ReSHAPE: A Framework for Dynamic Resizing and Scheduling of Homogeneous Applications in a Parallel Environment

Applications in science and engineering often require huge computational resources for solving problems within a reasonable time frame. Parallel supercomputers provide the computational infrastructure for solving such problems. A traditional application scheduler running on a parallel cluster only supports static scheduling where the number of processors allocated to an application remains fixed throughout the lifetime of execution of the job. Due to the unpredictability in job arrival times and varying resource requirements, static scheduling can result in idle system resources thereby decreasing the overall system throughput. In this paper we present a prototype framework called ReSHAPE, which supports dynamic resizing of parallel MPI applications executed on distributed memory platforms. The framework includes a scheduler that supports resizing of applications, an API to enable applications to interact with the scheduler, and a library that makes resizing viable. Applications executed using the ReSHAPE scheduler framework can expand to take advantage of additional free processors or can shrink to accommodate a high priority application, without getting suspended. In our research, we have mainly focused on structured applications that have two-dimensional data arrays distributed across a two-dimensional processor grid. The resize library includes algorithms for processor selection and processor mapping. Experimental results show that the ReSHAPE framework can improve individual job turn-around time and overall system throughput.Comment: 15 pages, 10 figures, 5 tables Submitted to International Conference on Parallel Processing (ICPP'07

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

Parallel Astronomical Data Processing with Python: Recipes for multicore machines

High performance computing has been used in various fields of astrophysical research. But most of it is implemented on massively parallel systems (supercomputers) or graphical processing unit clusters. With the advent of multicore processors in the last decade, many serial software codes have been re-implemented in parallel mode to utilize the full potential of these processors. In this paper, we propose parallel processing recipes for multicore machines for astronomical data processing. The target audience are astronomers who are using Python as their preferred scripting language and who may be using PyRAF/IRAF for data processing. Three problems of varied complexity were benchmarked on three different types of multicore processors to demonstrate the benefits, in terms of execution time, of parallelizing data processing tasks. The native multiprocessing module available in Python makes it a relatively trivial task to implement the parallel code. We have also compared the three multiprocessing approaches - Pool/Map, Process/Queue, and Parallel Python. Our test codes are freely available and can be downloaded from our website.Comment: 15 pages, 7 figures, 1 table, "for associated test code, see http://astro.nuigalway.ie/staff/navtejs", Accepted for publication in Astronomy and Computin

Maiter: An Asynchronous Graph Processing Framework for Delta-based Accumulative Iterative Computation

Myriad of graph-based algorithms in machine learning and data mining require parsing relational data iteratively. These algorithms are implemented in a large-scale distributed environment in order to scale to massive data sets. To accelerate these large-scale graph-based iterative computations, we propose delta-based accumulative iterative computation (DAIC). Different from traditional iterative computations, which iteratively update the result based on the result from the previous iteration, DAIC updates the result by accumulating the "changes" between iterations. By DAIC, we can process only the "changes" to avoid the negligible updates. Furthermore, we can perform DAIC asynchronously to bypass the high-cost synchronous barriers in heterogeneous distributed environments. Based on the DAIC model, we design and implement an asynchronous graph processing framework, Maiter. We evaluate Maiter on local cluster as well as on Amazon EC2 Cloud. The results show that Maiter achieves as much as 60x speedup over Hadoop and outperforms other state-of-the-art frameworks.Comment: ScienceCloud 2012, TKDE 201