Initalizing the system for use of the NetCDF is dependent on the system you are using and the compiler you are using. To load the default NetCDF, run the following command: module load netcdf. To use the parallel implementation of NetCDF, run the following command instead: module load pnetcdf. To load a particular version, use  module load netcdf/version. For example, use  module load netcdf/4.3.3.1 to load NetCDF version 4.3.3.1. You can use module spider netcdf to view available modules.

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 or 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

When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Non-interactive Batch Job (Serial Run)

A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. You must load the netcdf or pnetcdf module in your batch script before executing a program which is built with the netcdf library. Below is the example batch script that executes a program built with NetCDF:

#!/bin/bash
#SBATCH --job-name=job-name
#SBATCH --nodes=1 --ntasks-per-node=28
#SBATCH --account <project-account>

module load netcdf
cp foo.dat $TMPDIR
cd $TMPDIR
appname < foo.dat > foo.out
cp foo.out $SLURM_SUBMIT_DIR

Initalizing the system for use of the NetCDF is dependent on the system you are using and the compiler you are using. To load the default NetCDF, run the following command: module load netcdf. 

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 or 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

#!/bin/bash 
#SBATCH --job-name=job-name
#SBATCH --nodes=1 --ntasks-per-node=48 
#SBATCH --account <project-account> 

module load netcdf 
cp foo.dat $TMPDIR 
cd $TMPDIR 
appname < foo.dat > foo.out 
cp foo.out $SLURM_SUBMIT_DIR