Algorithmic Based Fault Tolerance Applied to High Performance Computing

We present a new approach to fault tolerance for High Performance Computing system. Our approach is based on a careful adaptation of the Algorithmic Based Fault Tolerance technique (Huang and Abraham, 1984) to the need of parallel distributed computation. We obtain a strongly scalable mechanism for fault tolerance. We can also detect and correct errors (bit-flip) on the fly of a computation. To assess the viability of our approach, we have developed a fault tolerant matrix-matrix multiplication subroutine and we propose some models to predict its running time. Our parallel fault-tolerant matrix-matrix multiplication scores 1.4 TFLOPS on 484 processors (cluster jacquard.nersc.gov) and returns a correct result while one process failure has happened. This represents 65% of the machine peak efficiency and less than 12% overhead with respect to the fastest failure-free implementation. We predict (and have observed) that, as we increase the processor count, the overhead of the fault tolerance drops significantly

Parallel detrended fluctuation analysis for fast event detection on massive PMU data

("(c) 2015 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.")Phasor measurement units (PMUs) are being rapidly deployed in power grids due to their high sampling rates and synchronized measurements. The devices high data reporting rates present major computational challenges in the requirement to process potentially massive volumes of data, in addition to new issues surrounding data storage. Fast algorithms capable of processing massive volumes of data are now required in the field of power systems. This paper presents a novel parallel detrended fluctuation analysis (PDFA) approach for fast event detection on massive volumes of PMU data, taking advantage of a cluster computing platform. The PDFA algorithm is evaluated using data from installed PMUs on the transmission system of Great Britain from the aspects of speedup, scalability, and accuracy. The speedup of the PDFA in computation is initially analyzed through Amdahl's Law. A revision to the law is then proposed, suggesting enhancements to its capability to analyze the performance gain in computation when parallelizing data intensive applications in a cluster computing environment

Parallel detrended fluctuation analysis for fast event detection on massive PMU data

("(c) 2015 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.")Phasor measurement units (PMUs) are being rapidly deployed in power grids due to their high sampling rates and synchronized measurements. The devices high data reporting rates present major computational challenges in the requirement to process potentially massive volumes of data, in addition to new issues surrounding data storage. Fast algorithms capable of processing massive volumes of data are now required in the field of power systems. This paper presents a novel parallel detrended fluctuation analysis (PDFA) approach for fast event detection on massive volumes of PMU data, taking advantage of a cluster computing platform. The PDFA algorithm is evaluated using data from installed PMUs on the transmission system of Great Britain from the aspects of speedup, scalability, and accuracy. The speedup of the PDFA in computation is initially analyzed through Amdahl's Law. A revision to the law is then proposed, suggesting enhancements to its capability to analyze the performance gain in computation when parallelizing data intensive applications in a cluster computing environment

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 useful for 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 four 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

Checkpoint and run-time adaptation with pluggable parallelisation

Enabling applications for computational Grids requires new approaches to develop applications that can effectively cope with resource volatility. Applications must be resilient to resource faults, adapting the behaviour to available resources. This paper describes an approach to application-level adaptation that efficiently supports application-level checkpointing. The key of this work is the concept of pluggable parallelisation, which localises parallelisation issues into multiple modules that can be (un)plugged to match resource availability. This paper shows how pluggable parallelisation can be extended to effectively support checkpointing and run-time adaptation. We present the developed pluggable mechanism that helps the programmer to include checkpointing in the base (sequential). Based on these mechanisms and on previous work on pluggable parallelisation, our approach is able to automatically add support for checkpointing in parallel execution environments. Moreover, applications can adapt from a sequential execution to a multi-cluster configuration. Adaptation can be performed by checkpointing the application and restarting on a different mode or can be performed during run-time. Pluggable parallelisation intrinsically promotes the separation of software functionality from fault-tolerance and adaptation issues facilitating their analysis and evolution. The work presented in this paper reinforces this idea by showing the feasibility of the approach and performance benefits that can be achieved.(undefined

Many-Task Computing and Blue Waters

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware

AspectGrid: Aspect-Oriented Fault-Tolerance in Grid Platforms

Migrating traditional scientific applications to computational Grids requires programming tools that can help programmers update application behaviour to this kind of platforms. Computational Grids are particularly suited for long running scientific applications, but they are also more prone to faults than desktop machines. The AspectGrid framework aims to develop methodologies and tools that can help Grid-enable scientific applications, particularly focusing on techniques based on aspect-oriented programming. In this paper we present the aspect-oriented approach taken in the AspectGrid framework to address faults in computational Grids. In the proposed approach, scientific applications are enhanced with fault-tolerance capability by plugging additional modules. The proposed technique is portable across operating systems and minimises the changes required to base applications