Multiple strategy process migration

The future of computing lies with distributed systems, i.e. a network of workstations controlled by a modern distributed operating system. By supporting load balancing and parallel execution, the overall performance of a distributed system can be improved dramatically. Process migration, the act of moving a running process from a highly loaded machine to a lightly loaded machine, could be used to support load balancing, parallel execution, reliability etc. This thesis identifies the problems past process migration facilities have had and determines the possible differing strategies that can be used to resolve these problems. The result of this analysis has led to a new design philosophy. This philosophy requires the design of a process migration facility and the design of an operating system to be conducted in parallel. Modern distributed operating systems follow the microkernel and client/server paradigms. Applying these design paradigms, in conjunction with the requirements of both process migration and a distributed operating system, results in a system where each resource is controlled by a separate server process. However, a process is a complex resource composed of simple resources such as data structures, an address space and communication state. For this reason, a process migration facility does not directly migrate the resources of a process. Instead, it requests the appropriate servers to transfer the resources. This novel solution yields a modular, high performance facility that is easy to create, debug and maintain. Furthermore, the design easily incorporates providing multiple migration strategies. In order to verify the validity of this design, a process migration facility was developed and tested within RHODOS (ResearcH Oriented Distributed Operating System). RHODOS is a modern microkernel and client/server based distributed operating system. In RHODOS, a process is composed of at least three separate resources: process state - maintained by a process manager, address space - maintained by a memory manager and communication state - maintained by an InterProcess Communication Manager (IPCM). The RHODOS multiple strategy migration manager utilises the services of the process, memory and IPC Managers to migrate the resources of a process. Performance testing of this facility indicates that this design is as fast or better than existing systems which use faster hardware. Furthermore, by studying the results of the performance test ing, the conditions under which a particular strategy should be employed have been identified. This thesis also addresses heterogeneous process migration. The current trend is to have islands of homogeneous workstations amid a sea of heterogeneity. From this situation and the current literature on the topic, heterogeneous process migration can be seen as too inefficient for general use. Instead, only homogeneous workstations should be used for process migration. This implies a need to locate homogeneous workstations. Entities called traders, which store and disseminate knowledge about the resources of several workstations, should be used to provide resource discovery. Resource discovery will enable the detection of homogeneous workstations to which processes can be migrated

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

Exploiting operating system services to efficiently checkpoint parallel applications in GENESIS

Recent research efforts of parallel processing on non-dedicated clusters have focused on high execution performance, parallelism management, transparent access to resources, and making clusters easy to use. However, as a collection of independent computers used by multiple users, clusters are susceptible to failure. This paper shows the development of a coordinated checkpointing facility for the GENESIS cluster operating system. This facility was developed by exploiting existing operating system services. High performance and low overheads are achieved by allowing the processes of a parallel application to continue executing during the creation of checkpoints, while maintaining low demands on cluster resources by using coordinated checkpointing.<br /

Characterization and functional analysis of seven flagellin genes in Rhizobium leguminosarum bv. viciae. Characterization of R. leguminosarum flagellins

<p>Abstract</p> <p>Background</p> <p><it>Rhizobium leguminosarum </it>bv. <it>viciae </it>establishes symbiotic nitrogen fixing partnerships with plant species belonging to the Tribe Vicieae, which includes the genera <it>Vicia, Lathyrus, Pisum </it>and <it>Lens</it>. Motility and chemotaxis are important in the ecology of <it>R. leguminosarum </it>to provide a competitive advantage during the early steps of nodulation, but the mechanisms of motility and flagellar assembly remain poorly studied. This paper addresses the role of the seven flagellin genes in producing a functional flagellum.</p> <p>Results</p> <p><it>R. leguminosarum </it>strains 3841 and VF39SM have seven flagellin genes (<it>flaA</it>, <it>flaB, flaC, flaD, flaE, flaH</it>, and <it>flaG</it>), which are transcribed separately. The predicted flagellins of 3841 are highly similar or identical to the corresponding flagellins in VF39SM. <it>flaA, flaB, flaC</it>, and <it>flaD </it>are in tandem array and are located in the main flagellar gene cluster. <it>flaH </it>and <it>flaG </it>are located outside of the flagellar/motility region while <it>flaE </it>is plasmid-borne. Five flagellin subunits (FlaA, FlaB, FlaC, FlaE, and FlaG) are highly similar to each other, whereas FlaD and FlaH are more distantly related. All flagellins exhibit conserved amino acid residues at the N- and C-terminal ends and are variable in the central regions. Strain 3841 has 1-3 plain subpolar flagella while strain VF39SM exhibits 4-7 plain peritrichous flagella. Three flagellins (FlaA/B/C) and five flagellins (FlaA/B/C/E/G) were detected by mass spectrometry in the flagellar filaments of strains 3841 and VF39SM, respectively. Mutation of <it>flaA </it>resulted in non-motile VF39SM and extremely reduced motility in 3841. Individual mutations of <it>flaB </it>and <it>flaC </it>resulted in shorter flagellar filaments and consequently reduced swimming and swarming motility for both strains. Mutant VF39SM strains carrying individual mutations in <it>flaD, flaE, flaH</it>, and <it>flaG </it>were not significantly affected in motility and filament morphology. The flagellar filament and the motility of 3841 strains with mutations in <it>flaD </it>and <it>flaG </it>were not significantly affected while <it>flaE </it>and <it>flaH </it>mutants exhibited shortened filaments and reduced swimming motility.</p> <p>Conclusion</p> <p>The results obtained from this study demonstrate that FlaA, FlaB, and FlaC are major components of the flagellar filament while FlaD and FlaG are minor components for <it>R. leguminosarum </it>strains 3841 and VF39SM. We also observed differences between the two strains, wherein FlaE and FlaH appear to be minor components of the flagellar filaments in VF39SM but these flagellin subunits may play more important roles in 3841. This paper also demonstrates that the flagellins of 3841 and VF39SM are possibly glycosylated.</p

Platform for reliable computing on clusters using group communications

Shared clusters represent an excellent platform for the execution of parallel applications given their low price/performance ratio and the presence of cluster infrastructure in many organisations. The focus of recent research efforts are on parallelism management, transport and efficient access to resources, and making clusters easy to use. In this thesis, we examine reliable parallel computing on clusters. The aim of this research is to demonstrate the feasibility of developing an operating system facility providing transport fault tolerance using existing, enhanced and newly built operating system services for supporting parallel applications. In particular, we use existing process duplication and process migration services, and synthesise a group communications facility for use in a transparent checkpointing facility. This research is carried out using the methods of experimental computer science. To provide a foundation for the synthesis of the group communications and checkpointing facilities, we survey and review related work in both fields. For group communications, we examine the V Distributed System, the x-kernel and Psync, the ISIS Toolkit, and Horus. We identify a need for services that consider the placement of processes on computers in the cluster. For Checkpointing, we examine Manetho, KeyKOS, libckpt, and Diskless Checkpointing. We observe the use of remote computer memories for storing checkpoints, and the use of copy-on-write mechanisms to reduce the time to create a checkpoint of a process. We propose a group communications facility providing two sets of services: user-oriented services and system-oriented services. User-oriented services provide transparency and target application. System-oriented services supplement the user-oriented services for supporting other operating systems services and do not provide transparency. Additional flexibility is achieved by providing delivery and ordering semantics independently. An operating system facility providing transparent checkpointing is synthesised using coordinated checkpointing. To ensure a consistent set of checkpoints are generated by the facility, instead of blindly blocking the processes of a parallel application, only non-deterministic events are blocked. This allows the processes of the parallel application to continue execution during the checkpoint operation. Checkpoints are created by adapting process duplication mechanisms, and checkpoint data is transferred to remote computer memories and disk for storage using the mechanisms of process migration. The services of the group communications facility are used to coordinate the checkpoint operation, and to transport checkpoint data to remote computer memories and disk. Both the group communications facility and the checkpointing facility have been implemented in the GENESIS cluster operating system and provide proof-of-concept. GENESIS uses a microkernel and client-server based operating system architecture, and is demonstrated to provide an appropriate environment for the development of these facilities. We design a number of experiments to test the performance of both the group communications facility and checkpointing facility, and to provide proof-of-performance. We present our approach to testing, the challenges raised in testing the facilities, and how we overcome them. For group communications, we examine the performance of a number of delivery semantics. Good speed-ups are observed and system-oriented group communication services are shown to provide significant performance advantages over user-oriented semantics in the presence of packet loss. For checkpointing, we examine the scalability of the facility given different levels of resource usage and a variable number of computers. Low overheads are observed for checkpointing a parallel application. It is made clear by this research that the microkernel and client-server based cluster operating system provide an ideal environment for the development of a high performance group communications facility and a transparent checkpointing facility for generating a platform for reliable parallel computing on clusters

Phylogeny and historical biogeography of Lauraceae

Phylogenetic relationships among 122 species of Lauraceae representing 44 of the 55 currently recognized genera are inferred from sequence variation in the chloroplast and nuclear genomes. The trnL-trnF, trnT-trnL, psbA-trnH, and rpll6 regions of cpDNA, and the 5' end of 26S rDNA resolved major lineages, while the ITS/5.8S region of rDNA resolved a large terminal lade. The phylogenetic estimate is used to assess morphology-based views of relationships and, with a temporal dimension added, to reconstruct the biogeographic history of the family. Results suggest Lauraceae radiated when trans-Tethyean migration was relatively easy, and basal lineages are established on either Gondwanan or Laurasian terrains by the Late Cretaceous. Most genera with Gondwanan histories place in Cryptocaryeae, but a small group of South American genera, the Chlorocardium-Mezilauruls lade, represent a separate Gondwanan lineage. Caryodaphnopsis and Neocinnamomum may be the only extant representatives of the ancient Lauraceae flora docu- mented in Mid- to Late Cretaceous Laurasian strata. Remaining genera place in a terminal Perseeae-Laureae lade that radiated in Early Eocene Laurasia. Therein, non-cupulate genera associate as the Persea group, and cupuliferous genera sort to Laureae of most classifications or Cinnamomeae sensu Kostermans. Laureae are Laurasian relicts in Asia. The Persea group and Cinnamomum group (of Cinnamomeae) show tropical amphi-Pacific disjunctions here credited to disruption of boreotropical ranges by Eocene-Oligocene climatic cooling. The Ocotea complex accommodates re- maining Cinnamomeae and shows a trans-Atlantic disjunction possibly derived from a Madrean-Tethyan ancestral distribution. These findings support Laurasian ancestry for most extant Lauraceae, with their considerable neotropical representation primarily derived from Early Miocene radiation of the Ocotea complex upon reaching South America

ELNAIS: A collaborative network on Aquatic Alien Species in Hellas (Greece)

ELNAIS is a dynamic online information platform aiming to collect and report spatial information on Aquatic Alien Species in Greek waters. It covers freshwater, marine and estuarine waters, including not only established aliens but also casual records and cryptogenic species. The ELNAIS system includes: News, List of Greek experts, Literature of findings in Greece, List of species with information on their first introduction date and source as well as photos and distribution maps. Data providers are the scientific community (publications, grey literature, and databases) as well as citizen scientists. ELNAIS provides a useful tool towards national obligations and commitments under both the European and global frameworks in respect to Non Indigenous Species (CBD, WFD, MSFD).JRC.H.1-Water Resource

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