NetCDF

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Developer: Unidata Platforms: NEC Nehalem Cluster Category: Storage Formats License: Open Source Website: Official NetCDF Homepage

Using NetCDF on Nehalem cluster

There are two versions of NetCDF instaled on Nehalem cluster:

• intel
• gnu

Example

This example shows the basic steps when using NetCDF.

Load the necessary module, for example the intel version:

module load tools/netcdf/4.3.3-intel-14.0.4

Simple program using NetCDF:

File: ex_netcdf.c

#include <stdlib.h>
#include <stdio.h>
#include <netcdf.h>

/* This is the name of the data file we will create. */
#define FILE_NAME "ex_netcdf.nc"

/* We are writing 2D data, a 6 x 12 grid. */
#define NDIMS 2
#define NX 60
#define NY 120

/* Handle errors by printing an error message and exiting with a
 * non-zero status. */
#define ERRCODE 2
#define ERR(e) {printf("Error: %s\n", nc_strerror(e)); exit(ERRCODE);}

int
main()
{
   int ncid, x_dimid, y_dimid, varid;
   int dimids[NDIMS];
   size_t chunks[NDIMS];
   int shuffle, deflate, deflate_level;
   int data_out[NX][NY];
   int x, y, retval;
      

   /* Set chunking, shuffle, and deflate. */
   shuffle = NC_SHUFFLE;
   deflate = 1;
   deflate_level = 1;

   /* Create some pretend data. If this wasn't an example program, we
    * would have some real data to write, for example, model output. */
   for (x = 0; x < NX; x++)
      for (y = 0; y < NY; y++)
         data_out[x][y] = x * NY + y;

   /* Create the file. The NC_NETCDF4 parameter tells netCDF to create
    * a file in netCDF-4/HDF5 standard. */
   if ((retval = nc_create(FILE_NAME, NC_NETCDF4, &ncid)))
      ERR(retval);

   /* Define the dimensions. */
   if ((retval = nc_def_dim(ncid, "x", NX, &x_dimid)))
      ERR(retval);
   if ((retval = nc_def_dim(ncid, "y", NY, &y_dimid)))
      ERR(retval);

   /* Set up variabe data. */
   dimids[0] = x_dimid;
   dimids[1] = y_dimid;
   chunks[0] = NX/4;
   chunks[1] = NY/4;
   /* Define the variable. */
   if ((retval = nc_def_var(ncid, "data", NC_INT, NDIMS,
                            dimids, &varid)))
      ERR(retval);
   if ((retval = nc_def_var_chunking(ncid, varid, 0, &chunks[0])))
      ERR(retval);
   if ((retval = nc_def_var_deflate(ncid, varid, shuffle, deflate,
                                    deflate_level)))
      ERR(retval);

   /* No need to explicitly end define mode for netCDF-4 files. Write
    * the pretend data to the file. */
   if ((retval = nc_put_var_int(ncid, varid, &data_out[0][0])))
      ERR(retval);

   /* Close the file. */
   if ((retval = nc_close(ncid)))
      ERR(retval);

   printf("*** SUCCESS writing example file simple_xy_nc4.nc!\n");
   return 0;
}

Compile with:

icc ex_netcdf.c -I /opt/tools/netcdf/4.3.3-intel-14.0.4/include/ -L /opt/tools/netcdf/4.3.3-intel-14.0.4/lib/ -lnetcdf

or if you have a fortran program

ifort ex_netcdf.f90 -I /opt/tools/netcdf/4.3.3-intel-14.0.4/include/ -L /opt/tools/netcdf/4.3.3-intel-14.0.4/lib/ -lnetcdff -lnetcdf

See also

• Software Development Tools, Compilers & Libraries

External links

• Official NetCDF Homepage