Programmer friendly and efficient distributed shared memory integrated into a distributed operating system

Distributed Shared Memory (DSM) provides programmers with a shared memory environment in systems where memory is not physically shared. Clusters of Workstations (COWs), an often untapped source of computing power, are characterised by a very low cost/performance ratio. The combination of Clusters of Workstations (COWs) with DSM provides an environment in which the programmer can use the well known approaches and methods of programming for physically shared memory systems and parallel processing can be carried out to make full use of the computing power and cost advantages of the COW. The aim of this research is to synthesise and develop a distributed shared memory system as an integral part of an operating system in order to provide application programmers with a convenient environment in which the development and execution of parallel applications can be done easily and efficiently, and which does this in a transparent manner. Furthermore, in order to satisfy our challenging design requirements we want to demonstrate that the operating system into which the DSM system is integrated should be a distributed operating system. In this thesis a study into the synthesis of a DSM system within a microkernel and client-server based distributed operating system which uses both strict and weak consistency models, with a write-invalidate and write-update based approach for consistency maintenance is reported. Furthermore a unique automatic initialisation system which allows the programmer to start the parallel execution of a group of processes with a single library call is reported. The number and location of these processes are determined by the operating system based on system load information. The DSM system proposed has a novel approach in that it provides programmers with a complete programming environment in which they are easily able to develop and run their code or indeed run existing shared memory code. A set of demanding DSM system design requirements are presented and the incentives for the placement of the DSM system with a distributed operating system and in particular in the memory management server have been reported. The new DSM system concentrated on an event-driven set of cooperating and distributed entities, and a detailed description of the events and reactions to these events that make up the operation of the DSM system is then presented. This is followed by a pseudocode form of the detailed design of the main modules and activities of the primitives used in the proposed DSM system. Quantitative results of performance tests and qualitative results showing the ease of programming and use of the RHODOS DSM system are reported. A study of five different application is given and the results of tests carried out on these applications together with a discussion of the results are given. A discussion of how RHODOS’ DSM allows programmers to write shared memory code in an easy to use and familiar environment and a comparative evaluation of RHODOS DSM with other DSM systems is presented. In particular, the ease of use and transparency of the DSM system have been demonstrated through the description of the ease with which a moderately inexperienced undergraduate programmer was able to convert, write and run applications for the testing of the DSM system. Furthermore, the description of the tests performed using physically shared memory shows that the latter is indistinguishable from distributed shared memory; this is further evidence that the DSM system is fully transparent. This study clearly demonstrates that the aim of the research has been achieved; it is possible to develop a programmer friendly and efficient DSM system fully integrated within a distributed operating system. It is clear from this research that client-server and microkernel based distributed operating system integrated DSM makes shared memory operations transparent and almost completely removes the involvement of the programmer beyond classical activities needed to deal with shared memory. The conclusion can be drawn that DSM, when implemented within a client-server and microkernel based distributed operating system, is one of the most encouraging approaches to parallel processing since it guarantees performance improvements with minimal programmer involvement

A new purple sulfur bacterium from saline littoral sediments, Thiorhodotvibrio winogradskyi gen. nov. and sp. nov.

Two strains of a new purple sulfur bacterium were isolated in pure culture from the littoral sediment of a saline lake (Mahoney Lake, Canada) and a marine microbial mat from the North Sea island of Mellum, respectively. Single cells were vibrioid-to spirilloid-shaped and motile by means of single polar flagella. Intracellular photosynthetic membranes were of the vesicular type. As photosynthetic pigments, bacteriochlorophyll a and the carotenoids lycopene, rhodopin, anhydrorhodovibrin, rhodovibrin and spirilloxanthin were present. Hydrogen sulfide and elemental sulfur were used under anoxic conditions for phototrophic growth. In addition one strain (06511) used thiosulfate. Carbon dioxide, acetate and pyruvate were utilized by both strains as carbon sources. Depending on the strain propionate, succinate, fumarate, malate, tartrate, malonate, glycerol or peptone may additionally serve as carbon sources in the light. Optimum growth rates were obtained at pH 7.2, 33 °C, 50 mol m-2 s-1 intensity of daylight fluorescent tubes and a salinity of 2.2–3.2% NaCl. During growth on sulfide, up to ten small sulfur globules were formed inside the cells. The strains grew microaerophilic in the dark and exhibited high specific respiration rates. No vitamins were required for growth. The DNA base composition was 61.0–62.4 mol% G+C. The newly isolated bacterium belongs to the family chromatiaceae and is described as a member of a new genus and species, Thiorhodovibrio winogradskyi gen. nov. and sp. nov. with the type strain SSP1, DSM No. 6702

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

Experimental study of radiative shocks at PALS facility

We report on the investigation of strong radiative shocks generated with the high energy, sub-nanosecond iodine laser at PALS. These shock waves are characterized by a developed radiative precursor and their dynamics is analyzed over long time scales (~50 ns), approaching a quasi-stationary limit. We present the first preliminary results on the rear side XUV spectroscopy. These studies are relevant to the understanding of the spectroscopic signatures of accretion shocks in Classical T Tauri Stars.Comment: 21 pages, 1 table, 7 figure

Automated parallel application creation and execution tool for clusters

This research investigated an automated approach to re-writing traditional sequential computer programs into parallel programs for networked computers. A tool was designed and developed for generating parallel programs automatically and also executing these parallel programs on a network of computers. Performance is maximized by utilising all idle resources

Single system image: A survey

Single system image is a computing paradigm where a number of distributed computing resources are aggregated and presented via an interface that maintains the illusion of interaction with a single system. This approach encompasses decades of research using a broad variety of techniques at varying levels of abstraction, from custom hardware and distributed hypervisors to specialized operating system kernels and user-level tools. Existing classification schemes for SSI technologies are reviewed, and an updated classification scheme is proposed. A survey of implementation techniques is provided along with relevant examples. Notable deployments are examined and insights gained from hands-on experience are summarized. Issues affecting the adoption of kernel-level SSI are identified and discussed in the context of technology adoption literature

Enhanced biosurfactant production through cloning of three genes and role of esterase in biosurfactant release

<p>Abstract</p> <p>Background</p> <p>Biosurfactants have been reported to utilize a number of immiscible substrates and thereby facilitate the biodegradation of panoply of polyaromatic hydrocarbons. Olive oil is one such carbon source which has been explored by many researchers. However, studying the concomitant production of biosurfactant and esterase enzyme in the presence of olive oil in the <it>Bacillus </it>species and its recombinants is a relatively novel approach.</p> <p>Results</p> <p><it>Bacillus </it>species isolated from endosulfan sprayed cashew plantation soil was cultivated on a number of hydrophobic substrates. Olive oil was found to be the best inducer of biosurfactant activity. The protein associated with the release of the biosurfactant was found to be an esterase. There was a twofold increase in the biosurfactant and esterase activities after the successful cloning of the biosurfactant genes from <it>Bacillus subtilis </it>SK320 into <it>E.coli. </it>Multiple sequence alignment showed regions of similarity and conserved sequences between biosurfactant and esterase genes, further confirming the symbiotic correlation between the two. Biosurfactants produced by <it>Bacillus subtilis </it>SK320 and recombinant strains <it>BioS a, BioS b, BioS c </it>were found to be effective emulsifiers, reducing the surface tension of water from 72 dynes/cm to as low as 30.7 dynes/cm.</p> <p>Conclusion</p> <p>The attributes of enhanced biosurfactant and esterase production by hyper-producing recombinant strains have many utilities from industrial viewpoint. This study for the first time has shown a possible association between biosurfactant production and esterase activity in any <it>Bacillus </it>species. Biosurfactant-esterase complex has been found to have powerful emulsification properties, which shows promising bioremediation, hydrocarbon biodegradation and pharmaceutical applications.</p

Architektur vernetzter Systeme. Seminar SS 1996 & WS 1996/97

Der vorliegende Interne Bericht enthält die Beiträge von Studenten zum Seminar "Architektur vernetzter Systeme", das im Sommersemester 1996 und im Wintersemester 1996/97 am Institut für Telematik der Universität Karlsruhe stattgefunden hat. Themen waren dabei Replikationsverfahren im Mobilumfeld sowie Dienste und Konzepte in verteilten Systemen als auch alternative Ansätze wie Memory-Consictency-Modelle

Caracterização genômica (taxonomia e simbiose) e fenotípica (controle biológico de fitopatógenos) de bactérias isoladas de feijoeiro da Coleção SEMIA : revisão taxonômica da Ordem Rhizobiales (Hyphomicrobiales)

A Coleção SEMIA existe oficialmente desde 1975 e é referência internacional na área de inoculantes. Essa coleção mantém mais de 1.200 estirpes de bactérias isoladas de nódulos de 171 leguminosas de importância agrícola, das quais 98 são recomendadas para o uso em inoculantes. Grande parte da Coleção SEMIA foi identificada utilizando características bioquímicas, PCR baseada em elementos repetitivos, identificações sorológicas e de planta hospedeira, e, menor número, o sequenciamento parcial do gene do 16S rRNA. Entretanto, ainda faltam informações taxonômicas das estirpes SEMIA, com base nos métodos moleculares baseados em análise de genomas aceitos atualmente. Em vista disso, o presente trabalho se propôs a i) elucidar o potencial das estirpes SEMIA para o controle biológico de fungos patogênicos e ii) resolver problemas de taxonomia dentro da Coleção SEMIA e da própria ordem Rhizobiales (Hyphomicrobiales). O capítulo I, “Rhizobia for biological control of plant diseases”, é uma revisão sobre os mecanismos empregados para a eficácia dos rizóbios no biocontrole de doenças causadas por diferentes classes de fitopatógenos. O capítulo II, intitulado “Rhizobium strains in the biological control of the phytopathogenic fungi Sclerotium (Athelia) rolfsii on the common bean” é um artigo de pesquisa que avaliou 78 isolados de feijão da coleção de cultura SEMIA para identificar agentes de biocontrole contra o fitopatógeno S. rolfsii. Demonstramos que estirpes estirpes isoladas de nódulos podem ser fortes antagonistas ao crescimento S. rolfsii e ser eficazes no controle da doença provocada pelo mesmo à campo. No Capítulo III, “Reclassification of Ochrobactrum lupini as a later heterotypic synonym of Ochrobactrum anthropi based on whole-genome sequence analysis”, demonstramos com dados filogenéticos, genômicos, fenotípicos e quimiotaxonômicos que O. lupini deve ser considerado a mesma espécie de O anthropi. O Capítulo IV, “Genomic metrics applied to Rhizobiales (Hyphomicrobiales): species reclassification, identification of unauthentic genomes and false type strains”, apresenta a taxonomia atualizada da ordem Hyphomicrobiales, com base em 270.400 comparações analisadas com um corte de 95% de ANI para extrair clusters de genoma com alta identidade através do uso da ferramenta ProKlust descrita. Esse trabalho originou uma série de propostas de reclassificações taxonômicas, além da descoberta de acessos de genoma que não era das estirpes-tipo genuínas utilizadas para as respectivas descrições de “suas espécies”, bem como casos de uso indevido do termo “estirpe-tipo” no banco de dados. No Capítulo IV, "Analysis of 95+ genomes from the common-bean branch from SEMIA collection: new genomospecies, alternative nitrogenases, horizontal gene transfer events, and unexpected genera of nodule-associated bacteria", sequenciamos os genomas de 96 estirpes SEMIA, relatando 15 clusters de genoespécies, bem como, 12 genoespécies isoladas, que surgiram de 1.322.500 comparações de ANI em pares entre as estirpes SEMIA e 1.053 genomas pertencentes a Burkholderiaceae, Comamonadaceae, Mycobacteriaceae, Rhizobiaceae, e Xanthomonadaceae. As estirpes foram identificadas como pertencentes a nove espécies diferentes de Rhizobium, Agrobacterium radiobacter, Pararhizobium giardinii, Paraburkholderia fungorum e as espécies putativas associadas a nódulos Mycobacterium monacense, Stenotrophomonas maltophilia e Variovorax guangxiensis. Cerca de um terço da coleção foi identificado como novas espécies potenciais. A análise do pangenoma das estirpes SEMIA resultou em 50.221 clusters de genes contendo 604.752 genes. A presença de genes relacionados às nitrogenases alternativas foi detectada entre representantes pertencentes a M. monacense, P. fungorum e V. guangxiens, bem como nas novas espécies putativas G11 e G9. A presença de homólogos nifH foi exclusiva para 55 estirpes pertencentes a Rhizobium. A detecção de sobreposição com sequências extracromossômicas foi encontrada apenas entre representantes de Rhizobium e P. fungorum. Vários genes de transposase foram localizados a montante e a jusante dos operons nifHDKENX e nifHDKE detectados, indicando eventos de transferência horizontal. Uma ampla distribuição filogenética foi encontrada no nível da família e um número notável (≥40) de genes transferidos putativos foram encontrados especialmente entre 12 estirpes, incluindo eventos de transferência putativos de outros domínios, como a família botânica Euphorbiaceae, Aspergillaceae e Siphoviridae. Conjuntos de genes biossintéticos putativos foram identificados. A reclassificação de mais de 25 espécies bacterianas também foi proposta com base nas comparações entre os genomas das estirpes-tipo.The SEMIA Collection has officially existed since 1975 and is an international reference in the field of inoculants. This collection holds more than 1,200 strains of bacteria isolated from the nodules of 171 legumes of agricultural importance, 98 of which are recommended for use in inoculants. A large part of the SEMIA Collection was identified using biochemical characteristics, PCR based on repetitive elements, serological and host plant identification, and, to a lesser extent, the partial sequencing of the 16S rRNA gene. However, taxonomic information on SEMIA strains is still lacking, based on currently accepted molecular genome-based methods. In view of this, the present work aimed to i) elucidate the potential of SEMIA strains for the biological control of pathogenic fungi and ii) solve taxonomy problems within the SEMIA Collection and the order Rhizobiales (Hyphomicrobiales) itself. Chapter I, “Rhizobia for biological control of plant diseases”, is a review regarding rhizobial mechanisms and efficacy to biocontrol diseases caused by different classes of plant pathogens. Chapter II, entitled “Rhizobium strains in the biological control of the phytopathogenic fungi Sclerotium (Athelia) rolfsii on the common bean” is a research article that evaluated 78 common bean isolates from SEMIA culture collection to identify biocontrol agents against the plant pathogen S. rolfsii. We demonstrated that root-isolated strains can be strong antagonists to S. rolfsii growth and be effective in controlling the disease caused by this pathogen in the field. In the Chapter III, “Reclassification of Ochrobactrum lupini as a later heterotypic synonym of Ochrobactrum anthropi based on whole-genome sequence analysis”, we demonstrated with phylogenetic, genomic, phenotypic, and chemotaxonomic data that O. lupini should be considered the same species of O. anthropi. The Chapter IV, “Genomic metrics applied to Rhizobiales (Hyphomicrobiales): species reclassification, identification of unauthentic genomes and false type strains”, presents the updated taxonomy of the order Hyphomicrobiales, based on 270,400 comparisons analyzed with a 95% ANI cut-off to extract high identity genome clusters using the described ProKlust tool. This work has led to a series of proposals for taxonomic reclassifications, in addition to discover of genome accessions that are not from the genuine type strains used for the respective species descriptions as well as cases of misuse of the term “type strain”. In the Chapter IV, “Analysis of 95+ genomes from the common-bean branch from SEMIA collection: new genomospecies, alternative nitrogenases, horizontal gene transfer events, and unexpected genera of nodule-associated bacteria”, we sequenced the genomes from 96 SEMIA strains, reporting 15 genospecies clusters as well as 12 isolated genospecies that arised from the 1,322,500 ANI pairwise comparisons between the SEMIA strains and 1,053 genomes belonging to Burkholderiaceae, Comamonadaceae, Mycobacteriaceae, Rhizobiaceae, and Xanthomonadaceae. The strains were identified as belonging to nine different Rhizobium species, Agrobacterium radiobacter, Pararhizobium giardinii, Paraburkholderia fungorum and the putative nodule-associated species Mycobacterium monacense, Stenotrophomonas maltophilia, and Variovorax guangxiensis. Around one-third of the collection were identified as new potential species. The pangenome analysis of SEMIA resulted in 50,221 gene clusters containing 604,752 genes. The presence of alternative nitrogenases relatedgenes was detected among representatives belonging to M. monacense, P. fungorum and V. guangxiens, as well as in the putative new species G11 and G9. The presence of nifH homologs was as exclusive to 55 strains belonging to Rhizobium. The detection of overlap with extrachromosomal sequences was found only among representatives from Rhizobium and P. fungorum. Multiple transposase genes were located upstream and downstream of the detected nifHDKENX and nifHDKE operons, indicating HGT events. A wide phylogenetic distribution was found at the family level and an outstanding number (≥40) of putative transferred genes were found especially among 12 strains, including putative transfer events from other Domains such as the botanical family Euphorbiaceae, Aspergillaceae, and Siphoviridae. Putative biosynthetic gene clusters were identified. Reclassification of over 25 bacterial species was also proposed based on the comparisons between the type-strain genomes