int main(int argc, char** argv) { extern int optind; char filename[256]; int i, j, rank, nprocs, verbose=1, err, nerrs=0; int ncid, cmode, varid, dimid[2], buf[NY][NX]; char str_att[128]; float float_att[100]; MPI_Offset global_ny, global_nx; MPI_Offset start[2], count[2]; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &nprocs); /* get command-line arguments */ while ((i = getopt(argc, argv, "hq")) != EOF) switch(i) { case 'q': verbose = 0; break; case 'h': default: if (rank==0) usage(argv[0]); MPI_Finalize(); return 1; } if (argv[optind] == NULL) strcpy(filename, "testfile.nc"); else snprintf(filename, 256, "%s", argv[optind]); MPI_Bcast(filename, 256, MPI_CHAR, 0, MPI_COMM_WORLD); if (verbose && rank == 0) printf("%s: example of using put_vara APIs\n",__FILE__); /* create a new file for writing ----------------------------------------*/ cmode = NC_CLOBBER | NC_64BIT_DATA; err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL, &ncid); ERR /* the global array is NY * (NX * nprocs) */ global_ny = NY; global_nx = NX * nprocs; for (i=0; i<NY; i++) for (j=0; j<NX; j++) buf[i][j] = rank; /* add a global attribute: a time stamp at rank 0 */ time_t ltime = time(NULL); /* get the current calendar time */ asctime_r(localtime(<ime), str_att); /* make sure the time string are consistent among all processes */ MPI_Bcast(str_att, strlen(str_att), MPI_CHAR, 0, MPI_COMM_WORLD); err = ncmpi_put_att_text(ncid, NC_GLOBAL, "history", strlen(str_att), &str_att[0]); ERR /* define dimensions x and y */ err = ncmpi_def_dim(ncid, "Y", global_ny, &dimid[0]); ERR err = ncmpi_def_dim(ncid, "X", global_nx, &dimid[1]); ERR /* define a 2D variable of integer type */ err = ncmpi_def_var(ncid, "var", NC_INT, 2, dimid, &varid); ERR /* add attributes to the variable */ strcpy(str_att, "example attribute of type text."); err = ncmpi_put_att_text(ncid, varid, "str_att_name", strlen(str_att), &str_att[0]); ERR for (i=0; i<8; i++) float_att[i] = i; err = ncmpi_put_att_float(ncid, varid, "float_att_name", NC_FLOAT, 8, &float_att[0]); ERR long long int64_att=10000000000LL; err = ncmpi_put_att_longlong(ncid, varid, "int64_att_name", NC_INT64, 1, &int64_att); ERR /* do not forget to exit define mode */ err = ncmpi_enddef(ncid); ERR /* now we are in data mode */ start[0] = 0; start[1] = NX * rank; count[0] = NY; count[1] = NX; err = ncmpi_put_vara_int_all(ncid, varid, start, count, &buf[0][0]); ERR err = ncmpi_close(ncid); ERR /* check if there is any PnetCDF internal malloc residue */ MPI_Offset malloc_size, sum_size; err = ncmpi_inq_malloc_size(&malloc_size); if (err == NC_NOERR) { MPI_Reduce(&malloc_size, &sum_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD); if (rank == 0 && sum_size > 0) printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n", sum_size); } MPI_Finalize(); return (nerrs > 0); }
int main(int argc, char **argv) { int i, j; int status; int ncid1, ncid2; int ndims, nvars, ngatts, unlimdimid; char name[NC_MAX_NAME]; nc_type type, vartypes[NC_MAX_VARS]; MPI_Offset attlen; MPI_Offset dimlen, shape[NC_MAX_VAR_DIMS], varsize, start[NC_MAX_VAR_DIMS]; void *valuep; int dimids[NC_MAX_DIMS], varids[NC_MAX_VARS]; int vardims[NC_MAX_VARS][NC_MAX_VAR_DIMS/16]; /* divided by 16 due to my memory limitation */ int varndims[NC_MAX_VARS], varnatts[NC_MAX_VARS]; params opts; int rank; int nprocs; MPI_Comm comm = MPI_COMM_WORLD; MPI_Init(&argc, &argv); MPI_Comm_size(MPI_COMM_WORLD, &nprocs); MPI_Comm_rank(MPI_COMM_WORLD, &rank); if (rank == 0) fprintf(stderr, "Testing independent read ... "); parse_read_args(argc, argv, rank, &opts); /********** START OF NETCDF ACCESS **************/ /* Read a netCDF file and write it out to another file */ /** * Open the input dataset - ncid1: * File name: "../data/test_int.nc" * Dataset API: Collective * And create the output dataset - ncid2: * File name: "testread.nc" * Dataset API: Collective */ status = ncmpi_open(comm, opts.infname, 0, MPI_INFO_NULL, &ncid1); if (status != NC_NOERR) handle_error(status); status = ncmpi_create(comm, opts.outfname, NC_CLOBBER, MPI_INFO_NULL, &ncid2); if (status != NC_NOERR) handle_error(status); /** * Inquire the dataset definitions of input dataset AND * Add dataset definitions for output dataset. */ status = ncmpi_inq(ncid1, &ndims, &nvars, &ngatts, &unlimdimid); if (status != NC_NOERR) handle_error(status); /* Inquire global attributes, assume CHAR attributes. */ for (i = 0; i < ngatts; i++) { status = ncmpi_inq_attname(ncid1, NC_GLOBAL, i, name); if (status != NC_NOERR) handle_error(status); status = ncmpi_inq_att (ncid1, NC_GLOBAL, name, &type, &attlen); if (status != NC_NOERR) handle_error(status); switch (type) { case NC_CHAR: valuep = (void *)malloc(attlen * sizeof(char)); status = ncmpi_get_att_text(ncid1, NC_GLOBAL, name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_text (ncid2, NC_GLOBAL, name, attlen, (char *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_SHORT: valuep = (void *)malloc(attlen * sizeof(short)); status = ncmpi_get_att_short(ncid1, NC_GLOBAL, name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_short (ncid2, NC_GLOBAL, name, type, attlen, (short *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_INT: valuep = (void *)malloc(attlen * sizeof(int)); status = ncmpi_get_att_int(ncid1, NC_GLOBAL, name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_int (ncid2, NC_GLOBAL, name, type, attlen, (int *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_FLOAT: valuep = (void *)malloc(attlen * sizeof(float)); status = ncmpi_get_att_float(ncid1, NC_GLOBAL, name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_float (ncid2, NC_GLOBAL, name, type, attlen, (float *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_DOUBLE: valuep = (void *)malloc(attlen * sizeof(double)); status = ncmpi_get_att_double(ncid1, NC_GLOBAL, name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_double (ncid2, NC_GLOBAL, name, type, attlen, (double *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; default: ; /* handle unexpected types */ } } /* Inquire dimension */ for (i = 0; i < ndims; i++) { status = ncmpi_inq_dim(ncid1, i, name, &dimlen); if (status != NC_NOERR) handle_error(status); if (i == unlimdimid) dimlen = NC_UNLIMITED; status = ncmpi_def_dim(ncid2, name, dimlen, dimids+i); if (status != NC_NOERR) handle_error(status); } /* Inquire variables */ for (i = 0; i < nvars; i++) { status = ncmpi_inq_var (ncid1, i, name, vartypes+i, varndims+i, vardims[i], varnatts+i); if (status != NC_NOERR) handle_error(status); status = ncmpi_def_var(ncid2, name, vartypes[i], varndims[i], vardims[i], varids+i); if (status != NC_NOERR) handle_error(status); /* var attributes, assume CHAR attributes */ for (j = 0; j < varnatts[i]; j++) { status = ncmpi_inq_attname(ncid1, varids[i], j, name); if (status != NC_NOERR) handle_error(status); status = ncmpi_inq_att (ncid1, varids[i], name, &type, &attlen); if (status != NC_NOERR) handle_error(status); switch (type) { case NC_CHAR: valuep = (void *)malloc(attlen * sizeof(char)); status = ncmpi_get_att_text(ncid1, varids[i], name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_text (ncid2, varids[i], name, attlen, (char *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_SHORT: valuep = (void *)malloc(attlen * sizeof(short)); status = ncmpi_get_att_short(ncid1, varids[i], name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_short (ncid2, varids[i], name, type, attlen, (short *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_INT: valuep = (void *)malloc(attlen * sizeof(int)); status = ncmpi_get_att_int(ncid1, varids[i], name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_int (ncid2, varids[i], name, type, attlen, (int *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_FLOAT: valuep = (void *)malloc(attlen * sizeof(float)); status = ncmpi_get_att_float(ncid1, varids[i], name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_float (ncid2, varids[i], name, type, attlen, (float *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_DOUBLE: valuep = (void *)malloc(attlen * sizeof(double)); status = ncmpi_get_att_double(ncid1, varids[i], name, valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_att_double (ncid2, varids[i], name, type, attlen, (double *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; default: ; /* handle unexpected types */ } } } /** * End Define Mode (switch to data mode) for output dataset * Dataset API: Collective */ status = ncmpi_enddef(ncid2); if (status != NC_NOERR) handle_error(status); /** * Read data of variables from input dataset (assume INT variables) * Write the data out to the corresponding variables in the output dataset * * Data Partition (Assume 4 processors): * square: 2-D, (Block, *), 25*100 from 100*100 * cube: 3-D, (Block, *, *), 25*100*100 from 100*100*100 * xytime: 3-D, (Block, *, *), 25*100*100 from 100*100*100 * time: 1-D, Block-wise, 25 from 100 * * Data Mode API: non-collective */ status = ncmpi_begin_indep_data(ncid1); if (status != NC_NOERR) handle_error(status); status =ncmpi_begin_indep_data(ncid2); if (status != NC_NOERR) handle_error(status); for (i = 0; i < NC_MAX_VAR_DIMS; i++) start[i] = 0; for (i = 0; i < nvars; i++) { varsize = 1; for (j = 0; j < varndims[i]; j++) { status = ncmpi_inq_dim(ncid1, vardims[i][j], name, shape + j); if (status != NC_NOERR) handle_error(status); if (j == 0) { shape[j] /= nprocs; start[j] = shape[j] * rank; } varsize *= shape[j]; } switch (vartypes[i]) { case NC_CHAR: break; case NC_SHORT: valuep = (void *)malloc(varsize * sizeof(short)); status = ncmpi_get_vara_short(ncid1, i, start, shape, (short *)valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_vara_short(ncid2, varids[i], start, shape, (short *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_INT: valuep = (void *)malloc(varsize * sizeof(int)); status = ncmpi_get_vara_int(ncid1, i, start, shape, (int *)valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_vara_int(ncid2, varids[i], start, shape, (int *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_FLOAT: valuep = (void *)malloc(varsize * sizeof(float)); status = ncmpi_get_vara_float(ncid1, i, start, shape, (float *)valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_vara_float(ncid2, varids[i], start, shape, (float *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; case NC_DOUBLE: valuep = (void *)malloc(varsize * sizeof(double)); status = ncmpi_get_vara_double(ncid1, i, start, shape, (double *)valuep); if (status != NC_NOERR) handle_error(status); status = ncmpi_put_vara_double(ncid2, varids[i], start, shape, (double *)valuep); if (status != NC_NOERR) handle_error(status); free(valuep); break; default: ; /* handle unexpected types */ } } status = ncmpi_end_indep_data(ncid1); if (status != NC_NOERR) handle_error(status); status = ncmpi_end_indep_data(ncid2); if (status != NC_NOERR) handle_error(status); status = ncmpi_sync(ncid1); if (status != NC_NOERR) handle_error(status); status = ncmpi_sync(ncid2); if (status != NC_NOERR) handle_error(status); /** * Close the datasets * Dataset API: collective */ status = ncmpi_close(ncid1); if (status != NC_NOERR) handle_error(status); status = ncmpi_close(ncid2); if (status != NC_NOERR) handle_error(status); /******************* END OF NETCDF ACCESS ****************/ if (rank == 0) fprintf(stderr, "OK\nInput file %s copied to: %s!\n", opts.infname, opts.outfname); MPI_Finalize(); return 0; }
/* Write an attribute with type conversion. */ static int nc4_put_att_tc(int ncid, int varid, const char *name, nc_type file_type, nc_type mem_type, int mem_type_is_long, size_t len, const void *op) { NC *nc; NC_HDF5_FILE_INFO_T *h5; if (!name || strlen(name) > NC_MAX_NAME) return NC_EBADNAME; LOG((3, "nc4_put_att_tc: ncid 0x%x varid %d name %s file_type %d " "mem_type %d len %d", ncid, varid, name, file_type, mem_type, len)); /* The length needs to be positive (cast needed for braindead systems with signed size_t). */ if((unsigned long) len > X_INT_MAX) return NC_EINVAL; /* Find metadata. */ if (!(nc = nc4_find_nc_file(ncid,NULL))) return NC_EBADID; /* get netcdf-4 metadata */ h5 = NC4_DATA(nc); assert(h5); #if 0 /*def USE_PNETCDF*/ /* Take care of files created/opened with parallel-netcdf library. */ if (h5->pnetcdf_file) { if (mem_type == NC_UBYTE) mem_type = NC_BYTE; switch(mem_type) { case NC_BYTE: return ncmpi_put_att_schar(nc->int_ncid, varid, name, file_type, len, op); case NC_CHAR: return ncmpi_put_att_text(nc->int_ncid, varid, name, len, op); case NC_SHORT: return ncmpi_put_att_short(nc->int_ncid, varid, name, file_type, len, op); case NC_INT: if (mem_type_is_long) return ncmpi_put_att_long(nc->int_ncid, varid, name, file_type, len, op); else return ncmpi_put_att_int(nc->int_ncid, varid, name, file_type, len, op); case NC_FLOAT: return ncmpi_put_att_float(nc->int_ncid, varid, name, file_type, len, op); case NC_DOUBLE: return ncmpi_put_att_double(nc->int_ncid, varid, name, file_type, len, op); case NC_NAT: default: return NC_EBADTYPE; } } #endif /* USE_PNETCDF */ /* Otherwise, handle things the netcdf-4 way. */ return nc4_put_att(ncid, nc, varid, name, file_type, mem_type, len, mem_type_is_long, op); }