sandbox/bderembl/libs/pnetcdf_bas.h
(Parallel) Netcdf interface for Basilisk
These input/output routines are meant to provide a simple way to store and read netcdf files. It relies on the pnetcdf library. This is an extension of the standard netcdf library, optimized for parallel computing. Hence, pnetcdf should be installed and linked at compilation time.
This file provides 3 routines:
create_nc({scalar1, vector1}, “filename.nc”);
which creates the structure of the netcdf file. This should be called only once for instance in an init event. Then one can use
write_nc();
to write a snapshot of the selected variables.
Last, the routine
read_nc({scalar1, vector1}, “filename.nc”);
reads the selected scalar from file “filename.nc”.
Notes: This routine only works for multigrids. It should work for 2d, layered and 3d variable.
- TODO: add units
- TODO: for 2d fields, no need to have a z dimension
#include <stdio.h>
#include <string.h>
#include <pnetcdf.h>
#define NDIMS 4
#define Z_NAME "z"
#define Y_NAME "y"
#define X_NAME "x"
#define REC_NAME "time"
#define LVL_NAME "level"
#if LAYERS == 0
int nl = 1;
int _layer = 0;
#endif
TODO: For the units attributes.
define UNITS “units”
define PRES_UNITS “hPa”
define TEMP_UNITS “celsius”
define MAX_ATT_LEN 80
Handle errors by printing an error message and exiting with a non-zero status
int nc_err;
static void handle_error(int status, int lineno)
{
fprintf(stderr, "Error at line %d: %s\n", lineno, ncmpi_strerror(status));
MPI_Abort(MPI_COMM_WORLD, 1);
}
User global variables: IDs for the netCDF file, dimensions, and variables.
int ncid;
scalar * nc_scalar_list;
char nc_file[80];
int nc_varid[1000];
int nc_rec = -1;
int rec_varid;
Netcdf creation
create_nc is used to create the netcdf file
void create_nc(scalar * list_out, char* file_out){
/* LOCAL IDs for the netCDF file, dimensions, and variables. */
int x_dimid, y_dimid, z_dimid, rec_dimid;
int z_varid, y_varid, x_varid;
int dimids[NDIMS];
// make it global variable
sprintf (nc_file,"%s", file_out);
nc_scalar_list = list_copy(list_out);
/* Create the file. */
if ((nc_err = ncmpi_create(MPI_COMM_WORLD, nc_file,
NC_CLOBBER, MPI_INFO_NULL,&ncid)))
handle_error(nc_err, __LINE__);
/* Define the dimensions. The record dimension is defined to have
* unlimited length - it can grow as needed. In this example it is
* the time dimension.*/
#if _MPI
int npx = mpi_dims[0];
int npy = mpi_dims[1];
#else
int npx = 1;
int npy = 1;
#endif
int Nloc = (1 << depth());
int Nx = Nloc*npx;
int Ny = Nloc*npy;
if ((nc_err = ncmpi_def_dim(ncid, REC_NAME, NC_UNLIMITED, &rec_dimid)))
handle_error(nc_err, __LINE__);
#if dimension > 2
#if _MPI
int npz = mpi_dims[2];
#else
int npz = 1;
#endif // MPI
int Nz = Nloc*npz;
if ((nc_err = ncmpi_def_dim(ncid, Z_NAME, Nz, &z_dimid)))
handle_error(nc_err, __LINE__);
#else // dimension > 2
int Nz = nl;
if ((nc_err = ncmpi_def_dim(ncid, LVL_NAME, nl, &z_dimid)))
handle_error(nc_err, __LINE__);
#endif
if ((nc_err = ncmpi_def_dim(ncid, Y_NAME, Ny, &y_dimid)))
handle_error(nc_err, __LINE__);
if ((nc_err = ncmpi_def_dim(ncid, X_NAME, Nx, &x_dimid)))
handle_error(nc_err, __LINE__);
/* Define the coordinate variables. We will only define coordinate
variables for lat and lon. Ordinarily we would need to provide
an array of dimension IDs for each variable's dimensions, but
since coordinate variables only have one dimension, we can
simply provide the address of that dimension ID (&y_dimid) and
similarly for (&x_dimid). */
if ((nc_err = ncmpi_def_var(ncid, REC_NAME, NC_FLOAT, 1, &rec_dimid,
&rec_varid)))
handle_error(nc_err, __LINE__);
#if dimension > 2
if ((nc_err = ncmpi_def_var(ncid, Z_NAME, NC_FLOAT, 1, &z_dimid,
&z_varid)))
handle_error(nc_err, __LINE__);
#else
if ((nc_err = ncmpi_def_var(ncid, LVL_NAME, NC_FLOAT, 1, &z_dimid,
&z_varid)))
handle_error(nc_err, __LINE__);
#endif
if ((nc_err = ncmpi_def_var(ncid, Y_NAME, NC_FLOAT, 1, &y_dimid,
&y_varid)))
handle_error(nc_err, __LINE__);
if ((nc_err = ncmpi_def_var(ncid, X_NAME, NC_FLOAT, 1, &x_dimid,
&x_varid)))
handle_error(nc_err, __LINE__);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. Both of the netCDF variables we are
creating share the same four dimensions. In C, the
unlimited dimension must come first on the list of dimids. */
dimids[0] = rec_dimid;
dimids[1] = z_dimid;
dimids[2] = y_dimid;
dimids[3] = x_dimid;
/* Define the netCDF variables */
int nvarout = 0;
for (scalar s in nc_scalar_list){
if ((nc_err = ncmpi_def_var(ncid, s.name, NC_FLOAT, NDIMS,
dimids, &nc_varid[nvarout])))
handle_error(nc_err, __LINE__);
nvarout += 1;
}
/* /\* Assign units attributes to the netCDF variables. *\/ */
/* if ((nc_err = nc_put_att_text(ncid, pres_varid, UNITS, */
/* strlen(PRES_UNITS), PRES_UNITS))) */
/* ERR(nc_err); */
/* if ((nc_err = nc_put_att_text(ncid, temp_varid, UNITS, */
/* strlen(TEMP_UNITS), TEMP_UNITS))) */
/* ERR(nc_err); */
/* End define mode. */
if ((nc_err = ncmpi_enddef(ncid)))
handle_error(nc_err, __LINE__);
/* write coordinates*/
float yc[Ny], xc[Nx];
double Delta = L0*1.0/Nx;
for (int i = 0; i < Nx; i++)
xc[i] = X0 + (i + 0.5)*Delta;
for (int i = 0; i < Ny; i++)
yc[i] = Y0 + (i + 0.5)*Delta;
float zc[Nz];
for (int i = 0; i < Nz; i++)
#if dimension > 2
zc[i] = Z0 + (i + 0.5)*Delta;
#else
zc[i] = i;
#endif
if ((nc_err = ncmpi_put_var_float_all(ncid, z_varid, &zc[0])))
handle_error(nc_err, __LINE__);
if ((nc_err = ncmpi_put_var_float_all(ncid, y_varid, &yc[0])))
handle_error(nc_err, __LINE__);
if ((nc_err = ncmpi_put_var_float_all(ncid, x_varid, &xc[0])))
handle_error(nc_err, __LINE__);
/* Close the file. */
if ((nc_err = ncmpi_close(ncid)))
handle_error(nc_err, __LINE__);
fprintf(stdout,"*** SUCCESS creating example file %s!\n", nc_file);
}
Write in netcdf
We use write_nc to dump a snapshot in the netcdf file at time t.
void write_nc() {
int Nloc = (1 << depth());
/* open file. */
if ((nc_err = ncmpi_open(MPI_COMM_WORLD,
nc_file, NC_WRITE, MPI_INFO_NULL, &ncid)))
handle_error(nc_err, __LINE__);
// write time
nc_rec += 1;
float loctime[1];
loctime[0] = t;
MPI_Offset startt[1], countt[1];
startt[0] = nc_rec; //time
countt[0] = 1;
if ((nc_err = ncmpi_put_vara_float_all(ncid, rec_varid, startt, countt,
&loctime[0])))
handle_error(nc_err, __LINE__);
#if dimension > 2
float * field = (float *)malloc(Nloc*Nloc*Nloc*sizeof(float));
#else
// float ** field = matrix_new (Nloc, Nloc, sizeof(float));
float * field = (float *)malloc(nl*Nloc*Nloc*sizeof(float));
#endif
/* The start and count arrays will tell the netCDF library where to
write our data. */
MPI_Offset start[NDIMS], count[NDIMS];
/* These settings tell netcdf to write one timestep of data. (The
setting of start[0] inside the loop below tells netCDF which
timestep to write.) */
start[0] = nc_rec; //time
#if dimension > 2
#if _MPI
start[1] = mpi_coords[2]*Nloc; //z
#else
start[1] = 0;
#endif // MPI
#else
start[1] = 0; //level
#endif
#if _MPI
start[2] = mpi_coords[1]*Nloc; //y
start[3] = mpi_coords[0]*Nloc; //x
#else
start[2] = 0; //y
start[3] = 0; //x
#endif
count[0] = 1;
#if dimension > 2
count[1] = Nloc; //z
#else
count[1] = nl;
#endif
count[2] = Nloc;
count[3] = Nloc;
int nv = -1;
for (scalar s in nc_scalar_list){
nv += 1;
foreach(noauto){
int i = point.i - GHOSTS;
int j = point.j - GHOSTS;
#if dimension > 2
int k = point.k - GHOSTS;
field[Nloc*Nloc*k + Nloc*j + i] = s[];
#else
for (_layer = 0; _layer < nl; _layer++){
int k = _layer;
field[Nloc*Nloc*k + Nloc*j + i] = s[];
}
_layer = 0;
#endif
}
if ((nc_err = ncmpi_put_vara_float_all(ncid, nc_varid[nv], start, count,
&field[0])))
// &field[0][0])))
handle_error(nc_err, __LINE__);
}
free(field);
/* Close the file. */
if ((nc_err = ncmpi_close(ncid)))
handle_error(nc_err, __LINE__);
}
Read a netcdf file
void read_nc(scalar * list_in, char* file_in){
int i, ret;
int ncfile, ndims, nvars, ngatts, unlimited;
int var_ndims, var_natts;
nc_type type;
char varname[NC_MAX_NAME+1];
int *dimids=NULL;
int Nloc = (1 << depth());
#if dimension > 2
float * field = (float *)malloc(Nloc*Nloc*Nloc*sizeof(float));
#else
// float ** field = matrix_new (Nloc, Nloc, sizeof(float));
float * field = (float *)malloc(Nloc*Nloc*nl*sizeof(float));
#endif
// float ** field = matrix_new (Nloc, Nloc, sizeof(float));
ret = ncmpi_open(MPI_COMM_WORLD, file_in, NC_NOWRITE, MPI_INFO_NULL,
&ncfile);
if (ret != NC_NOERR) handle_error(ret, __LINE__);
/* reader knows nothing about dataset, but we can interrogate with query
* routines: ncmpi_inq tells us how many of each kind of "thing"
* (dimension, variable, attribute) we will find in the file */
/* no communication needed after ncmpi_open: all processors have a cached
* view of the metadata once ncmpi_open returns */
ret = ncmpi_inq(ncfile, &ndims, &nvars, &ngatts, &unlimited);
if (ret != NC_NOERR) handle_error(ret, __LINE__);
MPI_Offset start[NDIMS], count[NDIMS];
// default (no MPI)
start[0] = 0; //time
start[1] = 0; //z or level
start[2] = 0;
start[3] = 0;
#if _MPI
#if dimension > 2
start[1] = mpi_coords[2]*Nloc;
#endif
start[2] = mpi_coords[1]*Nloc; //y
start[3] = mpi_coords[0]*Nloc; //x
#endif
count[0] = 1;
#if dimension > 2
count[1] = Nloc;
#else
count[1] = nl;
#endif
count[2] = Nloc;
count[3] = Nloc;
for (scalar s in list_in){
for(i=0; i<nvars; i++) {
ret = ncmpi_inq_var(ncfile, i, varname, &type, &var_ndims, dimids,
&var_natts);
if (ret != NC_NOERR) handle_error(ret, __LINE__);
if (strcmp(varname,s.name) == 0) {
fprintf(stdout,"Reading variable %s!\n", s.name);
if ((nc_err = ncmpi_get_vara_float_all(ncfile, i, start, count,
&field[0])))
handle_error(nc_err, __LINE__);
foreach(noauto){
int i = point.i - GHOSTS;
int j = point.j - GHOSTS;
#if dimension > 2
int k = point.k - GHOSTS;
s[] = field[Nloc*Nloc*k + Nloc*j + i];
#else
for (_layer = 0; _layer < nl; _layer++){
int k = _layer;
s[] = field[Nloc*Nloc*k + Nloc*j + i];
}
_layer = 0;
#endif
}
}
}
}
// matrix_free (field);
free(field);
ret = ncmpi_close(ncfile);
if (ret != NC_NOERR) handle_error(ret, __LINE__);
}
event cleanup (t = end)
{
free(nc_scalar_list);
}