ParallelIO

The Parallel IO libraries (PIO) are high-level parallel I/O C and Fortran libraries for applications that need to do netCDF I/O from large numbers of processors on a HPC system.

PIO provides a netCDF-like API, and allows users to designate some subset of processors to perform IO. Computational code calls netCDF-like functions to read and write data, and PIO uses the IO processors to perform all necessary IO.

Intracomm Mode

In Intracomm mode, PIO allows the user to designate some subset of processors to do all I/O. The I/O processors also participate in computational work.

Async Mode

PIO also supports the creation of multiple computation components, each containing many processors, and one shared set of IO processors. The computational components can perform write operation asynchronously, and the IO processors will take care of all storage interaction.

Website

For complete documentation, see our website at http://ncar.github.io/ParallelIO/.

Mailing List

The (low-traffic) PIO mailing list is at https://groups.google.com/forum/#!forum/parallelio, send email to the list at parallelio@googlegroups.com.

Testing

The results of our continuous integration testing with GitHub actions can be found on any of the Pull Requests on the GitHub site: https://github.com/NCAR/ParallelIO.

The results of our nightly tests on multiple platforms can be found on our cdash site at http://my.cdash.org/index.php?project=PIO.

Dependencies

PIO can use NetCDF (version 4.6.1+) and/or PnetCDF (version 1.9.0+) for I/O. NetCDF may be built with or without netCDF-4 features. NetCDF is required for PIO, PnetCDF is optional.

The NetCDF C library must be built with MPI, which requires that it be linked with an MPI-enabled version of HDF5. Optionally, NetCDF can be built with DAP support, which introduces a dependency on CURL. HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.

Building PIO

To build PIO, unpack the distribution tarball and do:

CC=mpicc FC=mpif90 ./configure --enable-fortran && make check install

For a full description of the available options and flags, try:

./configure --help

Note that environment variables CC and FC may need to be set to the MPI versions of the C and Fortran compiler. Also CPPFLAGS and LDFLAGS may need to be set to indicate the locations of one or more of the dependent libraries. (If using MPI compilers, the entire set of dependent libraries should be built with the same compilers.) For example:

export CC=mpicc
export FC=mpifort
export CPPFLAGS='-I/usr/local/netcdf-fortran-4.4.5_c_4.6.3_mpich-3.2/include -I/usr/local/netcdf-c-4.6.3_hdf5-1.10.5/include -I/usr/local/pnetcdf-1.11.0_shared/include'
export LDFLAGS='-L/usr/local/netcdf-c-4.6.3_hdf5-1.10.5/lib -L/usr/local/pnetcdf-1.11.0_shared/lib'
./configure --prefix=/usr/local/pio-2.4.2 --enable-fortran
make check
make install

Building with CMake

The typical configuration with CMake can be done as follows:

CC=mpicc FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/source

Full instructions for the cmake build can be found in the installation documentation.

References

Hartnett, E., Edwards, J., "THE PARALLELIO (PIO) C/FORTRAN LIBRARIES FOR SCALABLE HPC PERFORMANCE", 37th Conference on Environmental Information Processing Technologies, American Meteorological Society Annual Meeting, January, 2021. Retrieved on Feb 3, 2021, from [https://www.researchgate.net/publication/348169990_THE_PARALLELIO_PIO_CFORTRAN_LIBRARIES_FOR_SCALABLE_HPC_PERFORMANCE].

Hartnett, E., Edwards, J., "POSTER: THE PARALLELIO (PIO) C/FORTRAN LIBRARIES FOR SCALABLE HPC PERFORMANCE", 37th Conference on Environmental Information Processing Technologies, American Meteorological Society Annual Meeting, January, 2021. Retrieved on Feb 3, 2021, from [https://www.researchgate.net/publication/348170136_THE_PARALLELIO_PIO_CFORTRAN_LIBRARIES_FOR_SCALABLE_HPC_PERFORMANCE].