PnetCDF is a library providing high-performance parallel I/O while still maintaining file-format compatibility with Unidata's NetCDF, specifically the formats of CDF-1 and CDF-2. Although NetCDF supports parallel I/O starting from version 4, the files must be in HDF5 format. PnetCDF is currently the only choice for carrying out parallel I/O on files that are in classic formats (CDF-1 and 2). In addition, PnetCDF supports the CDF-5 file format, an extension of CDF-2, that supports more data types and allows users to define large dimensions, attributes, and variables (>2B elements).
Availability and Restrictions
Versions
The following versions of PnetCDF are available at OSC:
| Version | Owens | Pitzer | Cardinal |
|---|---|---|---|
| 1.7.0 | X* | ||
| 1.8.1 | X | ||
| 1.10.0 | X | ||
| 1.12.1 | X* | ||
| 1.12.3 | X |
You can use module spider pnetcdf to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work. On Cardinal the module name is different, use module spider parallel-netcdf to view available modules on Cardinal
Access
PnetCDF is available to all OSC users. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
Northwestern University and Argonne National Lab., Open source
Usage
Usage on Owens
Set-up
To initalize the system prior to using PnetCDF, run the following comand:
module load pnetcdf
Building With PnetDCF
With the PnetCDF module loaded, the following environment variables will be available for use:
| VARIABLE | USE |
|---|---|
| $PNETCDF_CFLAGS | Use during your compilation step for C or C++ programs. |
| $PNETCDF_FFLAGS | Use during your compilation step for Fortran programs. |
| $PNETCDF_LIBS |
Use when linking your program to PnetCDF. |
| $PNETCDF | Path to the PnetCDF installation directory |
For example, to build the code myprog.c with the pnetcdf library you would use:
mpicc -c $PNETCDF_CFLAGS myprog.c mpicc -o myprog myprog.o $PNETCDF_LIBS
Batch Usage
#!/bin/bash #SBATCH --job-name=AppNameJob #SBATCH --nodes=1 --ntasks-per-node=28 #SBATCH --account <project-account> srun ./myprog
