our studies reveal that the proposed sparse matrix inversion algorithm significantly reduces the time taken for obtaining the solution of the snake problem. In this paper, we present the results of our experimental work.

A Common-feature approach for testing present-value restrictions with financial data

It is well known that cointegration between the level of two variables (labeled Yt and yt in this paper) is a necessary condition to assess the empirical validity of a present-value model (PV and PVM, respectively, hereafter) linking them. The work on cointegration has been so prevalent that it is often overlooked that another necessary condition for the PVM to hold is that the forecast error entailed by the model is orthogonal to the past. The basis of this result is the use of rational expectations in forecasting future values of variables in the PVM. If this condition fails, the present-value equation will not be valid, since it will contain an additional term capturing the (non-zero) conditional expected value of future error terms. Our article has a few novel contributions, but two stand out. First, in testing for PVMs, we advise to split the restrictions implied by PV relationships into orthogonality conditions (or reduced rank restrictions) before additional tests on the value of parameters. We show that PV relationships entail a weak-form common feature relationship as in Hecq, Palm, and Urbain (2006) and in Athanasopoulos, Guillén, Issler and Vahid (2011) and also a polynomial serial-correlation common feature relationship as in Cubadda and Hecq (2001), which represent restrictions on dynamic models which allow several tests for the existence of PV relationships to be used. Because these relationships occur mostly with nancial data, we propose tests based on generalized method of moment (GMM) estimates, where it is straightforward to propose robust tests in the presence of heteroskedasticity. We also propose a robust Wald test developed to investigate the presence of reduced rank models. Their performance is evaluated in a Monte-Carlo exercise. Second, in the context of asset pricing, we propose applying a permanent-transitory (PT) decomposition based on Beveridge and Nelson (1981), which focus on extracting the long-run component of asset prices, a key concept in modern nancial theory as discussed in Alvarez and Jermann (2005), Hansen and Scheinkman (2009), and Nieuwerburgh, Lustig, Verdelhan (2010). Here again we can exploit the results developed in the common cycle literature to easily extract permament and transitory components under both long and also short-run restrictions. The techniques discussed herein are applied to long span annual data on long- and short-term interest rates and on price and dividend for the U.S. economy. In both applications we do not reject the existence of a common cyclical feature vector linking these two series. Extracting the long-run component shows the usefulness of our approach and highlights the presence of asset-pricing bubbles.

Forecasting multivariate time series under present-value-model short- and long-run co-movement restrictions

It is well known that cointegration between the level of two variables (e.g. prices and dividends) is a necessary condition to assess the empirical validity of a present-value model (PVM) linking them. The work on cointegration,namelyon long-run co-movements, has been so prevalent that it is often over-looked that another necessary condition for the PVM to hold is that the forecast error entailed by the model is orthogonal to the past. This amounts to investigate whether short-run co-movememts steming from common cyclical feature restrictions are also present in such a system. In this paper we test for the presence of such co-movement on long- and short-term interest rates and on price and dividend for the U.S. economy. We focuss on the potential improvement in forecasting accuracies when imposing those two types of restrictions coming from economic theory.

Forecasting Multivariate Time Series under Present-Value-Model Short- and Long-run Co-movement Restrictions

This paper has two original contributions. First, we show that the present value model (PVM hereafter), which has a wide application in macroeconomics and fi nance, entails common cyclical feature restrictions in the dynamics of the vector error-correction representation (Vahid and Engle, 1993); something that has been already investigated in that VECM context by Johansen and Swensen (1999, 2011) but has not been discussed before with this new emphasis. We also provide the present value reduced rank constraints to be tested within the log-linear model. Our second contribution relates to forecasting time series that are subject to those long and short-run reduced rank restrictions. The reason why appropriate common cyclical feature restrictions might improve forecasting is because it finds natural exclusion restrictions preventing the estimation of useless parameters, which would otherwise contribute to the increase of forecast variance with no expected reduction in bias. We applied the techniques discussed in this paper to data known to be subject to present value restrictions, i.e. the online series maintained and up-dated by Shiller. We focus on three different data sets. The fi rst includes the levels of interest rates with long and short maturities, the second includes the level of real price and dividend for the S&P composite index, and the third includes the logarithmic transformation of prices and dividends. Our exhaustive investigation of several different multivariate models reveals that better forecasts can be achieved when restrictions are applied to them. Moreover, imposing short-run restrictions produce forecast winners 70% of the time for target variables of PVMs and 63.33% of the time when all variables in the system are considered.