Runtime Adaptation of Scientific Service Workflows

Software landscapes are rather subject to change than being complete after having been built. Changes may be caused by a modified customer behavior, the shift to new hardware resources, or otherwise changed requirements. In such situations, several challenges arise. New architectural models have to be designed and implemented, existing software has to be integrated, and, finally, the new software has to be deployed, monitored, and, where appropriate, optimized during runtime under realistic usage scenarios. All of these situations often demand manual intervention, which causes them to be error-prone. This thesis addresses these types of runtime adaptation. Based on service-oriented architectures, an environment is developed that enables the integration of existing software (i.e., the wrapping of legacy software as web services). A workflow modeling tool that aims at an easy-to-use approach by separating the role of the workflow expert and the role of the domain expert. After the development of workflows, tools that observe the executing infrastructure and perform automatic scale-in and scale-out operations are presented. Infrastructure-as-a-Service providers are used to scale the infrastructure in a transparent and cost-efficient way. The deployment of necessary middleware tools is automatically done. The use of a distributed infrastructure can lead to communication problems. In order to keep workflows robust, these exceptional cases need to treated. But, in this way, the process logic of a workflow gets mixed up and bloated with infrastructural details, which yields an increase in its complexity. In this work, a module is presented that can deal automatically with infrastructural faults and that thereby allows to keep the separation of these two layers. When services or their components are hosted in a distributed environment, some requirements need to be addressed at each service separately. Although techniques as object-oriented programming or the usage of design patterns like the interceptor pattern ease the adaptation of service behavior or structures. Still, these methods require to modify the configuration or the implementation of each individual service. On the other side, aspect-oriented programming allows to weave functionality into existing code even without having its source. Since the functionality needs to be woven into the code, it depends on the specific implementation. In a service-oriented architecture, where the implementation of a service is unknown, this approach clearly has its limitations. The request/response aspects presented in this thesis overcome this obstacle and provide a SOA-compliant and new methods to weave functionality into the communication layer of web services. The main contributions of this thesis are the following: Shifting towards a service-oriented architecture: The generic and extensible Legacy Code Description Language and the corresponding framework allow to wrap existing software, e.g., as web services, which afterwards can be composed into a workflow by SimpleBPEL without overburdening the domain expert with technical details that are indeed handled by a workflow expert. Runtime adaption: Based on the standardized Business Process Execution Language an automatic scheduling approach is presented that monitors all used resources and is able to automatically provision new machines in case a scale-out becomes necessary. If the resource's load drops, e.g., because of less workflow executions, a scale-in is also automatically performed. The scheduling algorithm takes the data transfer between the services into account in order to prevent scheduling allocations that eventually increase the workflow's makespan due to unnecessary or disadvantageous data transfers. Furthermore, a multi-objective scheduling algorithm that is based on a genetic algorithm is able to additionally consider cost, in a way that a user can define her own preferences rising from optimized execution times of a workflow and minimized costs. Possible communication errors are automatically detected and, according to certain constraints, corrected. Adaptation of communication: The presented request/response aspects allow to weave functionality into the communication of web services. By defining a pointcut language that only relies on the exchanged documents, the implementation of services must neither be known nor be available. The weaving process itself is modeled using web services. In this way, the concept of request/response aspects is naturally embedded into a service-oriented architecture

GRID superscalar: a programming model for the Grid

Durant els darrers anys el Grid ha sorgit com una nova plataforma per la computació distribuïda. La tecnologia Gris permet unir diferents recursos de diferents dominis administratius i formar un superordinador virtual amb tots ells. Molts grups de recerca han dedicat els seus esforços a desenvolupar un conjunt de serveis bàsics per oferir un middleware de Grid: una capa que permet l'ús del Grid. De tota manera, utilitzar aquests serveis no és una tasca fácil per molts usuaris finals, cosa que empitjora si l'expertesa d'aquests usuaris no està relacionada amb la informàtica.Això té una influència negativa a l'hora de que la comunitat científica adopti la tecnologia Grid. Es veu com una tecnologia potent però molt difícil de fer servir. Per facilitar l'ús del Grid és necessària una capa extra que amagui la complexitat d'aquest i permeti als usuaris programar o portar les seves aplicacions de manera senzilla.Existeixen moltes propostes d'eines de programació pel Grid. En aquesta tesi fem un resum d'algunes d'elles, i podem veure que existeixen eines conscients i no-conscients del Grid (es programen especificant o no els detalls del Grid, respectivament). A més, molt poques d'aquestes eines poden explotar el paral·lelisme implícit de l'aplicació, i en la majoria d'elles, l'usuari ha de definir aquest paral·lelisme de manera explícita. Una altra característica que considerem important és si es basen en llenguatges de programació molt populars (com C++ o Java), cosa que facilita l'adopció per part dels usuaris finals.En aquesta tesi, el nostre objectiu principal ha estat crear un model de programació pel Grid basat en la programació seqüencial i els llenguatges més coneguts de la programació imperativa, capaç d'explotar el paral·lelisme implícit de les aplicacions i d'accelerar-les fent servir els recursos del Grid de manera concurrent. A més, com el Grid és de naturalesa distribuïda, heterogènia i dinàmica i degut també a que el nombre de recursos que pot formar un Grid pot ser molt gran, la probabilitat de que es produeixi una errada durant l'execució d'una aplicació és elevada. Per tant, un altre dels nostres objectius ha estat tractar qualsevol tipus d'error que pugui sorgir durant l'execució d'una aplicació de manera automàtica (ja siguin errors relacionats amb l'aplicació o amb el Grid). GRID superscalar (GRIDSs), la principal contribució d'aquesta tesi, és un model de programació que assoleix elsobjectius mencionats proporcionant una interfície molt petita i simple i un entorn d'execució que és capaç d'executar en paral·lel el codi proporcionat fent servir el Grid. La nostra interfície de programació permet a un usuari programar una aplicació no-conscient del Grid, amb llenguatges imperatius coneguts i populars (com C/C++, Java, Perl o Shell script) i de manera seqüencial, per tant dóna un pas important per ajudar als usuaris a adoptar la tecnologia Grid.Hem aplicat el nostre coneixement de l'arquitectura de computadors i el disseny de microprocessadors a l'entorn d'execució de GRIDSs. Tal com es fa a un processador superescalar, l'entorn d'execució de GRIDSs és capaç de realitzar un anàlisi de dependències entre les tasques que formen l'aplicació, i d'aplicar tècniques de renombrament per incrementar el seu paral·lelisme. GRIDSs genera automàticament a partir del codi principal de l'usuari un graf que descriu les dependències de dades en l'aplicació. També presentem casos d'ús reals del model de programació en els camps de la química computacional i la bioinformàtica, que demostren que els nostres objectius han estat assolits.Finalment, hem estudiat l'aplicació de diferents tècniques per detectar i tractar fallades: checkpoint, reintent i replicació de tasques. La nostra proposta és proporcionar un entorn capaç de tractar qualsevol tipus d'errors, de manera transparent a l'usuari sempre que sigui possible. El principal avantatge d'implementar aquests mecanismos al nivell del model de programació és que el coneixement a nivell de l'aplicació pot ser explotat per crear dinàmicament una estratègia de tolerància a fallades per cada aplicació, i evitar introduir sobrecàrrega en entorns lliures d'errors.During last years, the Grid has emerged as a new platform for distributed computing. The Grid technology allows joining different resources from different administrative domains and forming a virtual supercomputer with all of them.Many research groups have dedicated their efforts to develop a set of basic services to offer a Grid middleware: a layer that enables the use of the Grid. Anyway, using these services is not an easy task for many end users, even more if their expertise is not related to computer science. This has a negative influence in the adoption of the Grid technology by the scientific community. They see it as a powerful technology but very difficult to exploit. In order to ease the way the Grid must be used, there is a need for an extra layer which hides all the complexity of the Grid, and allows users to program or port their applications in an easy way.There has been many proposals of programming tools for the Grid. In this thesis we give an overview on some of them, and we can see that there exist both Grid-aware and Grid-unaware environments (programmed with or without specifying details of the Grid respectively). Besides, very few existing tools can exploit the implicit parallelism of the application and in the majority of them, the user must define the parallelism explicitly. Another important feature we consider is if they are based in widely used programming languages (as C++ or Java), so the adoption is easier for end users.In this thesis, our main objective has been to create a programming model for the Grid based on sequential programming and well-known imperative programming languages, able to exploit the implicit parallelism of applications and to speed them up by using the Grid resources concurrently. Moreover, because the Grid has a distributed, heterogeneous and dynamic nature and also because the number of resources that form a Grid can be very big, the probability that an error arises during an application's execution is big. Thus, another of our objectives has been to automatically deal with any type of errors which may arise during the execution of the application (application related or Grid related).GRID superscalar (GRIDSs), the main contribution of this thesis, is a programming model that achieves these mentioned objectives by providing a very small and simple interface and a runtime that is able to execute in parallel the code provided using the Grid. Our programming interface allows a user to program a Grid-unaware application with already known and popular imperative languages (such as C/C++, Java, Perl or Shell script) and in a sequential fashion, therefore giving an important step to assist end users in the adoption of the Grid technology.We have applied our knowledge from computer architecture and microprocessor design to the GRIDSs runtime. As it is done in a superscalar processor, the GRIDSs runtime system is able to perform a data dependence analysis between the tasks that form an application, and to apply renaming techniques in order to increase its parallelism. GRIDSs generates automatically from user's main code a graph describing the data dependencies in the application.We present real use cases of the programming model in the fields of computational chemistry and bioinformatics, which demonstrate that our objectives have been achieved.Finally, we have studied the application of several fault detection and treatment techniques: checkpointing, task retry and task replication. Our proposal is to provide an environment able to deal with all types of failures, transparently for the user whenever possible. The main advantage in implementing these mechanisms at the programming model level is that application-level knowledge can be exploited in order to dynamically create a fault tolerance strategy for each application, and avoiding to introduce overhead in error-free environments