Build PnetCDF Library

PnetCDF API Reference

  • PnetCDF C interface guide can be found  here.

Tutorial

  • A Quick Tutorial demonstrates some simple aspects of the library, with full code examples.
  • Additional example programs in C, Fortran 77, Fortran 90, and C++ are provided in all PnetCDF source releases under the directory "examples". Refer examples/README for brief descriptions of individual example programs.

Performance Tuning

  • For performance improvement, some general guide lines are available in  Questions and Answers.
  • I/O hints for PnetCDF describes some low-level tuning parameters
    • File offset alignment documents a way to adjust the layout of file header and variables in a dataset, and why/when you might want to do so
  • Nonblocking APIs are introduced as an I/O optimization in version 1.1. They can be used to aggregate multiple I/O requests into a larger one for better performance.
    • Usage: users first post multiple nonblocking I/O requests and then make a call to the wait API to commit the requests. The wait call combines all the pending requests into one bigger MPI I/O request.
    • Buffered write API describes the non-blocking routines that copy data to a temporary buffer. The advantage is the user buffers can freely be modified once the requests are posted.
  •  Subfiling is a mechanism to internally partition a netCDF file into multiple files (subfiles), making the netCDF data appear as a single file to users. Subfiling can reduce file access contention when a large number of processes make concurrent I/O requests to a shared file.

PnetCDF API design document

  • In each release, the file  doc/pnetcdf-api.pdf (built by running command 'make' in directory doc/) describes how the PnetCDF APIs are designed. We have designed the APIs to be more friendly to parallel I/O while maintaining file format compatibility with the serial version of NetCDF.

Unix man pages

  • Unix man pages for C, Fortran 77 and 90 are also available together with the release.
  • Unix commands: 'man pnetcdf', 'man pnetcdf_f77', and 'man pnetcdf_f90'

Publications and presentations

  • Jianwei Li, Wei-keng Liao, Alok Choudhary, Robert Ross, Rajeev Thakur, William Gropp, Rob Latham, Andrew Siegel, Brad Gallagher, and Michael Zingale. Parallel netCDF: A Scientific High-Performance I/O Interface]. In the Proceedings of Supercomputing Conference, November, 2003. ( PDF, 97k)
  • The above paper discusses the design of PnetCDF library and presents some performance results.
  • Jianwei Li's presentation from the SC 2003 conference ( PDF, 167k).

Hacking

Others

  • NetCDF-4 can use PnetCDF. We think this is great. More information: PnetcdfAndNetcdf4
  • Forrest Hoffman wrote an article about PnetCDF in the July 2004 issue of Linux Magazine.
  • The HDF group at NCSA ported a serial NetCDF code to one using PnetCDF. They posted  a writeup of their efforts . It's a little old but does provide some additional information to supplement doc/porting_notes.txt
  • PnetCDF user guide and other API references are still under construction.
  •  Unidata's serial NetCDF documentation sometimes comes in handy for comparison.