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Register a new userEnabling Loosely-Coupled Serial Job Execution on the IBM BlueGene/P Supercomputer and the SiCortex SC5832
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Added by
Ioan Raicu
Publication date
2008
fields
Informatics Engineering
and research's language is
English
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Our work addresses the enabling of the execution of highly parallel computations composed of loosely coupled serial jobs with no modifications to the respective applications, on large-scale systems. This approach allows new-and potentially far larger-classes of application to leverage systems such as the IBM Blue Gene/P supercomputer and similar emerging petascale architectures. We present here the challenges of I/O performance encountered in making this model practical, and show results using both micro-benchmarks and real applications on two large-scale systems, the BG/P and the SiCortex SC5832. Our preliminary benchmarks show that we can scale to 4096 processors on the Blue Gene/P and 5832 processors on the SiCortex with high efficiency, and can achieve thousands of tasks/sec sustained execution rates for parallel workloads of ordinary serial applications. We measured applications from two domains, economic energy modeling and molecular dynamics.
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We have extended the Falkon lightweight task execution framework to make loosely coupled programming on petascale systems a practical and useful programming model. This work studies and measures the performance factors involved in applying this approach to enable the use of petascale systems by a broader user community, and with greater ease. Our work enables the execution of highly parallel computations composed of loosely coupled serial jobs with no modifications to the respective applications. This approach allows a new-and potentially far larger-class of applications to leverage petascale systems, such as the IBM Blue Gene/P supercomputer. We present the challenges of I/O performance encountered in making this model practical, and show results using both microbenchmarks and real applications from two domains: economic energy modeling and molecular dynamics. Our benchmarks show that we can scale up to 160K processor-cores with high efficiency, and can achieve sustained execution rates of thousands of tasks per second.
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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.
In order to achieve near-time insights, scientific workflows tend to be organized in a flexible and dynamic way. Data-driven triggering of tasks has been explored as a way to support workflows that evolve based on the data. However, the overhead introduced by such dynamic triggering of tasks is an under-studied topic. This paper discusses different facets of dynamic task triggers. Particularly, we explore different ways of constructing a data-driven dynamic workflow and then evaluate the overheads introduced by such design decisions. We evaluate workflows with varying data size, percentage of interesting data, temporal data distribution, and number of tasks triggered. Finally, we provide advice based upon analysis of the evaluation results for users looking to construct data-driven scientific workflows.
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