State of the Art in Parallel Computing with R

R is a mature open-source programming language for statistical computing and graphics. Many areas of statistical research are experiencing rapid growth in the size of data sets. Methodological advances drive increased use of simulations. A common approach is to use parallel computing. This paper presents an overview of techniques for parallel computing with R on computer clusters, on multi-core systems, and in grid computing. It reviews sixteen different packages, comparing them on their state of development, the parallel technology used, as well as on usability, acceptance, and performance. Two packages (snow, Rmpi) stand out as particularly suited to general use on computer clusters. Packages for grid computing are still in development, with only one package currently available to the end user. For multi-core systems five different packages exist, but a number of issues pose challenges to early adopters. The paper concludes with ideas for further developments in high performance computing with R. Example code is available in the appendix.

Guaranteed bandwidth implementation of message passing interface on workstation clusters

Due to their wide availability, networks of workstations (NOW) are an attractive platform for parallel processing. Parallel programming environments such as Parallel Virtual Machine (PVM), and Message Passing Interface (MPI) offer the user a convenient way to express parallel computing and communication for a network of workstations. Currently, a number of MPI implementations are available that offer low (average ) latency and high bandwidth environments to users by utilizing an efficient MPI library specification and high speed networks. In addition to high bandwidth and low average latency requirements, mission critical distributed applications, audio/video communications require a completely different type of service, guaranteed bandwidth and worst case delays (worst case latency) to be guaranteed by underlying protocol. The hypothesis presented in this paper is that it is possible to provide an application a low level reliable transport protocol with performance and guaranteed bandwidth as close to the hardware on which it is executing. The hypothesis is proven by designing and implementing a reliable high performance message passing protocol interface which also provides the guaranteed bandwidth to MPI and to mission critical distributed MPI applications. This protocol interface works with the Fiber Distributed Data Interface (FDDI) driver which has been designed and implemented for Performance Technology Inc. commercial high performance FDDI product, the Station Management Software 7.3, and the ADI / MPICH (Argonne National Laboratory and Mississippi State University\u27s free MPI implementation)

"Virtual malleability" applied to MPI jobs to improve their execution in a multiprogrammed environment"

This work focuses on scheduling of MPI jobs when executing in shared-memory multiprocessors (SMPs). The objective was to obtain the best performance in response time in multiprogrammed multiprocessors systems using batch systems, assuming all the jobs have the same priority. To achieve that purpose, the benefits of supporting malleability on MPI jobs to reduce fragmentation and consequently improve the performance of the system were studied. The contributions made in this work can be summarized as follows:· Virtual malleability: A mechanism where a job is assigned a dynamic processor partition, where the number of processes is greater than the number of processors. The partition size is modified at runtime, according to external requirements such as the load of the system, by varying the multiprogramming level, making the job contend for resources with itself. In addition to this, a mechanism which decides at runtime if applying local or global process queues to an application depending on the load balancing between processes of it. · A job scheduling policy, that takes decisions such as how many processes to start with and the maximum multiprogramming degree based on the type and number of applications running and queued. Moreover, as soon as a job finishes execution and where there are queued jobs, this algorithm analyzes whether it is better to start execution of another job immediately or just wait until there are more resources available. · A new alternative to backfilling strategies for the problema of window execution time expiring. Virtual malleability is applied to the backfilled job, reducing its partition size but without aborting or suspending it as in traditional backfilling. The evaluation of this thesis has been done using a practical approach. All the proposals were implemented, modifying the three scheduling levels: queuing system, processor scheduler and runtime library. The impact of the contributions were studied under several types of workloads, varying machine utilization, communication and, balance degree of the applications, multiprogramming level, and job size. Results showed that it is possible to offer malleability over MPI jobs. An application obtained better performance when contending for the resources with itself than with other applications, especially in workloads with high machine utilization. Load imbalance was taken into account obtaining better performance if applying the right queue type to each application independently.The job scheduling policy proposed exploited virtual malleability by choosing at the beginning of execution some parameters like the number of processes and maximum multiprogramming level. It performed well under bursty workloads with low to medium machine utilizations. However as the load increases, virtual malleability was not enough. That is because, when the machine is heavily loaded, the jobs, once shrunk are not able to expand, so they must be executed all the time with a partition smaller than the job size, thus degrading performance. Thus, at this point the job scheduling policy concentrated just in moldability.Fragmentation was alleviated also by applying backfilling techniques to the job scheduling algorithm. Virtual malleability showed to be an interesting improvement in the window expiring problem. Backfilled jobs even on a smaller partition, can continue execution reducing memory swapping generated by aborts/suspensions In this way the queueing system is prevented from reinserting the backfilled job in the queue and re-executing it in the future.Postprint (published version

pCoR - a protoype for resource oriented computing

In this paper we present CoR a resource oriented computing model that address the question of how to integrate user-level fine-grained multithreading, communication and coordination into a cluster of symmetrical multiprocessor computers. To support the design of complex distributed application using the proposed paradigm we built pCoR a run-time system which has new areas that represents extensions to the strict shared memory and message passing models supported by other platforms: remote operations, dynamic domains, communication ports, multithreading management, shared memory, replication and partition are some of its distinguished features. In addition, it provides a thread-safe transport communication layer to take advantage of modern high-performance commodity hardware/software like Myrinet network