Unidata

2.2 Parallel Access for NetCDF Files

For netCDF-4 files only, parallel read/write access is possible on systems which support it, and only if parallel HDF5 was installed on the system before netCDF, and only if the HDF5 parallel compiler was used during the netCDF configure. (Parallel HDF5 requires the MPI library).

To use parallel access, open or create the file with nc_open_par (see nc_open_par) or nc_create_par (see nc_create_par). Only netCDF-4 files can be opened or created for parallel access.

The following example shows the creation of a file using parallel access, and how a program might write data to such a file.

     #include "netcdf.h"
     #include <mpi.h>
     #include <assert.h>
     #include "hdf5.h"
     #include <string.h>
     #include <stdlib.h>
     
     #define BAIL(e) do { \
     printf("Bailing out in file %s, line %d, error:%s.\n", __FILE__, __LINE__, nc_strerror(e)); \
     return e; \
     } while (0)
     
     #define FILE "test_par.nc"
     #define NDIMS 2
     #define DIMSIZE 24
     #define QTR_DATA (DIMSIZE*DIMSIZE/4)
     #define NUM_PROC 4
     
     int
     main(int argc, char **argv)
     {
         /* MPI stuff. */
         int mpi_namelen;
         char mpi_name[MPI_MAX_PROCESSOR_NAME];
         int mpi_size, mpi_rank;
         MPI_Comm comm = MPI_COMM_WORLD;
         MPI_Info info = MPI_INFO_NULL;
     
         /* Netcdf-4 stuff. */
         int ncid, v1id, dimids[NDIMS];
         size_t start[NDIMS], count[NDIMS];
     
         int data[DIMSIZE*DIMSIZE], j, i, res;
     
         /* Initialize MPI. */
         MPI_Init(&argc,&argv);
         MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
         MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
         MPI_Get_processor_name(mpi_name, &mpi_namelen);
         printf("mpi_name: %s size: %d rank: %d\n", mpi_name,
                mpi_size, mpi_rank);
     
         /* Create a parallel netcdf-4 file. */
         if ((res = nc_create_par(FILE, NC_NETCDF4|NC_MPIIO, comm,
                                  info, &ncid)))
             BAIL(res);
     
         /* Create two dimensions. */
         if ((res = nc_def_dim(ncid, "d1", DIMSIZE, dimids)))
            BAIL(res);
         if ((res = nc_def_dim(ncid, "d2", DIMSIZE, &dimids[1])))
            BAIL(res);
     
         /* Create one var. */
         if ((res = nc_def_var(ncid, "v1", NC_INT, NDIMS, dimids, &v1id)))
            BAIL(res);
     
         if ((res = nc_enddef(ncid)))
            BAIL(res);
     
         /* Set up slab for this process. */
         start[0] = mpi_rank * DIMSIZE/mpi_size;
         start[1] = 0;
         count[0] = DIMSIZE/mpi_size;
         count[1] = DIMSIZE;
         printf("mpi_rank=%d start[0]=%d start[1]=%d count[0]=%d count[1]=%d\n",
                mpi_rank, start[0], start[1], count[0], count[1]);
     
         /* Create phony data. We're going to write a 24x24 array of ints,
            in 4 sets of 144. */
         printf("mpi_rank*QTR_DATA=%d (mpi_rank+1)*QTR_DATA-1=%d\n",
                mpi_rank*QTR_DATA, (mpi_rank+1)*QTR_DATA);
         for (i=mpi_rank*QTR_DATA; i<(mpi_rank+1)*QTR_DATA; i++)
            data[i] = mpi_rank;
     
         /*if ((res = nc_var_par_access(ncid, v1id, NC_COLLECTIVE)))
           BAIL(res);*/
         if ((res = nc_var_par_access(ncid, v1id, NC_INDEPENDENT)))
            BAIL(res);
     
         /* Write slabs of phony data. */
         if ((res = nc_put_vara_int(ncid, v1id, start, count,
                                    &data[mpi_rank*QTR_DATA])))
            BAIL(res);
     
         /* Close the netcdf file. */
         if ((res = nc_close(ncid)))
             BAIL(res);
     
         /* Shut down MPI. */
         MPI_Finalize();
     
         return 0;
     }