Combining I/O operations for multiple array variables in parallel netCDF

Kui Gao*, Wei Keng Liao, Alok Choudhary, Robert Ross, Robert Latham

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Scopus citations

Abstract

Parallel netCDF (PnetCDF) is a popular library used in many scientific applications to store scientific datasets. It provides high-performance parallel I/O while maintaining file-format compatibility with Unidata's netCDF. Array variables comprise the bulk of the data in a netCDF dataset, and for accesses to large regions of single array variables, PnetCDF attains very high performance. However, the current PnetCDF interface only allows access to one array variable per call. If an application instead accesses a large number of small-sized array variables, this interface limitation can cause significant performance degradation, because high end network and storage systems deliver much higher performance with larger request sizes. Moreover, the record variables data is stored interleaved by record, and the contiguity information is lost, so the existing MPI-IO collective I/O optimization can not help. This paper presents a new mechanism for PnetCDF to combine multiple I/O operations for better I/O performance. This mechanism can be used in a new function that takes arguments for reading/writing multiple array variables, allowing application programmers to explicitly access multiple array variables in a single call. It can also be used in the implementation of asynchronous I/O functions, so that the combination is carried out implicitly, without changes to the application. Our performance results demonstrate significant improvement using well-known application benchmarks.

Original languageEnglish (US)
Title of host publication2009 IEEE International Conference on Cluster Computing and Workshops, CLUSTER '09
DOIs
StatePublished - Dec 21 2009
Event2009 IEEE International Conference on Cluster Computing and Workshops, CLUSTER '09 - New Orleans, LA, United States
Duration: Aug 31 2009Sep 4 2009

Publication series

NameProceedings - IEEE International Conference on Cluster Computing, ICCC
ISSN (Print)1552-5244

Other

Other2009 IEEE International Conference on Cluster Computing and Workshops, CLUSTER '09
CountryUnited States
CityNew Orleans, LA
Period8/31/099/4/09

Keywords

  • MPI-IO
  • Parallel netCDF
  • Parallel-IO

ASJC Scopus subject areas

  • Software
  • Hardware and Architecture
  • Signal Processing

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