int
main(void)
{
hid_t file=-1, dcpl=-1, space=-1, dset1=-1, dset2=-1;
hsize_t cur_size[2]= {8, 8};
H5D_space_status_t allocation;
int fill_val1 = 4444, fill_val2=5555;
if((file=H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) <0) goto error;
if((space=H5Screate_simple(2, cur_size, cur_size)) < 0) goto error;
if((dcpl=H5Pcreate(H5P_DATASET_CREATE)) < 0) goto error;
/* Create a dataset with space being allocated and fill value written */
if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY) < 0) goto error;
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_ALLOC) < 0) goto error;
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fill_val1) < 0) goto error;
if((dset1 = H5Dcreate2(file, "dset1", H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if(H5Dget_space_status(dset1, &allocation) < 0) goto error;
if(allocation == H5D_SPACE_STATUS_NOT_ALLOCATED) {
puts(" Got unallocated space instead of allocated.");
printf(" Got %d\n", allocation);
goto error;
}
if(H5Dclose(dset1) < 0) goto error;
/* Create a dataset with space allocation being delayed */
if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_LATE) < 0) goto error;
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_ALLOC) < 0) goto error;
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fill_val2) < 0) goto error;
if((dset2 = H5Dcreate2(file, "dset2", H5T_NATIVE_INT, space, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
goto error;
if(H5Dget_space_status(dset2, &allocation) < 0) goto error;
if(allocation != H5D_SPACE_STATUS_NOT_ALLOCATED) {
puts(" Got allocated space instead of unallocated.");
printf(" Got %d\n", allocation);
goto error;
}
if(H5Dclose(dset2) < 0) goto error;
if(H5Sclose(space) < 0) goto error;
if(H5Pclose(dcpl) < 0) goto error;
if(H5Fclose(file) < 0) goto error;
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Sclose(space);
H5Dclose(dset1);
H5Dclose(dset2);
H5Fclose(file);
} H5E_END_TRY;
return 1;
}
/*
* Create HDF5 data set.
*/
static static void SetupDataSet(void *fd, IOR_param_t * param)
{
char dataSetName[MAX_STR];
hid_t dataSetPropList;
int dataSetID;
static int dataSetSuffix = 0;
/* may want to use an extendable dataset (H5S_UNLIMITED) someday */
/* may want to use a chunked dataset (H5S_CHUNKED) someday */
/* need to reset suffix counter if newly-opened file */
if (newlyOpenedFile)
dataSetSuffix = 0;
/* may want to use individual access to each data set someday */
if (param->individualDataSets) {
dataSetID = (rank + rankOffset) % param->numTasks;
} else {
dataSetID = 0;
}
sprintf(dataSetName, "%s-%04d.%04d", "Dataset", dataSetID,
dataSetSuffix++);
if (param->open == WRITE) { /* WRITE */
/* create data set */
dataSetPropList = H5Pcreate(H5P_DATASET_CREATE);
/* check if hdf5 available */
#if defined (H5_VERS_MAJOR) && defined (H5_VERS_MINOR)
/* no-fill option not available until hdf5-1.6.x */
#if (H5_VERS_MAJOR > 0 && H5_VERS_MINOR > 5)
if (param->noFill == TRUE) {
if (rank == 0 && verbose >= VERBOSE_1) {
fprintf(stdout, "\nusing 'no fill' option\n");
}
HDF5_CHECK(H5Pset_fill_time(dataSetPropList,
H5D_FILL_TIME_NEVER),
"cannot set fill time for property list");
}
#else
char errorString[MAX_STR];
sprintf(errorString, "'no fill' option not available in %s",
test->apiVersion);
ERR(errorString);
#endif
#else
WARN("unable to determine HDF5 version for 'no fill' usage");
#endif
dataSet =
H5Dcreate(*(hid_t *) fd, dataSetName, H5T_NATIVE_LLONG,
dataSpace, dataSetPropList);
HDF5_CHECK(dataSet, "cannot create data set");
} else { /* READ or CHECK */
dataSet = H5Dopen(*(hid_t *) fd, dataSetName);
HDF5_CHECK(dataSet, "cannot create data set");
}
}
//--------------------------------------------------------------------------
// Function: DSetCreatPropList::setFillTime
///\brief Sets fill value writing time for dataset.
///\return Fill value writing time
///\exception H5::PropListIException
///\par Description
/// Valid values for fill value writing time include
/// \li \c H5D_FILL_TIME_NEVER
/// \li \c H5D_FILL_TIME_ALLOC.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void DSetCreatPropList::setFillTime(H5D_fill_time_t fill_time)
{
herr_t ret_value = H5Pset_fill_time(id, fill_time);
if( ret_value < 0 )
{
throw PropListIException("DSetCreatPropList::setFillTime",
"H5Pset_fill_time failed");
}
}
int main(int argc, char* argv[]) {
HDF5_CALL(H5open());
HDF5_HANDLE(plist, get_parameters(), H5Pclose);
HDF5_HANDLE(file, H5Fcreate("test.hdf5", H5F_ACC_TRUNC, H5P_DEFAULT, plist),
&H5Fclose);
hsize_t dims[D] = {0};
hsize_t cdims[D] = {64};
cdims[D - 1] = 1;
hsize_t maxs[D];
maxs[0] = H5S_UNLIMITED;
maxs[1] = H5S_UNLIMITED;
double fill = -1;
HDF5_HANDLE(space, H5Screate_simple(D, dims, maxs), &H5Sclose);
HDF5_HANDLE(dplist, H5Pcreate(H5P_DATASET_CREATE), &H5Pclose);
HDF5_CALL(H5Pset_chunk(dplist, D, cdims));
HDF5_CALL(H5Pset_fill_value(dplist, H5T_NATIVE_DOUBLE, &fill));
if (argc > 1 && argv[1][0] == '+') {
std::cout << "old" << std::endl;
HDF5_CALL(H5Pset_fill_time(dplist, H5D_FILL_TIME_IFSET));
HDF5_CALL(H5Pset_alloc_time(dplist, H5D_ALLOC_TIME_LATE));
} else if (argc > 1 && argv[1][0] == '-') {
std::cout << "new" << std::endl;
HDF5_CALL(H5Pset_fill_time(dplist, H5D_FILL_TIME_ALLOC));
HDF5_CALL(H5Pset_alloc_time(dplist, H5D_ALLOC_TIME_INCR));
} else {
std::cout << "default" << std::endl;
HDF5_CALL(H5Pset_fill_time(dplist, H5D_FILL_TIME_IFSET));
HDF5_CALL(H5Pset_alloc_time(dplist, H5D_ALLOC_TIME_EARLY));
}
HDF5_HANDLE(ds, H5Dcreate2(file, "dataset", H5T_IEEE_F64LE, space,
H5P_DEFAULT, dplist, H5P_DEFAULT),
&H5Dclose);
set_size(ds, 1, 1);
set_value(ds, 0, 0, .5);
set_size(ds, 1, 2);
set_value(ds, 0, 1, 1);
set_size(ds, 1, 3);
set_value(ds, 0, 2, 0);
set_size(ds, 3, 4);
return 0;
}
herr_t H5ARRAYmake( hid_t loc_id,
const char *dset_name,
const char *obversion,
const int rank,
const hsize_t *dims,
int extdim,
hid_t type_id,
hsize_t *dims_chunk,
void *fill_data,
int compress,
char *complib,
int shuffle,
int fletcher32,
const void *data)
{
hid_t dataset_id, space_id;
hsize_t *maxdims = NULL;
hid_t plist_id = 0;
unsigned int cd_values[6];
int chunked = 0;
int i;
/* Check whether the array has to be chunked or not */
if (dims_chunk) {
chunked = 1;
}
if(chunked) {
maxdims = malloc(rank*sizeof(hsize_t));
if(!maxdims) return -1;
for(i=0;i<rank;i++) {
if (i == extdim) {
maxdims[i] = H5S_UNLIMITED;
}
else {
maxdims[i] = dims[i] < dims_chunk[i] ? dims_chunk[i] : dims[i];
}
}
}
/* Create the data space for the dataset. */
if ( (space_id = H5Screate_simple( rank, dims, maxdims )) < 0 )
return -1;
if (chunked) {
/* Modify dataset creation properties, i.e. enable chunking */
plist_id = H5Pcreate (H5P_DATASET_CREATE);
if ( H5Pset_chunk ( plist_id, rank, dims_chunk ) < 0 )
return -1;
/* Set the fill value using a struct as the data type. */
if (fill_data) {
if ( H5Pset_fill_value( plist_id, type_id, fill_data ) < 0 )
return -1;
}
else {
if ( H5Pset_fill_time(plist_id, H5D_FILL_TIME_ALLOC) < 0 )
return -1;
}
/*
Dataset creation property list is modified to use
*/
/* Fletcher must be first */
if (fletcher32) {
if ( H5Pset_fletcher32( plist_id) < 0 )
return -1;
}
/* Then shuffle (not if blosc is activated) */
if ((shuffle) && (strcmp(complib, "blosc") != 0)) {
if ( H5Pset_shuffle( plist_id) < 0 )
return -1;
}
/* Finally compression */
if (compress) {
cd_values[0] = compress;
cd_values[1] = (int)(atof(obversion) * 10);
if (extdim <0)
cd_values[2] = CArray;
else
cd_values[2] = EArray;
/* The default compressor in HDF5 (zlib) */
if (strcmp(complib, "zlib") == 0) {
if ( H5Pset_deflate( plist_id, compress) < 0 )
return -1;
}
/* The Blosc compressor does accept parameters */
else if (strcmp(complib, "blosc") == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 6, cd_values) < 0 )
return -1;
}
/* The LZO compressor does accept parameters */
else if (strcmp(complib, "lzo") == 0) {
if ( H5Pset_filter( plist_id, FILTER_LZO, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
/* The bzip2 compress does accept parameters */
else if (strcmp(complib, "bzip2") == 0) {
if ( H5Pset_filter( plist_id, FILTER_BZIP2, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
else {
/* Compression library not supported */
fprintf(stderr, "Compression library not supported\n");
return -1;
}
}
/* Create the (chunked) dataset */
if ((dataset_id = H5Dcreate(loc_id, dset_name, type_id,
space_id, plist_id )) < 0 )
goto out;
}
else { /* Not chunked case */
/* Create the dataset. */
if ((dataset_id = H5Dcreate(loc_id, dset_name, type_id,
space_id, H5P_DEFAULT )) < 0 )
goto out;
}
/* Write the dataset only if there is data to write */
if (data)
{
if ( H5Dwrite( dataset_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data ) < 0 )
goto out;
}
/* Terminate access to the data space. */
if ( H5Sclose( space_id ) < 0 )
return -1;
/* End access to the property list */
if (plist_id)
if ( H5Pclose( plist_id ) < 0 )
goto out;
/* Release resources */
if (maxdims)
free(maxdims);
return dataset_id;
out:
H5Dclose( dataset_id );
H5Sclose( space_id );
if (maxdims)
free(maxdims);
if (dims_chunk)
free(dims_chunk);
return -1;
}
/* ------- begin -------------------------- init_aux_new.c -- --- */
void init_aux_new(void) {
/* Creates the HDF5 file for the auxiliary data */
const char routineName[] = "init_aux_new";
unsigned int *tmp;
double *tmp_double;
int i;
hid_t plist, ncid, file_dspace, ncid_atom, ncid_mol;
hid_t id_x, id_y, id_z, id_n, id_tmp;
hsize_t dims[4];
char group_name[ARR_STRLEN];
Atom *atom;
Molecule *molecule;
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS) ) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(AUX_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* Fill value */
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* Get group name */
sprintf(group_name, (atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s",
atom->ID);
if (( ncid_atom = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_atom_ncid[i] = ncid_atom;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_atom, ".", "nlevel",
&atom->Nlevel, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "nline",
&atom->Nline, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "ncontinuum",
&atom->Ncont, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atom, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_atom, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atom, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_atom, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_atom, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_atom, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = atom->Nlevel;
tmp = (unsigned int *) calloc(atom->Nlevel , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = atom->Nline;
tmp = (unsigned int *) calloc(atom->Nline , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
tmp = (unsigned int *) calloc(atom->Ncont , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, CONT_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
}
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_atom, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( H5LTset_attribute_string(ncid_atom, CONT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
}
/* --- variables --- */
dims[0] = atom->Nlevel;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (atom->n != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POP_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_pop[i] = id_tmp;
}
if (atom->nstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POPLTE_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
/* Radiative rates */
dims[0] = atom->Nline;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0) HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LINE_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijL[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiL[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, CONT_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijC[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiC[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* Get group name */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( ncid_mol = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_mol_ncid[i] = ncid_mol;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_mol, ".", "nlevel_vibr",
&molecule->Nv, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nline_molecule",
&molecule->Nrt, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nJ",
&molecule->NJ, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mol, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_mol, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mol, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_mol, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_mol, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_mol, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = molecule->Nv;
tmp = (unsigned int *) calloc(molecule->Nv, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->Nrt;
tmp = (unsigned int *) calloc(molecule->Nrt, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->NJ;
tmp = (unsigned int *) calloc(molecule->NJ, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, NJ_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_mol, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, NJ_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
/* --- variables --- */
dims[0] = molecule->Nv;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_mol, VLEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (molecule->nv != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_pop[i] = id_tmp;
}
if (molecule->nvstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
// TODO: molecule->Ediss, molecule->Tmin, molecule->Tmax
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active MOLECULES loop */
io.aux_ncid = ncid; /* Copy stuff to the IO data struct */
if (( H5Pclose(plist) ) < 0) HERR(routineName); /* Free hdf5 resources */
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- init_hdf5_indata.c --- */
void init_hdf5_indata_new(void)
/* Creates the netCDF file for the input data */
{
const char routineName[] = "init_hdf5_indata_new";
int i, PRD_angle_dep;
double *eweight, *eabund, *x, *y;
/* This value is harcoded for efficiency.
Maximum number of iterations ever needed */
int NMaxIter = 1500;
hid_t plist, ncid, file_dspace, ncid_input, ncid_atmos, ncid_mpi;
hsize_t dims[4];
bool_t XRD;
char startJ[MAX_LINE_SIZE], StokesMode[MAX_LINE_SIZE], angleSet[MAX_LINE_SIZE];
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(INPUTDATA_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Create groups */
if (( ncid_input = H5Gcreate(ncid, "/input", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_atmos = H5Gcreate(ncid, "/atmos", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_mpi = H5Gcreate(ncid, "/mpi", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* --- Definitions for the INPUT group --- */
/* attributes */
if ( atmos.NPRDactive > 0)
PRD_angle_dep = input.PRD_angle_dep;
else
PRD_angle_dep=0;
XRD = (input.XRD && atmos.NPRDactive > 0);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Magneto_optical",
(unsigned char *) &input.magneto_optical, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "PRD_angle_dep",
(unsigned char *) &PRD_angle_dep, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "XRD",
(unsigned char *) &XRD, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Background_polarization",
(unsigned char *) &input.backgr_pol, 1)) < 0) HERR(routineName);
switch (input.startJ) {
case UNKNOWN:
strcpy(startJ, "Unknown");
break;
case LTE_POPULATIONS:
strcpy(startJ, "LTE_POPULATIONS");
break;
case ZERO_RADIATION:
strcpy(startJ, "ZERO_RADIATION");
break;
case OLD_POPULATIONS:
strcpy(startJ, "OLD_POPULATIONS");
break;
case ESCAPE_PROBABILITY:
strcpy(startJ, "ESCAPE_PROBABILITY");
break;
case NEW_J:
strcpy(startJ, "NEW_J");
break;
case OLD_J:
strcpy(startJ, "OLD_J");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Start_J", startJ)) < 0)
HERR(routineName);
switch (input.StokesMode) {
case NO_STOKES:
strcpy(StokesMode, "NO_STOKES");
break;
case FIELD_FREE:
strcpy(StokesMode, "FIELD_FREE");
break;
case POLARIZATION_FREE:
strcpy(StokesMode, "POLARIZATION_FREE");
break;
case FULL_STOKES:
strcpy(StokesMode, "FULL_STOKES");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Stokes_mode",
StokesMode) ) < 0) HERR(routineName);
switch (atmos.angleSet.set) {
case SET_VERTICAL:
strcpy(angleSet, "SET_VERTICAL");
break;
case SET_GL:
strcpy(angleSet, "SET_GL");
break;
case SET_A2:
strcpy(angleSet, "SET_A2");
break;
case SET_A4:
strcpy(angleSet, "SET_A4");
break;
case SET_A6:
strcpy(angleSet, "SET_A6");
break;
case SET_A8:
strcpy(angleSet, "SET_A8");
break;
case SET_B4:
strcpy(angleSet, "SET_B4");
break;
case SET_B6:
strcpy(angleSet, "SET_B6");
break;
case SET_B8:
strcpy(angleSet, "SET_B8");
break;
case NO_SET:
strcpy(angleSet, "NO_SET");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Angle_set",
angleSet) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Atmos_file",
input.atmos_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Abundances_file",
input.abund_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Kurucz_PF_data",
input.pfData) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Iteration_limit",
&input.iterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "PRD_Iteration_limit",
&input.PRDiterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "N_max_iter",
&input.NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_delay",
&input.Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_order",
&input.Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_period",
&input.Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_N_max_iter",
&input.PRD_NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_delay",
&input.PRD_Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_order",
&input.PRD_Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_period",
&input.PRD_Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Metallicity",
&input.metallicity, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Lambda_reference",
&atmos.lambda_ref, 1) ) < 0) HERR(routineName);
/* --- Definitions for the ATMOS group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_atmos, ".", "nhydr",
&atmos.H->Nlevel, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nelements",
&atmos.Nelem, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nrays",
&geometry.Nrays, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = infile.nz;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_atmos_T = H5Dcreate(ncid_atmos, "temperature", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dcreate(ncid_atmos, "velocity_z", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dcreate(ncid_atmos, "height", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* --- Write some data that does not depend on xi, yi, ATMOS group --- */
/* arrays of number of elements */
eweight = (double *) malloc(atmos.Nelem * sizeof(double));
eabund = (double *) malloc(atmos.Nelem * sizeof(double));
for (i=0; i < atmos.Nelem; i++) {
eweight[i] = atmos.elements[i].weight;
eabund[i] = atmos.elements[i].abund;
}
dims[0] = atmos.Nelem;
if (( H5LTmake_dataset(ncid_atmos, "element_weight", 1, dims,
H5T_NATIVE_DOUBLE, eweight) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "element_abundance", 1, dims,
H5T_NATIVE_DOUBLE, eabund) ) < 0) HERR(routineName);
/* Not writing element_id for now
dims[1] = strlen;
if (( H5LTmake_dataset(ncid_atmos, "element_id", 2, dims,
H5T_C_S1, eID) ) < 0) HERR(routineName);
*/
free(eweight);
free(eabund);
dims[0] = geometry.Nrays;
if (( H5LTmake_dataset(ncid_atmos, "muz", 1, dims,
H5T_NATIVE_DOUBLE, geometry.muz) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "wmu", 1, dims,
H5T_NATIVE_DOUBLE, geometry.wmu) ) < 0) HERR(routineName);
x = (double *) malloc(mpi.nx * sizeof(double));
y = (double *) malloc(mpi.ny * sizeof(double));
for (i=0; i < mpi.nx; i++) x[i] = infile.x[mpi.xnum[i]];
for (i=0; i < mpi.ny; i++) y[i] = infile.y[mpi.ynum[i]];
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atmos, "x", 1, dims,
H5T_NATIVE_DOUBLE, x) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atmos, "y", 1, dims,
H5T_NATIVE_DOUBLE, y) ) < 0) HERR(routineName);
free(x);
free(y);
/* attributes */
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "moving",
(unsigned char *) &atmos.moving, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "stokes",
(unsigned char *) &atmos.Stokes, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "temperature", "units",
"K") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "velocity_z", "units",
"m s^-1") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "height", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "element_weight", "units",
"atomic_mass_units") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "x", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "y", "units",
"m") ) < 0) HERR(routineName);
/* --- Definitions for the MPI group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_mpi, ".", "nprocesses",
&mpi.size, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "niterations",
&NMaxIter, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mpi, XNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.xnum) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mpi, YNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.ynum) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
if (( file_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dcreate(ncid_mpi, TASK_MAP, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dcreate(ncid_mpi, TASK_NUMBER, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dcreate(ncid_mpi, ITER_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dcreate(ncid_mpi, CONV_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dcreate(ncid_mpi, DM_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dcreate(ncid_mpi, ZC_NAME, H5T_NATIVE_INT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = NMaxIter;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dcreate(ncid_mpi, DMH_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* attributes */
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_start",
&input.p15d_x0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_end",
&input.p15d_x1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_step",
&input.p15d_xst, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_start",
&input.p15d_y0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_end",
&input.p15d_y1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_step",
&input.p15d_yst, 1) ) < 0) HERR(routineName);
/* Tiago: most of the arrays involving Ntasks or rank as index are not
currently being written. They should eventually be migrated into
arrays of [ix, iy] and be written for each task. This is to
avoid causing problems with pool mode, where these quantities are
not known from the start.
*/
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
/* --- Copy stuff to the IO data struct --- */
io.in_ncid = ncid;
io.in_input_ncid = ncid_input;
io.in_atmos_ncid = ncid_atmos;
io.in_mpi_ncid = ncid_mpi;
return;
}
/*-------------------------------------------------------------------------
* Function: writer
*
* Purpose: Creates a *big* dataset.
*
* Return: Success: 0
*
* Failure: >0
*
* Programmer: Robb Matzke
* Wednesday, April 8, 1998
*
* Modifications:
* Robb Matzke, 15 Jul 1998
* Addresses are written to the file DNAME instead of stdout.
*
*-------------------------------------------------------------------------
*/
static int
writer (char* filename, hid_t fapl, fsizes_t testsize, int wrt_n)
{
hsize_t size1[4] = {8, 1024, 1024, 1024};
hsize_t size2[1] = {GB8LL};
hsize_t hs_start[1];
hsize_t hs_size[1];
hid_t file=-1, space1=-1, space2=-1, mem_space=-1, d1=-1, d2=-1;
int *buf = (int*)HDmalloc (sizeof(int) * WRT_SIZE);
int i, j;
FILE *out = HDfopen(DNAME, "w");
hid_t dcpl;
switch(testsize){
case LFILE:
TESTING("Large dataset write(2GB)");
/* reduce size1 to produce a 2GB dataset */
size1[1] = 1024/16;
size2[0] /= 16;
break;
case XLFILE:
TESTING("Extra large dataset write(4GB)");
/* reduce size1 to produce a 4GB dataset */
size1[1] = 1024/8;
size2[0] /= 8;
break;
case HUGEFILE:
TESTING("Huge dataset write");
/* Leave size1 as 32GB */
break;
case SFILE:
TESTING("small dataset write(1GB)");
/* reduce size1 to produce a 1GB dataset */
size1[1] = 1024/32;
size2[0] /= 32;
break;
case NOFILE:
/* what to do?? */
HDfprintf(stdout, "Unexpected file size of NOFILE\n");
goto error;
break;
default:
HDfprintf(stdout, "Unexpected file size(%d)\n", testsize);
goto error;
break;
}
/*
* We might be on a machine that has 32-bit files, so create an HDF5 file
* which is a family of files. Each member of the family will be 1GB
*/
if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) {
goto error;
}
/* Create simple data spaces according to the size specified above. */
if ((space1 = H5Screate_simple (4, size1, size1)) < 0 ||
(space2 = H5Screate_simple (1, size2, size2)) < 0) {
goto error;
}
/* Create the datasets */
/*
* The fix below is provided for bug#921
* H5Dcreate with H5P_DEFAULT creation properties
* will create a set of solid 1GB files; test will crash if quotas are enforced
* or it will take some time to write a file.
* We should create a dataset allocating space late and never writing fill values.
* EIP 4/8/03
*/
dcpl = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_LATE);
H5Pset_fill_time(dcpl, H5D_FILL_TIME_NEVER);
if((d1 = H5Dcreate2(file, "d1", H5T_NATIVE_INT, space1, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0 ||
(d2 = H5Dcreate2(file, "d2", H5T_NATIVE_INT, space2, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) {
goto error;
}
/* Write some things to them randomly */
hs_size[0] = WRT_SIZE;
if ((mem_space = H5Screate_simple (1, hs_size, hs_size)) < 0) goto error;
for (i=0; i<wrt_n; i++) {
/* start position must be at least hs_size from the end */
hs_start[0] = randll (size2[0]-hs_size[0], i);
HDfprintf (out, "#%03d 0x%016Hx\n", i, hs_start[0]);
if (H5Sselect_hyperslab (space2, H5S_SELECT_SET, hs_start, NULL,
hs_size, NULL) < 0) goto error;
for (j=0; j<WRT_SIZE; j++) {
buf[j] = i+1;
}
if (H5Dwrite (d2, H5T_NATIVE_INT, mem_space, space2,
H5P_DEFAULT, buf) < 0) goto error;
}
if (H5Dclose (d1) < 0) goto error;
if (H5Dclose (d2) < 0) goto error;
if (H5Sclose (mem_space) < 0) goto error;
if (H5Sclose (space1) < 0) goto error;
if (H5Sclose (space2) < 0) goto error;
if (H5Fclose (file) < 0) goto error;
HDfree (buf);
HDfclose(out);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Dclose(d1);
H5Dclose(d2);
H5Sclose(space1);
H5Sclose(space2);
H5Sclose(mem_space);
H5Fclose(file);
} H5E_END_TRY;
if (buf) HDfree(buf);
if (out) HDfclose(out);
return 1;
}
herr_t H5TBOmake_table( const char *table_title,
hid_t loc_id,
const char *dset_name,
char *version,
const char *class_,
hid_t type_id,
hsize_t nrecords,
hsize_t chunk_size,
void *fill_data,
int compress,
char *complib,
int shuffle,
int fletcher32,
const void *data )
{
hid_t dataset_id;
hid_t space_id;
hid_t plist_id;
hsize_t dims[1];
hsize_t dims_chunk[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
unsigned int cd_values[7];
int blosc_compcode;
char *blosc_compname = NULL;
dims[0] = nrecords;
dims_chunk[0] = chunk_size;
/* Create a simple data space with unlimited size */
if ( (space_id = H5Screate_simple( 1, dims, maxdims )) < 0 )
return -1;
/* Modify dataset creation properties, i.e. enable chunking */
plist_id = H5Pcreate (H5P_DATASET_CREATE);
if ( H5Pset_chunk ( plist_id, 1, dims_chunk ) < 0 )
return -1;
/* Set the fill value using a struct as the data type. */
if ( fill_data)
{
if ( H5Pset_fill_value( plist_id, type_id, fill_data ) < 0 )
return -1;
}
else {
if ( H5Pset_fill_time(plist_id, H5D_FILL_TIME_ALLOC) < 0 )
return -1;
}
/*
Dataset creation property list is modified to use filters
*/
/* Fletcher must be first */
if (fletcher32) {
if ( H5Pset_fletcher32( plist_id) < 0 )
return -1;
}
/* Then shuffle (blosc shuffles inplace) */
if ((shuffle && compress) && (strncmp(complib, "blosc", 5) != 0)) {
if ( H5Pset_shuffle( plist_id) < 0 )
return -1;
}
/* Finally compression */
if ( compress )
{
cd_values[0] = compress;
cd_values[1] = (int)(atof(version) * 10);
cd_values[2] = Table;
/* The default compressor in HDF5 (zlib) */
if (strcmp(complib, "zlib") == 0) {
if ( H5Pset_deflate( plist_id, compress) < 0 )
return -1;
}
/* The Blosc compressor does accept parameters */
else if (strcmp(complib, "blosc") == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 6, cd_values) < 0 )
return -1;
}
/* The Blosc compressor can use other compressors */
else if (strncmp(complib, "blosc:", 6) == 0) {
cd_values[4] = compress;
cd_values[5] = shuffle;
blosc_compname = complib + 6;
blosc_compcode = blosc_compname_to_compcode(blosc_compname);
cd_values[6] = blosc_compcode;
if ( H5Pset_filter( plist_id, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 7, cd_values) < 0 )
return -1;
}
/* The LZO compressor does accept parameters */
else if (strcmp(complib, "lzo") == 0) {
if ( H5Pset_filter( plist_id, FILTER_LZO, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
/* The bzip2 compress does accept parameters */
else if (strcmp(complib, "bzip2") == 0) {
if ( H5Pset_filter( plist_id, FILTER_BZIP2, H5Z_FLAG_OPTIONAL, 3, cd_values) < 0 )
return -1;
}
else {
/* Compression library not supported */
return -1;
}
}
/* Create the dataset. */
if ( (dataset_id = H5Dcreate( loc_id, dset_name, type_id, space_id,
H5P_DEFAULT, plist_id, H5P_DEFAULT )) < 0 )
goto out;
/* Only write if there is something to write */
if ( data )
{
/* Write data to the dataset. */
if ( H5Dwrite( dataset_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data ) < 0 )
goto out;
}
/* Terminate access to the data space. */
if ( H5Sclose( space_id ) < 0 )
goto out;
/* End access to the property list */
if ( H5Pclose( plist_id ) < 0 )
goto out;
/* Return the object unique ID for future references */
return dataset_id;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(dataset_id);
H5Sclose(space_id);
H5Pclose(plist_id);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: writer
*
* Purpose: Creates a *big* dataset.
*
* Return: Success: 0
*
* Failure: >0
*
* Programmer: Robb Matzke
* Wednesday, April 8, 1998
*
* Modifications:
* Robb Matzke, 15 Jul 1998
* Addresses are written to the file DNAME instead of stdout.
*
*-------------------------------------------------------------------------
*/
static int
writer(char* filename, hid_t fapl, int wrt_n)
{
hsize_t size1[4] = {8, 1024, 1024, 1024};
hsize_t size2[1] = {GB8LL};
hsize_t hs_start[1];
hsize_t hs_size[1];
hid_t file=-1, space1=-1, space2=-1, mem_space=-1, d1=-1, d2=-1;
int *buf = (int*)malloc (sizeof(int) * WRT_SIZE);
int i, j;
FILE *out = fopen(DNAME, "w");
hid_t dcpl;
TESTING("large dataset write");
/*
* We might be on a machine that has 32-bit files, so create an HDF5 file
* which is a family of files. Each member of the family will be 1GB
*/
if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl))<0) {
goto error;
}
/* Create simple data spaces according to the size specified above. */
if ((space1 = H5Screate_simple (4, size1, size1))<0 ||
(space2 = H5Screate_simple (1, size2, size2))<0) {
goto error;
}
/* Create the datasets */
/*
* The fix below is provided for bug#921
* H5Dcreate with H5P_DEFAULT creation properties
* will create a set of solid 1GB files; test will crash if quotas are enforced
* or it will take some time to write a file.
* We should create a dataset allocating space late and never writing fill values.
* EIP 4/8/03
if ((d1=H5Dcreate (file, "d1", H5T_NATIVE_INT, space1, H5P_DEFAULT))<0 ||
(d2=H5Dcreate (file, "d2", H5T_NATIVE_INT, space2, H5P_DEFAULT))<0) {
goto error;
}
*/
dcpl = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_LATE);
H5Pset_fill_time(dcpl, H5D_FILL_TIME_NEVER);
if ((d1=H5Dcreate (file, "d1", H5T_NATIVE_INT, space1, dcpl))<0 ||
(d2=H5Dcreate (file, "d2", H5T_NATIVE_INT, space2, dcpl))<0) {
goto error;
}
/* Write some things to them randomly */
hs_size[0] = WRT_SIZE;
if ((mem_space = H5Screate_simple (1, hs_size, hs_size))<0) goto error;
for (i=0; i<wrt_n; i++) {
hs_start[0] = randll (size2[0], i);
HDfprintf (out, "#%03d 0x%016Hx\n", i, hs_start[0]);
if (H5Sselect_hyperslab (space2, H5S_SELECT_SET, hs_start, NULL,
hs_size, NULL)<0) goto error;
for (j=0; j<WRT_SIZE; j++) {
buf[j] = i+1;
}
if (H5Dwrite (d2, H5T_NATIVE_INT, mem_space, space2,
H5P_DEFAULT, buf)<0) goto error;
}
if (H5Dclose (d1)<0) goto error;
if (H5Dclose (d2)<0) goto error;
if (H5Sclose (mem_space)<0) goto error;
if (H5Sclose (space1)<0) goto error;
if (H5Sclose (space2)<0) goto error;
if (H5Fclose (file)<0) goto error;
free (buf);
fclose(out);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Dclose(d1);
H5Dclose(d2);
H5Sclose(space1);
H5Sclose(space2);
H5Sclose(mem_space);
H5Fclose(file);
} H5E_END_TRY;
if (buf) free(buf);
if (out) fclose(out);
return 1;
}
