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NetCDF
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NetCDF (Network Common Data Form) 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. The project homepage is hosted by the Unidata program at the University Corporation for Atmospheric Research (UCAR). |
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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