NetCDF

NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

Availability & Restrictions

NetCDF is available without restriction to all OSC users.

The following versions of NetCDF are available at OSC:

Version Glenn Oakley
3.6.2 X  
4.1.3   X

Usage

Set-up

To initalize either system prior to using NetCDF, run the following comand:

module load netcdf

To use the parallel implementation of netcdf, run the following command instead:

module load pnetcdf

Building With NetDCF

With the netcdf library loaded, the following environment variables will be available for use:

Variable Use
$NETCDF_CFLAGS Use during your compilation step for C programs.
$NETCDF_FFLAGS Use during your compilation step for Fortran programs.
$NETCDF_LIBS Use when linking your program to NetCDF.

Similarly, when the pnetcdf module is loaded, the following environment variables will be available:

VARIABLE USE
$PNETCDF_CFLAGS Use during your compilation step for C programs.
$PNETCDF_FFLAGS Use during your compilation step for Fortran programs.
$PNETCDF_LIBS Use when linking your program to NetCDF.

 

For example, to build the code myprog.c with the netcdf library you would use:

icc -c $NETCDF_CFLAGS myprog.c
icc -o myprog myprog.o $NETCDF_LIBS

Batch Usage

You must load the netcdf or pnetcdf module in your batch script before executing a program which is built with the netcdf library

#PBS -N AppNameJob
#PBS -l nodes=1:ppn=12

module load netcdf
cd $PBS_O_WORKDIR
cp foo.dat $TMPDIR
cd $TMPDIR

appname < foo.dat > foo.out

cp foo.out $PBS_O_WORKDIR

Further Reading

See Also

  • hdf5 software page
Service: