//----------------------------------------------------------------
// Return a negative value when failed, otherwise return 0
int read_var_from_netcdf(int file_id, const char *var_name, struct Type type)
{
int TIMES=1;
int LATS=local_box_size[1];
int LONS=local_box_size[0];
assert(var_name != 0);
assert(var_data != 0);
int varidp,ndims,nvars,ngatts,unlimited;
nc_type xtypep;
//int dataset_id = H5Dopen2(file_id, var_name, H5P_DEFAULT);
int dataset_id = ncmpi_inq_varid(file_id, var_name, &varidp);
MPI_Offset start[]={local_box_offset[2],local_box_offset[1],local_box_offset[0]};
MPI_Offset count[]={TIMES,LATS,LONS};
dataset_id = ncmpi_inq_vartype(file_id,varidp, &xtypep);
// if (dataset_id !=0)
// terminate_with_error_msg("ERROR: Failed to open NetCDF dataset for variable %s\n", var_name);
int read_error = 0;
if (type.atomic_type == DOUBLE)
read_error = ncmpi_get_vara_double(file_id, varidp, start, count, var_data);
else if (type.atomic_type == FLOAT){
ncmpi_begin_indep_data(file_id);
read_error = ncmpi_get_vara_float(file_id, varidp, start, count, (float *)var_data);
ncmpi_end_indep_data(file_id);
if (read_error != NC_NOERR)
terminate_with_error_msg("ERROR: Can not read the data for the variable %s \n", var_name);
}
else if (type.atomic_type == INT)
read_error = ncmpi_get_vara_int(file_id, varidp, start, count, var_data);
// else if (type.atomic_type == UINT)
// read_error = ncmpi_get_vara_uint(file_id, varidp, start, count, var_data);
// else if (type.atomic_type == CHAR)
// read_error = ncmpi_get_vara_char(file_id, varidp, start, count, var_data);
else if (type.atomic_type == UCHAR)
read_error = ncmpi_get_vara_uchar(file_id, varidp, start, count, var_data);
else
terminate_with_error_msg("ERROR: Unsupported type. Type = %d\n", type.atomic_type);
if (read_error < 0)
return -1;
return 0;
}
//----------------------------------------------------------------
// Open the first NETCDF file and query all the types for all the variables
static void determine_var_types()
{
assert(netcdf_file_names != 0);
assert(netcdf_var_names != 0);
struct Type type;
int plist_id,i = 0,varidp,ndimsp;
int file_id = ncmpi_open(MPI_COMM_WORLD,netcdf_file_names[0], NC_NOWRITE, MPI_INFO_NULL, &plist_id);
if (file_id != NC_NOERR)
terminate_with_error_msg("ERROR: Cannot open file %s\n", netcdf_file_names[0]);
var_types = (struct Type *)calloc(var_count, sizeof(*var_types));
nc_type xtypep;
for (i = 0; i < var_count; ++i)
{
int dataset_id = ncmpi_inq_varid (plist_id, netcdf_var_names[i], &varidp);
dataset_id = ncmpi_inq_vartype(plist_id,varidp, &xtypep);
if (dataset_id != NC_NOERR)
terminate_with_error_msg("ERROR: Cannot read the datatype of the variable %s\n", netcdf_var_names[i]);
int num_dims = ncmpi_inq_varndims(plist_id,varidp,&ndimsp);
if (ndimsp > 3 )
{
//TODO:probably we can make it more clever to handle more dimensions as they are not related to the variable itself on netcdf
type.atomic_type = INVALID; // we don't support arrays of more than 3 dimension
return;
}
else if (xtypep == NC_FLOAT || xtypep == NC_INT)
{
type.num_values = 1;
}
else // we don't support HD5_COMPOUND datatype for example
{
type.atomic_type = INVALID;
}
type.atomic_type = from_netcdf_atomic_type(xtypep);
var_types[i] = type;
if (var_types[i].atomic_type == INVALID)
terminate_with_error_msg("ERROR: The datatype of the %s variable is not supported\n", netcdf_var_names[i]);
}
ncmpi_close(plist_id);
}
void BIL_Pio_read_nc_blocks(MPI_Comm all_readers_comm, MPI_Comm io_comm,
int num_blocks, BIL_Block* blocks) {
int i;
for (i = 0; i < num_blocks; i++) {
int fp;
BIL_Timing_fopen_start(all_readers_comm);
assert(ncmpi_open(io_comm, blocks[i].file_name, NC_NOWRITE,
BIL->io_hints, &fp) == NC_NOERR);
BIL_Timing_fopen_stop(all_readers_comm);
ncmpi_begin_indep_data(fp);
// Find the id, type, and size of the variable.
int var_id;
assert(ncmpi_inq_varid(fp, blocks[i].var_name, &var_id) == NC_NOERR);
nc_type var_type;
assert(ncmpi_inq_vartype(fp, var_id, &var_type) == NC_NOERR);
// Create extra variables specifically for the netCDF API.
MPI_Offset nc_dim_starts[BIL_MAX_NUM_DIMS];
MPI_Offset nc_dim_sizes[BIL_MAX_NUM_DIMS];
int j;
for (j = 0; j < blocks[i].num_dims; j++) {
nc_dim_starts[j] = blocks[i].starts[j];
nc_dim_sizes[j] = blocks[i].sizes[j];
}
MPI_Datatype nc_var_type;
BIL_Pio_nc_to_mpi_type(var_type, &nc_var_type, &(blocks[i].var_size));
// Allocate room for data and read it independently.
blocks[i].data = BIL_Misc_malloc(blocks[i].total_size * blocks[i].var_size);
BIL_Timing_io_start(all_readers_comm);
assert(ncmpi_get_vara(fp, var_id, nc_dim_starts, nc_dim_sizes,
blocks[i].data, blocks[i].total_size,
nc_var_type) == NC_NOERR);
BIL_Timing_io_stop(all_readers_comm,
blocks[i].total_size * blocks[i].var_size);
// Clean up.
ncmpi_end_indep_data(fp);
ncmpi_close(fp);
}
}
