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Array files for computational chemistry: MP2 energies.

Alan R Ford1, Tomasz Janowski, Peter Pulay

  • 1Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA. arford@astate.edu

Journal of Computational Chemistry
|February 15, 2007
PubMed
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Array files (AF) offer a straightforward message-passing system for distributed disk storage, simplifying parallel computing for large datasets in computational chemistry and beyond. This approach enhances efficiency and programming ease for complex calculations.

Area of Science:

  • Computational Chemistry
  • High-Performance Computing
  • Data Storage Systems

Background:

  • Handling large datasets in scientific applications requires efficient storage and access methods.
  • Parallel computing environments necessitate specialized data management strategies.
  • Existing systems may present programming complexities for distributed data.

Purpose of the Study:

  • To introduce Array Files (AF), a message-passing implementation for distributed disk storage.
  • To demonstrate the utility of AF for parallelizing computational chemistry applications.
  • To simplify the programming effort for applications handling large disk-based data.

Main Methods:

  • Developed a message-passing implementation named Array Files (AF).
  • Designed AF for transparent distributed storage and access of large data files.

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  • Stored individual records (0.1-32 MB) on single nodes, avoiding striping.

    • Main Results:

    • Implemented second-order Møller-Plesset (MP2) energies using AF.
    • AF implementation achieved efficiency comparable to hand-coded programs.
    • AF system significantly simplifies programming for complex calculations like Coupled Cluster energies.

    Conclusions:

    • Array Files provide an efficient and user-friendly solution for distributed disk storage in scientific computing.
    • AF is particularly beneficial for parallelizing computational chemistry tasks.
    • The system's design facilitates easier development of complex, data-intensive applications.