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NetCDF
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| 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. |
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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