Design and Evaluation of a Collective IO Model for Loosely Coupled Petascale Programming

Loosely coupled programming is a powerful paradigm for rapidly creating higher-level applications from scientific programs on petascale systems, typically using scripting languages. This paradigm is a form of many-task computing (MTC) which focuses on the passing of data between programs as ordinary files rather than messages. While it has the significant benefits of decoupling producer and consumer and allowing existing application programs to be executed in parallel with no recoding, its typical implementation using shared file systems places a high performance burden on the overall system and on the user who will analyze and consume the downstream data. Previous efforts have achieved great speedups with loosely coupled programs, but have done so with careful manual tuning of all shared file system access. In this work, we evaluate a prototype collective IO model for file-based MTC. The model enables efficient and easy distribution of input data files to computing nodes and gathering of output results from them. It eliminates the need for such manual tuning and makes the programming of large-scale clusters using a loosely coupled model easier. Our approach, inspired by in-memory approaches to collective operations for parallel programming, builds on fast local file systems to provide high-speed local file caches for parallel scripts, uses a broadcast approach to handle distribution of common input data, and uses efficient scatter/gather and caching techniques for input and output. We describe the design of the prototype model, its implementation on the Blue Gene/P supercomputer, and present preliminary measurements of its performance on synthetic benchmarks and on a large-scale molecular dynamics application.Comment: IEEE Many-Task Computing on Grids and Supercomputers (MTAGS08) 200

Mixing multi-core CPUs and GPUs for scientific simulation software

Recent technological and economic developments have led to widespread availability of multi-core CPUs and specialist accelerator processors such as graphical processing units (GPUs). The accelerated computational performance possible from these devices can be very high for some applications paradigms. Software languages and systems such as NVIDIA's CUDA and Khronos consortium's open compute language (OpenCL) support a number of individual parallel application programming paradigms. To scale up the performance of some complex systems simulations, a hybrid of multi-core CPUs for coarse-grained parallelism and very many core GPUs for data parallelism is necessary. We describe our use of hybrid applica- tions using threading approaches and multi-core CPUs to control independent GPU devices. We present speed-up data and discuss multi-threading software issues for the applications level programmer and o er some suggested areas for language development and integration between coarse-grained and ne-grained multi-thread systems. We discuss results from three common simulation algorithmic areas including: partial di erential equations; graph cluster metric calculations and random number generation. We report on programming experiences and selected performance for these algorithms on: single and multiple GPUs; multi-core CPUs; a CellBE; and using OpenCL. We discuss programmer usability issues and the outlook and trends in multi-core programming for scienti c applications developers

Peer to Peer Information Retrieval: An Overview

Peer-to-peer technology is widely used for file sharing. In the past decade a number of prototype peer-to-peer information retrieval systems have been developed. Unfortunately, none of these have seen widespread real- world adoption and thus, in contrast with file sharing, information retrieval is still dominated by centralised solutions. In this paper we provide an overview of the key challenges for peer-to-peer information retrieval and the work done so far. We want to stimulate and inspire further research to overcome these challenges. This will open the door to the development and large-scale deployment of real-world peer-to-peer information retrieval systems that rival existing centralised client-server solutions in terms of scalability, performance, user satisfaction and freedom

Distributed-Memory Breadth-First Search on Massive Graphs

This chapter studies the problem of traversing large graphs using the breadth-first search order on distributed-memory supercomputers. We consider both the traditional level-synchronous top-down algorithm as well as the recently discovered direction optimizing algorithm. We analyze the performance and scalability trade-offs in using different local data structures such as CSR and DCSC, enabling in-node multithreading, and graph decompositions such as 1D and 2D decomposition.Comment: arXiv admin note: text overlap with arXiv:1104.451