Shared Memory Parallel Subgraph Enumeration

The subgraph enumeration problem asks us to find all subgraphs of a target graph that are isomorphic to a given pattern graph. Determining whether even one such isomorphic subgraph exists is NP-complete---and therefore finding all such subgraphs (if they exist) is a time-consuming task. Subgraph enumeration has applications in many fields, including biochemistry and social networks, and interestingly the fastest algorithms for solving the problem for biochemical inputs are sequential. Since they depend on depth-first tree traversal, an efficient parallelization is far from trivial. Nevertheless, since important applications produce data sets with increasing difficulty, parallelism seems beneficial. We thus present here a shared-memory parallelization of the state-of-the-art subgraph enumeration algorithms RI and RI-DS (a variant of RI for dense graphs) by Bonnici et al. [BMC Bioinformatics, 2013]. Our strategy uses work stealing and our implementation demonstrates a significant speedup on real-world biochemical data---despite a highly irregular data access pattern. We also improve RI-DS by pruning the search space better; this further improves the empirical running times compared to the already highly tuned RI-DS.Comment: 18 pages, 12 figures, To appear at the 7th IEEE Workshop on Parallel / Distributed Computing and Optimization (PDCO 2017

Towards Implicit Parallel Programming for Systems

Multi-core processors require a program to be decomposable into independent parts that can execute in parallel in order to scale performance with the number of cores. But parallel programming is hard especially when the program requires state, which many system programs use for optimization, such as for example a cache to reduce disk I/O. Most prevalent parallel programming models do not support a notion of state and require the programmer to synchronize state access manually, i.e., outside the realms of an associated optimizing compiler. This prevents the compiler to introduce parallelism automatically and requires the programmer to optimize the program manually. In this dissertation, we propose a programming language/compiler co-design to provide a new programming model for implicit parallel programming with state and a compiler that can optimize the program for a parallel execution. We define the notion of a stateful function along with their composition and control structures. An example implementation of a highly scalable server shows that stateful functions smoothly integrate into existing programming language concepts, such as object-oriented programming and programming with structs. Our programming model is also highly practical and allows to gradually adapt existing code bases. As a case study, we implemented a new data processing core for the Hadoop Map/Reduce system to overcome existing performance bottlenecks. Our lambda-calculus-based compiler automatically extracts parallelism without changing the program's semantics. We added further domain-specific semantic-preserving transformations that reduce I/O calls for microservice programs. The runtime format of a program is a dataflow graph that can be executed in parallel, performs concurrent I/O and allows for non-blocking live updates

Towards Implicit Parallel Programming for Systems

Multi-core processors require a program to be decomposable into independent parts that can execute in parallel in order to scale performance with the number of cores. But parallel programming is hard especially when the program requires state, which many system programs use for optimization, such as for example a cache to reduce disk I/O. Most prevalent parallel programming models do not support a notion of state and require the programmer to synchronize state access manually, i.e., outside the realms of an associated optimizing compiler. This prevents the compiler to introduce parallelism automatically and requires the programmer to optimize the program manually. In this dissertation, we propose a programming language/compiler co-design to provide a new programming model for implicit parallel programming with state and a compiler that can optimize the program for a parallel execution. We define the notion of a stateful function along with their composition and control structures. An example implementation of a highly scalable server shows that stateful functions smoothly integrate into existing programming language concepts, such as object-oriented programming and programming with structs. Our programming model is also highly practical and allows to gradually adapt existing code bases. As a case study, we implemented a new data processing core for the Hadoop Map/Reduce system to overcome existing performance bottlenecks. Our lambda-calculus-based compiler automatically extracts parallelism without changing the program's semantics. We added further domain-specific semantic-preserving transformations that reduce I/O calls for microservice programs. The runtime format of a program is a dataflow graph that can be executed in parallel, performs concurrent I/O and allows for non-blocking live updates

Towards Implicit Parallel Programming for Systems

Multi-core processors require a program to be decomposable into independent parts that can execute in parallel in order to scale performance with the number of cores. But parallel programming is hard especially when the program requires state, which many system programs use for optimization, such as for example a cache to reduce disk I/O. Most prevalent parallel programming models do not support a notion of state and require the programmer to synchronize state access manually, i.e., outside the realms of an associated optimizing compiler. This prevents the compiler to introduce parallelism automatically and requires the programmer to optimize the program manually. In this dissertation, we propose a programming language/compiler co-design to provide a new programming model for implicit parallel programming with state and a compiler that can optimize the program for a parallel execution. We define the notion of a stateful function along with their composition and control structures. An example implementation of a highly scalable server shows that stateful functions smoothly integrate into existing programming language concepts, such as object-oriented programming and programming with structs. Our programming model is also highly practical and allows to gradually adapt existing code bases. As a case study, we implemented a new data processing core for the Hadoop Map/Reduce system to overcome existing performance bottlenecks. Our lambda-calculus-based compiler automatically extracts parallelism without changing the program's semantics. We added further domain-specific semantic-preserving transformations that reduce I/O calls for microservice programs. The runtime format of a program is a dataflow graph that can be executed in parallel, performs concurrent I/O and allows for non-blocking live updates

Towards Implicit Parallel Programming for Systems

Multi-core processors require a program to be decomposable into independent parts that can execute in parallel in order to scale performance with the number of cores. But parallel programming is hard especially when the program requires state, which many system programs use for optimization, such as for example a cache to reduce disk I/O. Most prevalent parallel programming models do not support a notion of state and require the programmer to synchronize state access manually, i.e., outside the realms of an associated optimizing compiler. This prevents the compiler to introduce parallelism automatically and requires the programmer to optimize the program manually. In this dissertation, we propose a programming language/compiler co-design to provide a new programming model for implicit parallel programming with state and a compiler that can optimize the program for a parallel execution. We define the notion of a stateful function along with their composition and control structures. An example implementation of a highly scalable server shows that stateful functions smoothly integrate into existing programming language concepts, such as object-oriented programming and programming with structs. Our programming model is also highly practical and allows to gradually adapt existing code bases. As a case study, we implemented a new data processing core for the Hadoop Map/Reduce system to overcome existing performance bottlenecks. Our lambda-calculus-based compiler automatically extracts parallelism without changing the program's semantics. We added further domain-specific semantic-preserving transformations that reduce I/O calls for microservice programs. The runtime format of a program is a dataflow graph that can be executed in parallel, performs concurrent I/O and allows for non-blocking live updates

Towards Implicit Parallel Programming for Systems

Multi-core processors require a program to be decomposable into independent parts that can execute in parallel in order to scale performance with the number of cores. But parallel programming is hard especially when the program requires state, which many system programs use for optimization, such as for example a cache to reduce disk I/O. Most prevalent parallel programming models do not support a notion of state and require the programmer to synchronize state access manually, i.e., outside the realms of an associated optimizing compiler. This prevents the compiler to introduce parallelism automatically and requires the programmer to optimize the program manually. In this dissertation, we propose a programming language/compiler co-design to provide a new programming model for implicit parallel programming with state and a compiler that can optimize the program for a parallel execution. We define the notion of a stateful function along with their composition and control structures. An example implementation of a highly scalable server shows that stateful functions smoothly integrate into existing programming language concepts, such as object-oriented programming and programming with structs. Our programming model is also highly practical and allows to gradually adapt existing code bases. As a case study, we implemented a new data processing core for the Hadoop Map/Reduce system to overcome existing performance bottlenecks. Our lambda-calculus-based compiler automatically extracts parallelism without changing the program's semantics. We added further domain-specific semantic-preserving transformations that reduce I/O calls for microservice programs. The runtime format of a program is a dataflow graph that can be executed in parallel, performs concurrent I/O and allows for non-blocking live updates

Operating system support for warehouse-scale computing

Modern applications are increasingly backed by large-scale data centres. Systems software in these data centre environments, however, faces substantial challenges: the lack of uniform resource abstractions makes sharing and resource management inefficient, infrastructure software lacks end-to-end access control mechanisms, and work placement ignores the effects of hardware heterogeneity and workload interference. In this dissertation, I argue that uniform, clean-slate operating system (OS) abstractions designed to support distributed systems can make data centres more efficient and secure. I present a novel distributed operating system for data centres, focusing on two OS components: the abstractions for resource naming, management and protection, and the scheduling of work to compute resources. First, I introduce a reference model for a decentralised, distributed data centre OS, based on pervasive distributed objects and inspired by concepts in classic 1980s distributed OSes. Translucent abstractions free users from having to understand implementation details, but enable introspection for performance optimisation. Fine-grained access control is supported by combining storable, communicable identifier capabilities, and context-dependent, ephemeral handle capabilities. Finally, multi-phase I/O requests implement optimistically concurrent access to objects while supporting diverse application-level consistency policies. Second, I present the DIOS operating system, an implementation of my model as an extension to Linux. The DIOS system call API is centred around distributed objects, globally resolvable names, and translucent references that carry context-sensitive object meta-data. I illustrate how these concepts support distributed applications, and evaluate the performance of DIOS in microbenchmarks and a data-intensive MapReduce application. I find that it offers improved, finegrained isolation of resources, while permitting flexible sharing. Third, I present the Firmament cluster scheduler, which generalises prior work on scheduling via minimum-cost flow optimisation. Firmament can flexibly express many scheduling policies using pluggable cost models; it makes high-quality placement decisions based on fine-grained information about tasks and resources; and it scales the flow-based scheduling approach to very large clusters. In two case studies, I show that Firmament supports policies that reduce colocation interference between tasks and that it successfully exploits flexibility in the workload to improve the energy efficiency of a heterogeneous cluster. Moreover, my evaluation shows that Firmament scales the minimum-cost flow optimisation to clusters of tens of thousands of machines while still making sub-second placement decisions.St John's College Supplementary Emolument Fund DARP

Scalable collision detection for distributed virtual environments

PhD ThesisDistributed Virtual Environments (DVEs) provide a mechanism whereby dispersed users can interact with one-another within a shared \'irtual world. DVEs commonly allow users to interact with one-another in ways analogous to the real-world, e.g. mimicking Newtonian physics. A scalable DVE should enable large numbers of users to participate simultaneously, regardless of the In geographical location and hardware configurations of individual users. addition, these users should perceive a mutually-consistent virtual world in which each user perceives a consistent series of events in real-time. Collision detection and response is a fundamental requirement of most virtual environments and simulations. It is a computationally-expensive operation which must be perfonned at frequent intervals in all virtual environments which simulate the motion of solid objects. Collision detection has received large amounts of research interest and as a result a number of efficient collision detection algorithms have been proposed. However, these collision detection approaches are designed to detect collisions efficiently in simulations run on a single machine and are not capable of overcoming problems associated with scalability and consistency, which are of paramount importance in DVEs. This thesis presents a new collision detection approach, tenned distributed collision detection, which provides high-levels of scalability, consistency and responsiveness. This thesis presents the algorithms and theory which underpin the distributed collision detection approach and provides experimental results demonstrating its scalability and responsiveness

Hadoop-cc (collaborative caching) in real time HDFS

Data is being generated at an enormous rate, due to online activities and use of resources related to computing. To access and handle such enormous amount of data spread, dis- tributed systems is an efficient mechanism. One such widely used distributed filesystem is Hadoop distributed filesystem (HDFS). HDFS follows a cluster approach in order to store huge amounts of data, it is scalable and works on low commodity. It uses MapRe- duce framework to perform analysis and carry computations parallely on these large data sets. Hadoop follows the master/slave architecture decoupling system metadata and appli- cation data where metadata is stored on dedicated server NameNode and application data on DataNodes. In this thesis work, study was performed on Hadoop Architecture, behaviour of filesys- tem and MapReduce in detail and concluded that processing of MapReduce is slow which was further confirmed by initial analysis and experiments performed on default Hadoop configuration. It is known that accessing data from cache is much faster as compared to disk access. Collaborative caching is one such mechanism in which the cache distributed over the clients or dedicated servers or storage devices form a single cache to serve the re- quests. This mechanism helps in improving the performance, reducing access latency and increasing the throughput. This coupled with prefetching enhances the performance. In order to enhance and improve the performance of MapReduce, the thesis proposes solution of new design of HDFS by introducing caching references, collaborative caching along with prefetching coupled with Modified-ARC cache replacement. Each of the DataN- odes would have a dedicated Cache Manager to maintain information about its local cache, remote caches and follow cache replacement algorithm. Initial analysis led to conclusion that caching references too help in improving performance. Modified-ARC helps in orga- nizing the cache in a different way as recent, frequent and history of evicted items which is a better cache replacement policy and improves the execution time and performance of MapReduce.The evaluation of the results were done by comparing the results obtained with that of default configuration in psuedo-distributed and fully distributed mode