/*----< test_attr_types() >---------------------------------------------------*/
static
int test_attr_types(char *filename,
int format)
{
int i, err, rank, ncid, cmode, nerrs=0, attr=0;
MPI_Info info=MPI_INFO_NULL;
MPI_Comm comm=MPI_COMM_WORLD;
nc_type xtype[5]={NC_UBYTE, NC_USHORT, NC_UINT, NC_INT64, NC_UINT64};
MPI_Comm_rank(comm, &rank);
cmode = NC_CLOBBER|format;
/* create a file in CDF-1 or CDF-2 format */
err = ncmpi_create(comm, filename, cmode, info, &ncid); ERR
for (i=0; i<5; i++) {
char name[32];
sprintf(name, "gattr_%d", i);
err = ncmpi_put_att_int(ncid, NC_GLOBAL, name, xtype[i], 1, &attr);
if (err != NC_ESTRICTCDF2) {
printf("Error (line=%d): expecting NC_ESTRICTCDF2 but got %s\n", __LINE__,nc_err_code_name(err));
nerrs++;
}
}
err = ncmpi_close(ncid); ERR
return nerrs;
}
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 a parallel-nedcdf file.
*
* We assume here that localData is a scalar.
*
* Pnetcdf uses row-major format (same as FFTW).
*
* \param[in] filename : PnetCDF filename
* \param[in] starts : offset to where to start reading data
* \param[in] counts : number of elements read (3D sub-domain inside global)
* \param[in] gsizes : global sizes
* \param[in] localData : actual data buffer (size : nx*ny*nz*sizeof(float))
*
*/
void write_pnetcdf(const std::string &filename,
MPI_Offset starts[3],
MPI_Offset counts[3],
int gsizes[3],
float *localData)
{
int myRank;
MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
// netcdf file id
int ncFileId;
int err;
// file creation mode
int ncCreationMode = NC_CLOBBER;
// CDF-5 is almost mandatory for very large files (>= 2x10^9 cells)
// not useful here
bool useCDF5 = false;
if (useCDF5)
ncCreationMode = NC_CLOBBER|NC_64BIT_DATA;
else // use CDF-2 file format
ncCreationMode = NC_CLOBBER|NC_64BIT_OFFSET;
// verbose log ?
//bool pnetcdf_verbose = false;
int nbVar=1;
int dimIds[3], varIds[nbVar];
//MPI_Offset write_size, sum_write_size;
MPI_Info mpi_info_used;
//char str[512];
// time measurement variables
//float write_timing, max_write_timing, write_bw;
/*
* Create NetCDF file
*/
err = ncmpi_create(MPI_COMM_WORLD, filename.c_str(),
ncCreationMode,
MPI_INFO_NULL, &ncFileId);
if (err != NC_NOERR) {
printf("Error: ncmpi_create() file %s (%s)\n",filename.c_str(),ncmpi_strerror(err));
MPI_Abort(MPI_COMM_WORLD, -1);
exit(1);
}
/*
* Define global dimensions
*/
err = ncmpi_def_dim(ncFileId, "x", gsizes[0], &dimIds[0]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_dim(ncFileId, "y", gsizes[1], &dimIds[1]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_dim(ncFileId, "z", gsizes[2], &dimIds[2]);
PNETCDF_HANDLE_ERROR;
/*
* Define variables to write (give a name)
*/
nc_type ncDataType = NC_FLOAT;
MPI_Datatype mpiDataType = MPI_FLOAT;
err = ncmpi_def_var(ncFileId, "data", ncDataType, 3, dimIds, &varIds[0]);
PNETCDF_HANDLE_ERROR;
/*
* global attributes
*/
// did we use CDF-2 or CDF-5
{
int useCDF5_int = useCDF5 ? 1 : 0;
err = ncmpi_put_att_int(ncFileId, NC_GLOBAL, "CDF-5 mode", NC_INT, 1, &useCDF5_int);
PNETCDF_HANDLE_ERROR;
}
/*
* exit the define mode
*/
err = ncmpi_enddef(ncFileId);
PNETCDF_HANDLE_ERROR;
/*
* Get all the MPI_IO hints used
*/
err = ncmpi_get_file_info(ncFileId, &mpi_info_used);
PNETCDF_HANDLE_ERROR;
// copy data to write in intermediate buffer
int nItems = counts[IX]*counts[IY]*counts[IZ];
{
// debug
// printf("Pnetcdf [rank=%d] starts=%lld %lld %lld, counts =%lld %lld %lld, gsizes=%d %d %d\n",
// myRank,
// starts[0],starts[1],starts[2],
// counts[0],counts[1],counts[2],
// gsizes[0],gsizes[1],gsizes[2]);
/*
* make sure PNetCDF doesn't complain when starts is outside of global domain
* bound. When nItems is null, off course we don't write anything, but starts
* offset have to be inside global domain.
* So there is no harm, setting starts to origin.
*/
if (nItems == 0) {
starts[0]=0;
starts[1]=0;
starts[2]=0;
}
err = ncmpi_put_vara_all(ncFileId,
varIds[0],
starts,
counts,
localData,
nItems,
mpiDataType);
PNETCDF_HANDLE_ERROR;
}
/*
* close the file
*/
err = ncmpi_close(ncFileId);
PNETCDF_HANDLE_ERROR;
} // write_pnetcdf
int
main(int argc, char **argv) { /* create foo.nc */
int stat; /* return status */
int ncid; /* netCDF id */
/* dimension ids */
int lat_dim;
int lon_dim;
int time_dim;
/* dimension lengths */
size_t lat_len = 10;
size_t lon_len = 5;
size_t time_len = NC_UNLIMITED;
/* variable ids */
int lat_id;
int lon_id;
int time_id;
int z_id;
int t_id;
int p_id;
int rh_id;
/* rank (number of dimensions) for each variable */
# define RANK_lat 1
# define RANK_lon 1
# define RANK_time 1
# define RANK_z 3
# define RANK_t 3
# define RANK_p 3
# define RANK_rh 3
/* variable shapes */
int lat_dims[RANK_lat];
int lon_dims[RANK_lon];
int time_dims[RANK_time];
int z_dims[RANK_z];
int t_dims[RANK_t];
int p_dims[RANK_p];
int rh_dims[RANK_rh];
/* attribute vectors */
double z_valid_range[2];
double p__FillValue[1];
int rh__FillValue[1];
int stat=0;
MPI_Init(&argc, &argv);
/* enter define mode */
stat = ncmpi_create(MPI_COMM_WORLD, "foo.nc", NC_CLOBBER, MPI_INFO_NULL, &ncid);
check_err(stat,__LINE__,__FILE__);
/* define dimensions */
stat = ncmpi_def_dim(ncid, "lat", lat_len, &lat_dim);
check_err(stat,__LINE__,__FILE__);
stat = ncmpi_def_dim(ncid, "lon", lon_len, &lon_dim);
check_err(stat,__LINE__,__FILE__);
stat = ncmpi_def_dim(ncid, "time", time_len, &time_dim);
check_err(stat,__LINE__,__FILE__);
/* define variables */
lat_dims[0] = lat_dim;
stat = ncmpi_def_var(ncid, "lat", NC_INT, RANK_lat, lat_dims, &lat_id);
check_err(stat,__LINE__,__FILE__);
lon_dims[0] = lon_dim;
stat = ncmpi_def_var(ncid, "lon", NC_INT, RANK_lon, lon_dims, &lon_id);
check_err(stat,__LINE__,__FILE__);
time_dims[0] = time_dim;
stat = ncmpi_def_var(ncid, "time", NC_INT, RANK_time, time_dims, &time_id);
check_err(stat,__LINE__,__FILE__);
z_dims[0] = time_dim;
z_dims[1] = lat_dim;
z_dims[2] = lon_dim;
stat = ncmpi_def_var(ncid, "z", NC_FLOAT, RANK_z, z_dims, &z_id);
check_err(stat,__LINE__,__FILE__);
t_dims[0] = time_dim;
t_dims[1] = lat_dim;
t_dims[2] = lon_dim;
stat = ncmpi_def_var(ncid, "t", NC_FLOAT, RANK_t, t_dims, &t_id);
check_err(stat,__LINE__,__FILE__);
p_dims[0] = time_dim;
p_dims[1] = lat_dim;
p_dims[2] = lon_dim;
stat = ncmpi_def_var(ncid, "p", NC_DOUBLE, RANK_p, p_dims, &p_id);
check_err(stat,__LINE__,__FILE__);
rh_dims[0] = time_dim;
rh_dims[1] = lat_dim;
rh_dims[2] = lon_dim;
stat = ncmpi_def_var(ncid, "rh", NC_INT, RANK_rh, rh_dims, &rh_id);
check_err(stat,__LINE__,__FILE__);
/* assign attributes */
stat = ncmpi_put_att_text(ncid, lat_id, "units", 13, "degrees_north");
check_err(stat,__LINE__,__FILE__);
stat = ncmpi_put_att_text(ncid, lon_id, "units", 12, "degrees_east");
check_err(stat,__LINE__,__FILE__);
stat = ncmpi_put_att_text(ncid, time_id, "units", 7, "seconds");
check_err(stat,__LINE__,__FILE__);
stat = ncmpi_put_att_text(ncid, z_id, "units", 6, "meters");
check_err(stat,__LINE__,__FILE__);
z_valid_range[0] = 0;
z_valid_range[1] = 5000;
stat = ncmpi_put_att_double(ncid, z_id, "valid_range", NC_DOUBLE, 2, z_valid_range);
check_err(stat,__LINE__,__FILE__);
p__FillValue[0] = -9999;
stat = ncmpi_put_att_double(ncid, p_id, "_FillValue", NC_DOUBLE, 1, p__FillValue);
check_err(stat,__LINE__,__FILE__);
rh__FillValue[0] = -1;
stat = ncmpi_put_att_int(ncid, rh_id, "_FillValue", NC_INT, 1, rh__FillValue);
check_err(stat,__LINE__,__FILE__);
/* leave define mode */
stat = ncmpi_enddef (ncid);
check_err(stat,__LINE__,__FILE__);
{ /* store lat */
static int lat[] = {0, 10, 20, 30, 40, 50, 60, 70, 80, 90};
ncmpi_begin_indep_data(ncid);
stat = ncmpi_put_var_int(ncid, lat_id, lat);
ncmpi_end_indep_data(ncid);
check_err(stat,__LINE__,__FILE__);
}
{ /* store lon */
static int lon[] = {-140, -118, -96, -84, -52};
ncmpi_begin_indep_data(ncid);
stat = ncmpi_put_var_int(ncid, lon_id, lon);
ncmpi_end_indep_data(ncid);
check_err(stat,__LINE__,__FILE__);
}
stat = ncmpi_close(ncid);
check_err(stat,__LINE__,__FILE__);
MPI_Finalize();
return 0;
}
/*
* adapted from HydroRunBaseMpi::outputPnetcdf
*
* assumes here that localData have size nx,ny,nz (no ghostWidth)
*
* see : test_pnetcdf_write.cpp
*
* Note that if ghostIncluded is false local_data must be sized upon nx,ny,nz
* if not size must be nx+2*ghostWidth,ny+2*ghostWidth,nz+2*ghostWidth
*
*/
void write_pnetcdf(const std::string &filename,
HostArray<double> &localData,
ConfigMap &configMap)
{
int myRank;
MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
// read local domain sizes
int nx=configMap.getInteger("mesh","nx",32);
int ny=configMap.getInteger("mesh","ny",32);
int nz=configMap.getInteger("mesh","nz",32);
// read mpi geometry
int mx=configMap.getInteger("mpi","mx",1);
int my=configMap.getInteger("mpi","my",1);
int mz=configMap.getInteger("mpi","mz",1);
// MPI cartesian coordinates
// myRank = mpiCoord[0] + mx*mpiCoord[1] + mx*my*mpiCoord[2]
int mpiCoord[3];
{
mpiCoord[2] = myRank/(mx*my);
mpiCoord[1] = (myRank - mx*my*mpiCoord[2])/mx;
mpiCoord[0] = myRank - mx*my*mpiCoord[2] -mx*mpiCoord[1];
}
bool ghostIncluded = configMap.getBool("output", "ghostIncluded",false);
int ghostWidth = configMap.getInteger("mesh","ghostWidth",3);
// global size
int NX=nx*mx, NY=ny*my, NZ=nz*mz;
int gsizes[3];
gsizes[IZ] = NX;
gsizes[IY] = NY;
gsizes[IX] = NZ;
if ( ghostIncluded ) {
gsizes[IZ] += 2*ghostWidth;
gsizes[IY] += 2*ghostWidth;
gsizes[IX] += 2*ghostWidth;
}
// netcdf file id
int ncFileId;
int err;
// file creation mode
int ncCreationMode = NC_CLOBBER;
bool useCDF5 = configMap.getBool("output","pnetcdf_cdf5",false);
if (useCDF5)
ncCreationMode = NC_CLOBBER|NC_64BIT_DATA;
else // use CDF-2 file format
ncCreationMode = NC_CLOBBER|NC_64BIT_OFFSET;
// verbose log ?
bool pnetcdf_verbose = configMap.getBool("output","pnetcdf_verbose",false);
int nbVar=8;
int dimIds[3], varIds[nbVar];
MPI_Offset write_size, sum_write_size;
MPI_Info mpi_info_used;
char str[512];
// time measurement variables
double write_timing, max_write_timing, write_bw;
/*
* writing parameter (offset and size)
*/
MPI_Offset starts[3] = {0};
MPI_Offset counts[3] = {nz, ny, nx};
// take care that row-major / column major format
starts[IZ] = mpiCoord[IX]*nx;
starts[IY] = mpiCoord[IY]*ny;
starts[IX] = mpiCoord[IZ]*nz;
if ( ghostIncluded ) {
if ( mpiCoord[IX] == 0 )
counts[IZ] += ghostWidth;
if ( mpiCoord[IY] == 0 )
counts[IY] += ghostWidth;
if ( mpiCoord[IZ] == 0 )
counts[IX] += ghostWidth;
if ( mpiCoord[IX] == mx-1 )
counts[IZ] += ghostWidth;
if ( mpiCoord[IY] == my-1 )
counts[IY] += ghostWidth;
if ( mpiCoord[IZ] == mz-1 )
counts[IX] += ghostWidth;
starts[IZ] += ghostWidth;
starts[IY] += ghostWidth;
starts[IX] += ghostWidth;
if ( mpiCoord[IX] == 0 )
starts[IZ] -= ghostWidth;
if ( mpiCoord[IY] == 0 )
starts[IY] -= ghostWidth;
if ( mpiCoord[IZ] == 0 )
starts[IX] -= ghostWidth;
}
/*
* Create NetCDF file
*/
err = ncmpi_create(MPI_COMM_WORLD, filename.c_str(),
ncCreationMode,
MPI_INFO_NULL, &ncFileId);
if (err != NC_NOERR) {
printf("Error: ncmpi_create() file %s (%s)\n",filename.c_str(),ncmpi_strerror(err));
MPI_Abort(MPI_COMM_WORLD, -1);
exit(1);
}
/*
* Define dimensions
*/
err = ncmpi_def_dim(ncFileId, "x", gsizes[0], &dimIds[0]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_dim(ncFileId, "y", gsizes[1], &dimIds[1]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_dim(ncFileId, "z", gsizes[2], &dimIds[2]);
PNETCDF_HANDLE_ERROR;
/*
* Define variables
*/
nc_type ncDataType = NC_DOUBLE;
MPI_Datatype mpiDataType = MPI_DOUBLE;
err = ncmpi_def_var(ncFileId, "rho", ncDataType, 3, dimIds, &varIds[ID]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "E", ncDataType, 3, dimIds, &varIds[IP]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "rho_vx", ncDataType, 3, dimIds, &varIds[IU]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "rho_vy", ncDataType, 3, dimIds, &varIds[IV]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "rho_vz", ncDataType, 3, dimIds, &varIds[IW]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "Bx", ncDataType, 3, dimIds, &varIds[IA]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "By", ncDataType, 3, dimIds, &varIds[IB]);
PNETCDF_HANDLE_ERROR;
err = ncmpi_def_var(ncFileId, "Bz", ncDataType, 3, dimIds, &varIds[IC]);
PNETCDF_HANDLE_ERROR;
/*
* global attributes
*/
// did we use CDF-2 or CDF-5
{
int useCDF5_int = useCDF5 ? 1 : 0;
err = ncmpi_put_att_int(ncFileId, NC_GLOBAL, "CDF-5 mode", NC_INT, 1, &useCDF5_int);
PNETCDF_HANDLE_ERROR;
}
/*
* exit the define mode
*/
err = ncmpi_enddef(ncFileId);
PNETCDF_HANDLE_ERROR;
/*
* Get all the MPI_IO hints used
*/
err = ncmpi_get_file_info(ncFileId, &mpi_info_used);
PNETCDF_HANDLE_ERROR;
int nItems = counts[IX]*counts[IY]*counts[IZ];
for (int iVar=0; iVar<nbVar; iVar++) {
double *data = &(localData(0,0,0,iVar));
err = ncmpi_put_vara_all(ncFileId, varIds[iVar], starts, counts, data, nItems, mpiDataType);
PNETCDF_HANDLE_ERROR;
}
/*
* close the file
*/
err = ncmpi_close(ncFileId);
PNETCDF_HANDLE_ERROR;
} // write_pnetcdf
static
int tst_norm(char *filename, int cmode)
{
int ncid, dimid, varid;
int dimids[NDIMS];
/* unnormalized UTF-8 encoding for Unicode 8-character "Hello" in Greek: */
unsigned char uname_utf8[] = {
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x80, /* COMBINING GRAVE ACCENT */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x81, /* COMBINING ACUTE ACCENT */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x82, /* COMBINING CIRCUMFLEX ACCENT */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x83, /* COMBINING TILDE */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x88, /* COMBINING DIAERESIS */
0x41, /* LATIN CAPITAL LETTER A */
0xCC, 0x8A, /* COMBINING RING ABOVE */
0x43, /* LATIN CAPITAL LETTER C */
0xCC, 0xA7, /* COMBINING CEDILLA */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x80, /* COMBINING GRAVE ACCENT */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x81, /* COMBINING ACUTE ACCENT */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x82, /* COMBINING CIRCUMFLEX ACCENT */
0x45, /* LATIN CAPITAL LETTER E */
0xCC, 0x88, /* COMBINING DIAERESIS */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x80, /* COMBINING GRAVE ACCENT */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x81, /* COMBINING ACUTE ACCENT */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x82, /* COMBINING CIRCUMFLEX ACCENT */
0x49, /* LATIN CAPITAL LETTER I */
0xCC, 0x88, /* COMBINING DIAERESIS */
0x4E, /* LATIN CAPITAL LETTER N */
0xCC, 0x83, /* COMBINING TILDE */
0x00
};
/* NFC normalized UTF-8 encoding for same Unicode string: */
unsigned char nname_utf8[] = {
0xC3, 0x80, /* LATIN CAPITAL LETTER A WITH GRAVE */
0xC3, 0x81, /* LATIN CAPITAL LETTER A WITH ACUTE */
0xC3, 0x82, /* LATIN CAPITAL LETTER A WITH CIRCUMFLEX */
0xC3, 0x83, /* LATIN CAPITAL LETTER A WITH TILDE */
0xC3, 0x84, /* LATIN CAPITAL LETTER A WITH DIAERESIS */
0xC3, 0x85, /* LATIN CAPITAL LETTER A WITH RING ABOVE */
0xC3, 0x87, /* LATIN CAPITAL LETTER C WITH CEDILLA */
0xC3, 0x88, /* LATIN CAPITAL LETTER E WITH GRAVE */
0xC3, 0x89, /* LATIN CAPITAL LETTER E WITH ACUTE */
0xC3, 0x8A, /* LATIN CAPITAL LETTER E WITH CIRCUMFLEX */
0xC3, 0x8B, /* LATIN CAPITAL LETTER E WITH DIAERESIS */
0xC3, 0x8C, /* LATIN CAPITAL LETTER I WITH GRAVE */
0xC3, 0x8D, /* LATIN CAPITAL LETTER I WITH ACUTE */
0xC3, 0x8E, /* LATIN CAPITAL LETTER I WITH CIRCUMFLEX */
0xC3, 0x8F, /* LATIN CAPITAL LETTER I WITH DIAERESIS */
0xC3, 0x91, /* LATIN CAPITAL LETTER N WITH TILDE */
0x00
};
/* Unnormalized name used for dimension, variable, and attribute value */
#define UNAME ((char *) uname_utf8)
#define UNAMELEN (sizeof uname_utf8)
/* Normalized name */
#define NNAME ((char *) nname_utf8)
#define NNAMELEN (sizeof nname_utf8)
char name_in[UNAMELEN + 1], strings_in[UNAMELEN + 1];
nc_type att_type;
MPI_Offset att_len;
int err, dimid_in, varid_in, attnum_in;
int attvals[] = {42};
#define ATTNUM ((sizeof attvals)/(sizeof attvals[0]))
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL,&ncid); ERR
/* Define dimension with unnormalized Unicode UTF-8 encoded name */
err = ncmpi_def_dim(ncid, UNAME, NX, &dimid); ERR
dimids[0] = dimid;
/* Define variable with same name */
err = ncmpi_def_var(ncid, UNAME, NC_CHAR, NDIMS, dimids, &varid); ERR
/* Create string attribute with same value */
err = ncmpi_put_att_text(ncid, varid, UNITS, UNAMELEN, UNAME); ERR
/* Create int attribute with same name */
err = ncmpi_put_att_int(ncid, varid, UNAME, NC_INT, ATTNUM, attvals); ERR
/* Try to create dimension and variable with NFC-normalized
* version of same name. These should fail, as unnormalized name
* should have been normalized in library, so these are attempts to
* create duplicate netCDF objects. */
if ((err = ncmpi_def_dim(ncid, NNAME, NX, &dimid)) != NC_ENAMEINUSE) {
printf("Error at line %d: expecting error code %d but got %d\n",__LINE__,NC_ENAMEINUSE,err);
return 1;
}
if ((err=ncmpi_def_var(ncid, NNAME, NC_CHAR, NDIMS, dimids, &varid)) != NC_ENAMEINUSE) {
printf("Error at line %d: expecting error code %d but got %d\n",__LINE__,NC_ENAMEINUSE,err);
return 1;
}
err = ncmpi_enddef(ncid); ERR
/* Write string data, UTF-8 encoded, to the file */
err = ncmpi_put_var_text_all(ncid, varid, UNAME); ERR
err = ncmpi_close(ncid); ERR
/* Check it out. */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, MPI_INFO_NULL, &ncid); ERR
err = ncmpi_inq_varid(ncid, UNAME, &varid); ERR
err = ncmpi_inq_varname(ncid, varid, name_in); ERR
err = strncmp(NNAME, name_in, NNAMELEN); ERR
err = ncmpi_inq_varid(ncid, NNAME, &varid_in); ERR
if ((err = ncmpi_inq_dimid(ncid, UNAME, &dimid_in)) || dimid != dimid_in)
{printf("Error at line %d\n",__LINE__);return 1;}
if ((err = ncmpi_inq_dimid(ncid, NNAME, &dimid_in)) || dimid != dimid_in)
{printf("Error at line %d\n",__LINE__);return 1;}
err = ncmpi_inq_att(ncid, varid, UNITS, &att_type, &att_len); ERR
if ( att_type != NC_CHAR || att_len != UNAMELEN)
{printf("Error at line %d\n",__LINE__);return 1;}
err = ncmpi_get_att_text(ncid, varid, UNITS, strings_in); ERR
strings_in[UNAMELEN] = '\0';
err = strncmp(UNAME, strings_in, UNAMELEN); ERR
if ((err = ncmpi_inq_attid(ncid, varid, UNAME, &attnum_in)) || ATTNUM != attnum_in)
{printf("Error at line %d\n",__LINE__);return 1;}
if ((err = ncmpi_inq_attid(ncid, varid, NNAME, &attnum_in)) || ATTNUM != attnum_in)
{printf("Error at line %d\n",__LINE__);return 1;}
err = ncmpi_close(ncid); ERR
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);
}