/****************************************************************
**
** test_vlstrings_special(): Test VL string code for special
** string cases, nil and zero-sized.
**
****************************************************************/
static void
test_vlstrings_special(void)
{
const char *wdata[SPACE1_DIM1] = {"", "two", "three", "\0"};
const char *wdata2[SPACE1_DIM1] = {NULL, NULL, NULL, NULL};
char *rdata[SPACE1_DIM1]; /* Information read in */
char *fill; /* Fill value */
hid_t fid1; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hid_t dcpl; /* Dataset creation property list ID */
hsize_t dims1[] = {SPACE1_DIM1};
unsigned i; /* counting variable */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
MESSAGE(5, ("Testing Special VL Strings\n"));
/* Create file */
fid1 = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid1, FAIL, "H5Fcreate");
/* Create dataspace for datasets */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
CHECK(sid1, FAIL, "H5Screate_simple");
/* Create a datatype to refer to */
tid1 = H5Tcopy(H5T_C_S1);
CHECK(tid1, FAIL, "H5Tcopy");
ret = H5Tset_size(tid1,H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
/* Create a dataset */
dataset = H5Dcreate2(fid1, "Dataset3", tid1, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(dataset, FAIL, "H5Dcreate2");
/* Read from dataset before writing data */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Check data read in */
for(i = 0; i < SPACE1_DIM1; i++)
if(rdata[i] != NULL)
TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i,rdata[i]);
/* Write dataset to disk */
ret = H5Dwrite(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
CHECK(ret, FAIL, "H5Dwrite");
/* Read dataset from disk */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Compare data read in */
for(i = 0; i < SPACE1_DIM1; i++) {
if(HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n",(int)i,(int)strlen(wdata[i]),(int)i,(int)strlen(rdata[i]));
continue;
} /* end if */
if((wdata[i] == NULL && rdata[i] != NULL) || (rdata[i] == NULL && wdata[i] != NULL)) {
TestErrPrintf("VL data values don't match!\n");
continue;
} /* end if */
if(HDstrcmp(wdata[i], rdata[i]) != 0 ) {
TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n",(int)i,wdata[i],(int)i,rdata[i]);
continue;
} /* end if */
} /* end for */
/* Reclaim the read VL data */
ret = H5Dvlen_reclaim(tid1, sid1, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dvlen_reclaim");
/* Close Dataset */
ret = H5Dclose(dataset);
CHECK(ret, FAIL, "H5Dclose");
/* Create another dataset to test nil strings */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
CHECK(dcpl, FAIL, "H5Pcreate");
/* Set the fill value for the second dataset */
fill = NULL;
ret = H5Pset_fill_value(dcpl, tid1, &fill);
CHECK(ret, FAIL, "H5Pset_fill_value");
dataset = H5Dcreate2(fid1, "Dataset4", tid1, sid1, H5P_DEFAULT, dcpl, H5P_DEFAULT);
CHECK(dataset, FAIL, "H5Dcreate2");
/* Close dataset creation property list */
ret = H5Pclose(dcpl);
CHECK(ret, FAIL, "H5Pclose");
/* Read from dataset before writing data */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Check data read in */
for(i = 0; i < SPACE1_DIM1; i++)
if(rdata[i] != NULL)
TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i,rdata[i]);
/* Try to write nil strings to disk. */
ret = H5Dwrite(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata2);
CHECK(ret, FAIL, "H5Dwrite");
/* Read nil strings back from disk */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Check data read in */
for(i = 0; i < SPACE1_DIM1; i++)
if(rdata[i] != NULL)
TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i,rdata[i]);
/* Close Dataset */
ret = H5Dclose(dataset);
CHECK(ret, FAIL, "H5Dclose");
/* Close datatype */
ret = H5Tclose(tid1);
CHECK(ret, FAIL, "H5Tclose");
/* Close disk dataspace */
ret = H5Sclose(sid1);
CHECK(ret, FAIL, "H5Sclose");
/* Close file */
ret = H5Fclose(fid1);
CHECK(ret, FAIL, "H5Fclose");
}
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_WR_H5_MPH( struct param_record param,
const struct mph_envi *mph )
{
register unsigned short ni = 0;
hid_t mph_type[NFIELDS];
const int compress = 0;
const char *mph_names[NFIELDS] = {
"product_name", "proc_stage", "ref_doc",
"acquisition_station", "proc_center", "proc_time",
"software_version",
"sensing_start", "sensing_stop",
"phase", "cycle", "rel_orbit", "abs_orbit", "state_vector_time",
"delta_ut1",
"x_position", "y_position", "z_position",
"x_velocity", "y_velocity", "z_velocity",
"vector_source", "utc_sbt_time", "sat_binary_time", "clock_step",
"leap_utc", "leap_sign", "leap_err",
"product_err", "tot_size", "sph_size", "num_dsd", "dsd_size",
"num_data_sets"
};
/*
* define user-defined data types of the Table-fields
*/
mph_type[0] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[0], (size_t) ENVI_FILENAME_SIZE );
mph_type[1] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[1], (size_t) 2 );
mph_type[2] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[2], (size_t) 24 );
mph_type[3] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[3], (size_t) 21 );
mph_type[4] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[4], (size_t) 7 );
mph_type[5] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[5], (size_t) UTC_STRING_LENGTH );
mph_type[6] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[6], (size_t) 15 );
mph_type[7] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[7], (size_t) UTC_STRING_LENGTH );
mph_type[8] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[8], (size_t) UTC_STRING_LENGTH );
mph_type[9] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[9], (size_t) 2 );
mph_type[10] = H5Tcopy( H5T_NATIVE_SHORT );
mph_type[11] = H5Tcopy( H5T_NATIVE_INT );
mph_type[12] = H5Tcopy( H5T_NATIVE_INT );
mph_type[13] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[13], (size_t) UTC_STRING_LENGTH );
mph_type[14] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[15] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[16] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[17] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[18] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[19] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[20] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[21] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[21], (size_t) 3 );
mph_type[22] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[22], (size_t) UTC_STRING_LENGTH );
mph_type[23] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[24] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[25] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[25], (size_t) UTC_STRING_LENGTH );
mph_type[26] = H5Tcopy( H5T_NATIVE_SHORT );
mph_type[27] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[27], (size_t) 2 );
mph_type[28] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[28], (size_t) 2 );
mph_type[29] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[30] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[31] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[32] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[33] = H5Tcopy( H5T_NATIVE_UINT );
/*
* create table
*/
(void) H5TBmake_table( "Main Product Header", param.hdf_file_id, "MPH",
NFIELDS, 1, mph_size, mph_names, mph_offs,
mph_type, 1, NULL, compress, mph );
/*
* create some attributes for quick access
*/
(void) H5LTset_attribute_int( param.hdf_file_id, "/", "abs_orbit",
&mph->abs_orbit, 1 );
/*
* close interface
*/
do {
(void) H5Tclose( mph_type[ni] );
} while ( ++ni < NFIELDS );
}
int main (int argc, char ** argv)
{
char filename [256];
int rank, size, gidx, i, j, k,l;
MPI_Comm comm_dummy = MPI_COMM_WORLD; /* MPI_Comm is defined through adios_read.h */
enum ADIOS_DATATYPES attr_type;
void * data = NULL;
uint64_t start[] = {0,0,0,0,0,0,0,0,0,0};
uint64_t count[MAX_DIMS], hcount[MAX_DIMS], bytes_read = 0;
herr_t h5_err;
char h5name[256],aname[256],fname[256];
int dims [MAX_DIMS];
int h5rank[MAX_DIMS];
int h5i, level;
hid_t grp_id [GMAX+1], space_id, dataset_id;
hid_t memspace_id, dataspace_id, att_id;
char ** grp_name;
hid_t type_id;
hid_t h5_type_id;
hsize_t adims;
if (argc < 2) {
printf("Usage: %s <BP-file> <HDF5-file>\n", argv[0]);
return 1;
}
MPI_Init(&argc, &argv);
h5_err = H5Eset_auto(NULL, NULL );
ADIOS_FILE * f = adios_fopen (argv[1], comm_dummy);
HDF5_FILE = H5Fcreate(argv[2],H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* create the complex types for HDF5 */
complex_real_id = H5Tcreate (H5T_COMPOUND, sizeof (complex_real_t));
H5Tinsert (complex_real_id, "real", HOFFSET(complex_real_t,re), H5T_NATIVE_FLOAT);
H5Tinsert (complex_real_id, "imaginary", HOFFSET(complex_real_t,im), H5T_NATIVE_FLOAT);
complex_double_id = H5Tcreate (H5T_COMPOUND, sizeof (complex_double_t));
H5Tinsert (complex_double_id, "real", HOFFSET(complex_double_t,re), H5T_NATIVE_DOUBLE);
H5Tinsert (complex_double_id, "imaginary", HOFFSET(complex_double_t,im), H5T_NATIVE_DOUBLE);
if (f == NULL) {
if (DEBUG) printf ("%s\n", adios_errmsg());
return -1;
}
/* For all groups */
for (gidx = 0; gidx < f->groups_count; gidx++) {
if (DEBUG) printf("Group %s:\n", f->group_namelist[gidx]);
ADIOS_GROUP * g = adios_gopen (f, f->group_namelist[gidx]);
if (g == NULL) {
if (DEBUG) printf ("%s\n", adios_errmsg());
return -1;
}
/* First create all of the groups */
grp_id [0] = HDF5_FILE;
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
strcpy(h5name,g->var_namelist[i]);
grp_name = bp_dirparser (h5name, &level);
for (j = 0; j < level-1; j++) {
grp_id [j + 1] = H5Gopen (grp_id [j], grp_name [j]);
if (grp_id [j + 1] < 0) {
grp_id [j + 1] = H5Gcreate (grp_id [j], grp_name [j], 0);
}
}
for (j=1; j<level; j++) {
H5Gclose(grp_id[j]);
}
}
/* Now we can write data into these scalars */
/* For all variables */
if (DEBUG) printf(" Variables=%d:\n", g->vars_count);
for (i = 0; i < g->vars_count; i++) {
ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
uint64_t total_size = adios_type_size (v->type, v->value);
for (j = 0; j < v->ndim; j++)
total_size *= v->dims[j];
strcpy(h5name,g->var_namelist[i]);
if (DEBUG) printf(" %-9s %s", adios_type_to_string(v->type), g->var_namelist[i]);
h5_err = bp_getH5TypeId (v->type, &h5_type_id);
if (v->type==adios_string) H5Tset_size(h5_type_id,strlen(v->value));
if (v->ndim == 0) {
/* Scalars do not need to be read in, we get it from the metadata
when using adios_inq_var */
if (DEBUG) printf(" = %s\n", value_to_string(v->type, v->value, 0));
// add the hdf5 dataset, these are scalars
for (h5i = 0;h5i<MAX_DIMS;h5i++)
count[0] = 0;
count[0] = 1; // we are writing just 1 element, RANK=1
h5_err = bp_getH5TypeId (v->type, &h5_type_id);
H5LTmake_dataset(HDF5_FILE,h5name,1,count,h5_type_id,v->value);
} else {
h5_err = readVar(g, v, h5name);
}
adios_free_varinfo (v);
} /* variables */
/* For all attributes */
if (DEBUG) printf(" Attributes=%d:\n", g->attrs_count);
for (i = 0; i < g->attrs_count; i++) {
enum ADIOS_DATATYPES atype;
int asize;
void *adata;
adios_get_attr_byid (g, i, &atype, &asize, &adata);
grp_name = bp_dirparser (g->attr_namelist[i], &level);
strcpy(aname,grp_name[level-1]);
// the name of the attribute is the last in the array
// we then need to concat the rest together
strcpy(fname,"/");
for (j=0;j<level-1;j++) {
strcat(fname,grp_name[j]);
}
h5_err = bp_getH5TypeId (atype, &h5_type_id);
// let's create the attribute
adims = 1;
if (atype==adios_string) H5Tset_size(h5_type_id,strlen(adata));
space_id = H5Screate(H5S_SCALAR); // just a scalar
att_id = H5Acreate(HDF5_FILE, g->attr_namelist[i], h5_type_id, space_id,H5P_DEFAULT);
h5_err = H5Awrite(att_id, h5_type_id, adata);
h5_err = H5Aclose(att_id);
h5_err = H5Sclose(space_id);
if (DEBUG) printf(" %-9s %s = %s\n", adios_type_to_string(atype),
g->attr_namelist[i], value_to_string(atype, adata, 0));
free(adata);
} /* attributes */
adios_gclose (g);
} /* groups */
adios_fclose (f);
h5_err = H5Fclose(HDF5_FILE);
MPI_Finalize();
return 0;
}
int
main (int argc, char *argv[])
{
inp_t input_params;
mdl_t source_mdl;
net_t network;
int cell_index;
int verbose = 1;
char *input_file;
/* Parse options and command line arguments. Diplay help
message if no (or more than one) argument is given. */
{
int opt;
static struct option longopts[] = {
{"help", no_argument, NULL, 'h'},
{"version", no_argument, NULL, 'V'},
{"verbose", no_argument, NULL, 'v'},
{"quiet", no_argument, NULL, 'q'},
{0, 0, 0, 0}
};
while ((opt = getopt_long (argc, argv, "hVvq", longopts, NULL)) != -1)
{
switch (opt)
{
case 'h':
usage ();
return EXIT_SUCCESS;
break;
case 'V':
version ();
return EXIT_SUCCESS;
break;
case 'v':
verbose = 2;
break;
case 'q':
verbose = 0;
break;
default:
usage ();
return EXIT_FAILURE;
}
};
argc -= optind;
argv += optind;
if (argc != 1)
{
usage ();
return EXIT_FAILURE;
}
input_file = argv[0];
}
/* Read the input file */
if( read_input_file_names (input_file, &input_params.files, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Read the chemical network file */
if( read_network (input_params.files.chem_file, &network, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Read the input file */
if( read_input (input_file, &input_params, &network, verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
/* Read the source model file */
if( read_source (input_params.files.source_file, &source_mdl, &input_params,
verbose) != EXIT_SUCCESS )
{
return EXIT_FAILURE;
}
// Hdf5 files, datatype and dataspace
hid_t fid, datatype, dataspace, dataset, tsDataset, tsDataspace, speciesDataset, speciesDataspace, speciesType;
datatype = H5Tcopy(H5T_NATIVE_DOUBLE);
hsize_t dimsf[ ROUTE_DATASET_RANK ]={ source_mdl.n_cells, source_mdl.ts.n_time_steps, input_params.output.n_output_species, N_OUTPUT_ROUTES };
fid = H5Fcreate( "astrochem_output.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dataspace = H5Screate_simple( ABUNDANCE_DATASET_RANK, dimsf, NULL);
// Add Atributes
hid_t simpleDataspace = H5Screate(H5S_SCALAR);
hid_t attrType = H5Tcopy(H5T_C_S1);
H5Tset_size ( attrType, MAX_CHAR_FILENAME );
H5Tset_strpad(attrType,H5T_STR_NULLTERM);
hid_t attrNetwork = H5Acreate( fid, "chem_file", attrType, simpleDataspace, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite( attrNetwork, attrType, realpath( input_params.files.chem_file, NULL ) );
H5Aclose( attrNetwork );
hid_t attrModel = H5Acreate( fid, "source_file", attrType, simpleDataspace, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite( attrModel, attrType, realpath( input_params.files.source_file, NULL ) );
H5Aclose( attrModel );
H5Tclose( attrType );
H5Sclose( simpleDataspace );
// Define chunk property
hsize_t chunk_dims[ ROUTE_DATASET_RANK ] = { 1, 1, input_params.output.n_output_species, N_OUTPUT_ROUTES };
hid_t prop_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(prop_id, ABUNDANCE_DATASET_RANK , chunk_dims);
// Create dataset
dataset = H5Dcreate(fid, "Abundances", datatype, dataspace, H5P_DEFAULT, prop_id, H5P_DEFAULT);
int i;
hid_t dataspaceRoute, route_t_datatype, r_t_datatype, route_prop_id, routeGroup;
hid_t routeDatasets[ input_params.output.n_output_species ];
if (input_params.output.trace_routes)
{
// Create route dataspace
dataspaceRoute = H5Screate_simple( ROUTE_DATASET_RANK, dimsf, NULL);
// Create route datatype
r_t_datatype = H5Tcreate (H5T_COMPOUND, sizeof(r_t));
H5Tinsert( r_t_datatype, "reaction_number", HOFFSET(r_t, reaction_no ), H5T_NATIVE_INT);
H5Tinsert( r_t_datatype, "reaction_rate", HOFFSET(r_t, rate), H5T_NATIVE_DOUBLE);
route_t_datatype = H5Tcreate (H5T_COMPOUND, sizeof(rout_t));
H5Tinsert( route_t_datatype, "formation_rate", HOFFSET(rout_t, formation ), r_t_datatype );
H5Tinsert( route_t_datatype, "destruction_rate", HOFFSET(rout_t, destruction ), r_t_datatype );
// Define route chunk property
route_prop_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk( route_prop_id, ROUTE_DATASET_RANK, chunk_dims);
// Create each named route dataset
routeGroup = H5Gcreate( fid, "Routes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
char routeName[6] = "route_";
char tempName[ MAX_CHAR_SPECIES + sizeof( routeName ) ];
for( i = 0; i < input_params.output.n_output_species ; i++ )
{
strcpy( tempName, routeName );
strcat( tempName, network.species[input_params.output.output_species_idx[i]].name );
routeDatasets[i] = H5Dcreate( routeGroup, tempName, route_t_datatype, dataspaceRoute, H5P_DEFAULT, route_prop_id, H5P_DEFAULT);
}
}
// Timesteps and species
hsize_t n_ts = source_mdl.ts.n_time_steps;
hsize_t n_species = input_params.output.n_output_species ;
tsDataspace = H5Screate_simple( 1, &n_ts, NULL);
speciesDataspace = H5Screate_simple( 1, &n_species, NULL);
speciesType = H5Tcopy (H5T_C_S1);
H5Tset_size (speciesType, MAX_CHAR_SPECIES );
H5Tset_strpad(speciesType,H5T_STR_NULLTERM);
// Create ts and species datasets
tsDataset = H5Dcreate(fid, "TimeSteps", datatype, tsDataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
speciesDataset = H5Dcreate(fid, "Species", speciesType, speciesDataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
double* convTs = (double*) malloc( sizeof(double)* source_mdl.ts.n_time_steps );
for( i=0; i< source_mdl.ts.n_time_steps; i++ )
{
convTs[i] = source_mdl.ts.time_steps[i] / CONST_MKSA_YEAR;
}
H5Dwrite( tsDataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, convTs );
char speciesName [ input_params.output.n_output_species ][ MAX_CHAR_SPECIES ];
for( i = 0; i < input_params.output.n_output_species ; i++ )
{
strcpy( speciesName[i], network.species[input_params.output.output_species_idx[i]].name );
}
H5Dwrite( speciesDataset, speciesType, H5S_ALL, H5S_ALL, H5P_DEFAULT, speciesName );
free( convTs );
H5Dclose( tsDataset );
H5Dclose( speciesDataset );
H5Tclose( speciesType );
H5Sclose( tsDataspace );
H5Sclose( speciesDataspace );
#ifdef HAVE_OPENMP
/*Initialize lock*/
omp_init_lock(&lock);
/* Solve the ODE system for each cell. */
{
#pragma omp parallel for schedule (dynamic, 1)
#endif
for (cell_index = 0; cell_index < source_mdl.n_cells; cell_index++)
{
if (verbose >= 1)
fprintf (stdout, "Computing abundances in cell %d...\n",
cell_index);
if( full_solve ( fid, dataset, routeDatasets, dataspace, dataspaceRoute, datatype, route_t_datatype, cell_index, &input_params, source_mdl.mode,
&source_mdl.cell[cell_index], &network, &source_mdl.ts, verbose) != EXIT_SUCCESS )
{
exit (EXIT_FAILURE);
}
if (verbose >= 1)
fprintf (stdout, "Done with cell %d.\n", cell_index);
}
#ifdef HAVE_OPENMP
}
/*Finished lock mechanism, destroy it*/
omp_destroy_lock(&lock);
#endif
/*
* Close/release hdf5 resources.
*/
if (input_params.output.trace_routes)
{
for( i = 0; i < input_params.output.n_output_species ; i++ )
{
H5Dclose(routeDatasets[i] );
}
H5Sclose(dataspaceRoute);
H5Gclose(routeGroup);
H5Pclose(route_prop_id);
H5Tclose(r_t_datatype);
H5Tclose(route_t_datatype);
}
H5Dclose(dataset);
H5Pclose(prop_id);
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(fid);
free_input (&input_params);
free_mdl (&source_mdl);
free_network (&network);
return (EXIT_SUCCESS);
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
Particle dst_buf[NRECORDS+NRECORDS_ADD];
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( p_data[0].name),
sizeof( p_data[0].lati),
sizeof( p_data[0].longi),
sizeof( p_data[0].pressure),
sizeof( p_data[0].temperature)};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
herr_t status;
int i;
/* Append particles */
Particle particle_in[ NRECORDS_ADD ] =
{{ "eight",80,80, 8.0f, 80.0},
{"nine",90,90, 9.0f, 90.0} };
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_02.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* make a table */
status=H5TBmake_table( "Table Title",file_id,TABLE_NAME,NFIELDS,NRECORDS,
dst_size, field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
/* append two records */
status=H5TBappend_records(file_id, TABLE_NAME,NRECORDS_ADD, dst_size, dst_offset, dst_sizes,
&particle_in );
/* read the table */
status=H5TBread_table( file_id, TABLE_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* print it by rows */
for (i=0; i<NRECORDS+NRECORDS_ADD; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
/****************************************************************
**
** test_write_vl_string_attribute(): Test basic VL string code.
** Tests writing VL strings as attributes
**
****************************************************************/
static void test_write_vl_string_attribute(void)
{
hid_t file, root, dataspace, att;
hid_t type;
herr_t ret;
char *string_att_check = NULL;
/* Open the file */
file = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(file, FAIL, "H5Fopen");
/* Create a datatype to refer to. */
type = H5Tcopy (H5T_C_S1);
CHECK(type, FAIL, "H5Tcopy");
ret = H5Tset_size (type, H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
root = H5Gopen2(file, "/", H5P_DEFAULT);
CHECK(root, FAIL, "H5Gopen2");
dataspace = H5Screate(H5S_SCALAR);
CHECK(dataspace, FAIL, "H5Screate");
/* Test creating a "normal" sized string attribute */
att = H5Acreate2(root, "test_scalar", type, dataspace, H5P_DEFAULT, H5P_DEFAULT);
CHECK(att, FAIL, "H5Acreate2");
ret = H5Awrite(att, type, &string_att);
CHECK(ret, FAIL, "H5Awrite");
ret = H5Aread(att, type, &string_att_check);
CHECK(ret, FAIL, "H5Aread");
if(HDstrcmp(string_att_check,string_att) != 0)
TestErrPrintf("VL string attributes don't match!, string_att=%s, string_att_check=%s\n",string_att,string_att_check);
H5free_memory(string_att_check);
string_att_check = NULL;
ret = H5Aclose(att);
CHECK(ret, FAIL, "HAclose");
/* Test creating a "large" sized string attribute */
att = H5Acreate2(root, "test_scalar_large", type, dataspace, H5P_DEFAULT, H5P_DEFAULT);
CHECK(att, FAIL, "H5Acreate2");
string_att_write = (char*)HDcalloc((size_t)8192, sizeof(char));
HDmemset(string_att_write, 'A', (size_t)8191);
ret = H5Awrite(att, type, &string_att_write);
CHECK(ret, FAIL, "H5Awrite");
ret = H5Aread(att, type, &string_att_check);
CHECK(ret, FAIL, "H5Aread");
if(HDstrcmp(string_att_check,string_att_write) != 0)
TestErrPrintf("VL string attributes don't match!, string_att_write=%s, string_att_check=%s\n",string_att_write,string_att_check);
H5free_memory(string_att_check);
string_att_check = NULL;
/* The attribute string written is freed below, in the test_read_vl_string_attribute() test */
/* HDfree(string_att_write); */
ret = H5Aclose(att);
CHECK(ret, FAIL, "HAclose");
ret = H5Gclose(root);
CHECK(ret, FAIL, "H5Gclose");
ret = H5Tclose(type);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Sclose(dataspace);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Fclose(file);
CHECK(ret, FAIL, "H5Fclose");
return;
}
/****************************************************************
**
** test_vl_rewrite(): Test basic VL string code.
** Tests I/O on VL strings when lots of objects in the file
** have been linked/unlinked.
**
****************************************************************/
static void test_vl_rewrite(void)
{
hid_t file1, file2; /* File IDs */
hid_t type; /* VL string datatype ID */
hid_t space; /* Scalar dataspace */
char name[256]; /* Buffer for names & data */
int i; /* Local index variable */
herr_t ret; /* Generic return value */
/* Create the VL string datatype */
type = H5Tcopy(H5T_C_S1);
CHECK(type, FAIL, "H5Tcopy");
ret = H5Tset_size(type, H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
/* Create the scalar dataspace */
space = H5Screate(H5S_SCALAR);
CHECK(space, FAIL, "H5Screate");
/* Open the files */
file1 = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(file1, FAIL, "H5Fcreate");
file2 = H5Fcreate(DATAFILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(file1, FAIL, "H5Fcreate");
/* Create in file 1 */
for(i=0; i<REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
write_scalar_dset(file1, type, space, name, name);
}
/* Effectively copy data from file 1 to 2 */
for(i=0; i<REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
read_scalar_dset(file1, type, space, name, name);
write_scalar_dset(file2, type, space, name, name);
}
/* Read back from file 2 */
for(i = 0; i < REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
read_scalar_dset(file2, type, space, name, name);
} /* end for */
/* Remove from file 2. */
for(i = 0; i < REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
ret = H5Ldelete(file2, name, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Ldelete");
} /* end for */
/* Effectively copy from file 1 to file 2 */
for(i = 0; i < REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
read_scalar_dset(file1, type, space, name, name);
write_scalar_dset(file2, type, space, name, name);
} /* end for */
/* Close everything */
ret = H5Tclose(type);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Sclose(space);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Fclose(file1);
CHECK(ret, FAIL, "H5Fclose");
ret = H5Fclose(file2);
CHECK(ret, FAIL, "H5Fclose");
return;
} /* end test_vl_rewrite() */
/*-------------------------------------------------------------------------
* Function: gent_att_compound_vlstr
*
* Purpose: Generate a dataset and a group.
* Both has an attribute with a compound datatype consisting
* of a variable length string
*
*-------------------------------------------------------------------------
*/
static void gent_att_compound_vlstr(hid_t loc_id)
{
typedef struct { /* Compound structure for the attribute */
int i;
char *v;
} s1;
hsize_t dim[1] = {1}; /* Dimension size */
hid_t sid = -1; /* Dataspace ID */
hid_t tid = -1; /* Datatype ID */
hid_t aid = -1; /* Attribute ID */
hid_t did = -1; /* Dataset ID */
hid_t gid = -1; /* Group ID */
hid_t vl_str_tid = -1; /* Variable length datatype ID */
hid_t cmpd_tid = -1; /* Compound datatype ID */
hid_t null_sid = -1; /* Null dataspace ID */
s1 buf; /* Buffer */
buf.i = 9;
buf.v = "ThisIsAString";
/* Create an integer datatype */
if((tid = H5Tcopy(H5T_NATIVE_INT)) < 0)
goto error;
/* Create a variable length string */
if((vl_str_tid = H5Tcopy(H5T_C_S1)) < 0)
goto error;
if(H5Tset_size(vl_str_tid, H5T_VARIABLE) < 0)
goto error;
/* Create a compound datatype with a variable length string and an integer */
if((cmpd_tid = H5Tcreate(H5T_COMPOUND, sizeof(s1))) < 0)
goto error;
if(H5Tinsert(cmpd_tid, "i", HOFFSET(s1, i), tid) < 0)
goto error;
if(H5Tinsert(cmpd_tid, "v", HOFFSET(s1, v), vl_str_tid) < 0)
goto error;
/* Create a dataset */
if((null_sid = H5Screate(H5S_NULL)) < 0)
goto error;
if((did = H5Dcreate2(loc_id, DATASET_ATTR, H5T_NATIVE_INT, null_sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Attach an attribute with the compound datatype to the dataset */
if((sid = H5Screate_simple(1, dim, dim)) < 0)
goto error;
if((aid = H5Acreate2(did, ATTR, cmpd_tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Write the attribute */
buf.i = 9;
buf.v = "ThisIsAString";
if(H5Awrite(aid, cmpd_tid, &buf) < 0)
goto error;
/* Close the dataset and its attribute */
if(H5Dclose(did) < 0)
goto error;
if(H5Aclose(aid) < 0)
goto error;
/* Create a group */
if((gid = H5Gcreate2(loc_id, GROUP_ATTR, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* Attach an attribute with the compound datatype to the group */
if((aid = H5Acreate2(gid, ATTR, cmpd_tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(H5Awrite(aid, cmpd_tid, &buf) < 0)
goto error;
/* Close the group and its attribute */
if(H5Aclose(aid) < 0)
goto error;
if(H5Gclose(gid) < 0)
goto error;
/* Close dataspaces */
if(H5Sclose(sid) < 0)
goto error;
if(H5Sclose(null_sid) < 0)
goto error;
/* Close datatypes */
if(H5Tclose(tid) < 0)
goto error;
if(H5Tclose(vl_str_tid) < 0)
goto error;
if(H5Tclose(cmpd_tid) < 0)
goto error;
error:
H5E_BEGIN_TRY {
H5Tclose(tid);
H5Tclose(vl_str_tid);
H5Tclose(cmpd_tid);
H5Sclose(null_sid);
H5Sclose(sid);
H5Dclose(did);
H5Aclose(aid);
H5Gclose(gid);
} H5E_END_TRY;
} /* gen_att_compound_vlstr() */
/*-------------------------------------------------------------------------
* Function: test_multi
*
* Purpose: Tests the file handle interface for MUTLI driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Tuesday, Sept 24, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
test_multi(void)
{
hid_t file=(-1), fapl, fapl2=(-1), dset=(-1), space=(-1);
hid_t root, attr, aspace, atype;
hid_t access_fapl = -1;
char filename[1024];
int *fhandle2=NULL, *fhandle=NULL;
hsize_t file_size;
H5FD_mem_t mt, memb_map[H5FD_MEM_NTYPES];
hid_t memb_fapl[H5FD_MEM_NTYPES];
haddr_t memb_addr[H5FD_MEM_NTYPES];
const char *memb_name[H5FD_MEM_NTYPES];
char sv[H5FD_MEM_NTYPES][32];
hsize_t dims[2]= {MULTI_SIZE, MULTI_SIZE};
hsize_t adims[1]= {1};
char dname[]="dataset";
char meta[] = "this is some metadata on this file";
int i, j;
int buf[MULTI_SIZE][MULTI_SIZE];
TESTING("MULTI file driver");
/* Set file access property list for MULTI driver */
fapl = h5_fileaccess();
HDmemset(memb_map, 0, sizeof memb_map);
HDmemset(memb_fapl, 0, sizeof memb_fapl);
HDmemset(memb_name, 0, sizeof memb_name);
HDmemset(memb_addr, 0, sizeof memb_addr);
HDmemset(sv, 0, sizeof sv);
for(mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
memb_fapl[mt] = H5P_DEFAULT;
memb_map[mt] = H5FD_MEM_SUPER;
}
memb_map[H5FD_MEM_DRAW] = H5FD_MEM_DRAW;
memb_map[H5FD_MEM_BTREE] = H5FD_MEM_BTREE;
memb_map[H5FD_MEM_GHEAP] = H5FD_MEM_GHEAP;
sprintf(sv[H5FD_MEM_SUPER], "%%s-%c.h5", 's');
memb_name[H5FD_MEM_SUPER] = sv[H5FD_MEM_SUPER];
memb_addr[H5FD_MEM_SUPER] = 0;
sprintf(sv[H5FD_MEM_BTREE], "%%s-%c.h5", 'b');
memb_name[H5FD_MEM_BTREE] = sv[H5FD_MEM_BTREE];
memb_addr[H5FD_MEM_BTREE] = HADDR_MAX/4;
sprintf(sv[H5FD_MEM_DRAW], "%%s-%c.h5", 'r');
memb_name[H5FD_MEM_DRAW] = sv[H5FD_MEM_DRAW];
memb_addr[H5FD_MEM_DRAW] = HADDR_MAX/2;
sprintf(sv[H5FD_MEM_GHEAP], "%%s-%c.h5", 'g');
memb_name[H5FD_MEM_GHEAP] = sv[H5FD_MEM_GHEAP];
memb_addr[H5FD_MEM_GHEAP] = (HADDR_MAX/4)*3;
if(H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, TRUE) < 0)
TEST_ERROR;
h5_fixname(FILENAME[4], fapl, filename, sizeof filename);
if((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Test wrong ways to reopen multi files */
if(test_multi_opens(filename) < 0)
TEST_ERROR;
/* Reopen the file */
if((file=H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
/* Create and write data set */
if((space=H5Screate_simple(2, dims, NULL)) < 0)
TEST_ERROR;
/* Retrieve the access property list... */
if ((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* Check that the driver is correct */
if(H5FD_MULTI != H5Pget_driver(access_fapl))
TEST_ERROR;
/* ...and close the property list */
if (H5Pclose(access_fapl) < 0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* Before any data is written, the raw data file is empty. So
* the file size is only the size of b-tree + HADDR_MAX/4.
*/
if(file_size < HADDR_MAX/4 || file_size > HADDR_MAX/2)
TEST_ERROR;
if((dset=H5Dcreate2(file, dname, H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
for(i=0; i<MULTI_SIZE; i++)
for(j=0; j<MULTI_SIZE; j++)
buf[i][j] = i*10000+j;
if(H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
TEST_ERROR;
if((fapl2=H5Pcreate(H5P_FILE_ACCESS)) < 0)
TEST_ERROR;
if(H5Pset_multi_type(fapl2, H5FD_MEM_SUPER) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, fapl2, (void **)&fhandle) < 0)
TEST_ERROR;
if(*fhandle<0)
TEST_ERROR;
if(H5Pset_multi_type(fapl2, H5FD_MEM_DRAW) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, fapl2, (void **)&fhandle2) < 0)
TEST_ERROR;
if(*fhandle2<0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* After the data is written, the file size is huge because the
* beginning of raw data file is set at HADDR_MAX/2. It's supposed
* to be (HADDR_MAX/2 + 128*128*4)
*/
if(file_size < HADDR_MAX/2 || file_size > HADDR_MAX)
TEST_ERROR;
if(H5Sclose(space) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Pclose(fapl2) < 0)
TEST_ERROR;
/* Create and write attribute for the root group. */
if((root = H5Gopen2(file, "/", H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Attribute string. */
if((atype = H5Tcopy(H5T_C_S1)) < 0)
TEST_ERROR;
if(H5Tset_size(atype, strlen(meta) + 1) < 0)
TEST_ERROR;
if(H5Tset_strpad(atype, H5T_STR_NULLTERM) < 0)
TEST_ERROR;
/* Create and write attribute */
if((aspace = H5Screate_simple(1, adims, NULL)) < 0)
TEST_ERROR;
if((attr = H5Acreate2(root, "Metadata", atype, aspace, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Awrite(attr, atype, meta) < 0)
TEST_ERROR;
/* Close IDs */
if(H5Tclose(atype) < 0)
TEST_ERROR;
if(H5Sclose(aspace) < 0)
TEST_ERROR;
if(H5Aclose(attr) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Sclose(space);
H5Dclose(dset);
H5Pclose(fapl);
H5Pclose(fapl2);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
int main(void)
{
hid_t fil,spc,set;
hid_t cs6, cmp, fix;
hid_t cmp1, cmp2, cmp3;
hid_t plist;
hid_t array_dt;
hsize_t dim[2];
hsize_t cdim[4];
char string5[5];
float fok[2] = {1234., 2341.};
float fnok[2] = {5678., 6785.};
float *fptr;
char *data = NULL;
int result = 0;
herr_t error = 1;
printf("%-70s", "Testing alignment in compound datatypes");
strcpy(string5, "Hi!");
HDunlink(fname);
fil = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (fil < 0) {
puts("*FAILED*");
return 1;
}
H5E_BEGIN_TRY {
(void)H5Ldelete(fil, setname, H5P_DEFAULT);
} H5E_END_TRY;
cs6 = H5Tcopy(H5T_C_S1);
H5Tset_size(cs6, sizeof(string5));
H5Tset_strpad(cs6, H5T_STR_NULLPAD);
cmp = H5Tcreate(H5T_COMPOUND, sizeof(fok) + sizeof(string5) + sizeof(fnok));
H5Tinsert(cmp, "Awkward length", 0, cs6);
cdim[0] = sizeof(fok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp, "Ok", sizeof(string5), array_dt);
H5Tclose(array_dt);
cdim[0] = sizeof(fnok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp, "Not Ok", sizeof(fok) + sizeof(string5), array_dt);
H5Tclose(array_dt);
fix = h5tools_get_native_type(cmp);
cmp1 = H5Tcreate(H5T_COMPOUND, sizeof(fok));
cdim[0] = sizeof(fok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp1, "Ok", 0, array_dt);
H5Tclose(array_dt);
cmp2 = H5Tcreate(H5T_COMPOUND, sizeof(string5));
H5Tinsert(cmp2, "Awkward length", 0, cs6);
cmp3 = H5Tcreate(H5T_COMPOUND, sizeof(fnok));
cdim[0] = sizeof(fnok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp3, "Not Ok", 0, array_dt);
H5Tclose(array_dt);
plist = H5Pcreate(H5P_DATASET_XFER);
if((error = H5Pset_preserve(plist, 1)) < 0)
goto out;
/*
* Create a small dataset, and write data into it we write each field
* in turn so that we are avoid alignment issues at this point
*/
dim[0] = 1;
spc = H5Screate_simple(1, dim, NULL);
set = H5Dcreate2(fil, setname, cmp, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(set, cmp1, spc, H5S_ALL, plist, fok);
H5Dwrite(set, cmp2, spc, H5S_ALL, plist, string5);
H5Dwrite(set, cmp3, spc, H5S_ALL, plist, fnok);
H5Dclose(set);
/* Now open the set, and read it back in */
data = malloc(H5Tget_size(fix));
if(!data) {
perror("malloc() failed");
abort();
}
set = H5Dopen2(fil, setname, H5P_DEFAULT);
H5Dread(set, fix, spc, H5S_ALL, H5P_DEFAULT, data);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
out:
if(error < 0) {
result = 1;
puts("*FAILED - HDF5 library error*");
} else if(fok[0] != fptr[0] || fok[1] != fptr[1]
|| fnok[0] != fptr[2] || fnok[1] != fptr[3]) {
char *mname;
result = 1;
mname = H5Tget_member_name(fix, 0);
printf("%14s (%2d) %6s = %s\n",
mname ? mname : "(null)", (int)H5Tget_member_offset(fix,0),
string5, (char *)(data + H5Tget_member_offset(fix, 0)));
if(mname)
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
mname = H5Tget_member_name(fix, 1);
printf("Data comparison:\n"
"%14s (%2d) %6f = %f\n"
" %6f = %f\n",
mname ? mname : "(null)", (int)H5Tget_member_offset(fix,1),
fok[0], fptr[0],
fok[1], fptr[1]);
if(mname)
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 2));
mname = H5Tget_member_name(fix, 2);
printf("%14s (%2d) %6f = %f\n"
" %6f = %6f\n",
mname ? mname : "(null)", (int)H5Tget_member_offset(fix,2),
fnok[0], fptr[0],
fnok[1], fptr[1]);
if(mname)
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
printf("\n"
"Short circuit\n"
" %6f = %f\n"
" %6f = %f\n"
" %6f = %f\n"
" %6f = %f\n",
fok[0], fptr[0],
fok[1], fptr[1],
fnok[0], fptr[2],
fnok[1], fptr[3]);
puts("*FAILED - compound type alignmnent problem*");
} else {
puts(" PASSED");
}
if(data)
free(data);
H5Sclose(spc);
H5Tclose(cmp);
H5Tclose(cmp1);
H5Tclose(cmp2);
H5Tclose(cmp3);
H5Pclose(plist);
H5Fclose(fil);
HDunlink(fname);
fflush(stdout);
return result;
}
IbHdf5::IbHdf5(const QString &tableName, const QString &filePath, QObject *parent)
: m_tableName(tableName)
, m_filePath(filePath)
, QObject(parent)
{
// struct Record2
// {
// uint timestamp;
// char* timeString;
// double open;
// double high;
// double low;
// double close;
// uint volume;
// char* sqlTimeFrame;
// };
m_nFields = 8;
// m_dst_size = sizeof(Record2);
m_dst_offset[0] = HOFFSET(Record2, timestamp);
m_dst_offset[1] = HOFFSET(Record2, timeString);
m_dst_offset[2] = HOFFSET(Record2, open);
m_dst_offset[3] = HOFFSET(Record2, high);
m_dst_offset[4] = HOFFSET(Record2, low);
m_dst_offset[5] = HOFFSET(Record2, close);
m_dst_offset[6] = HOFFSET(Record2, volume);
m_dst_offset[7] = HOFFSET(Record2, sqlTimeFrame);
m_dst_sizes[0] = sizeof(uint);
m_dst_sizes[1] = 64;
m_dst_sizes[2] = sizeof(double);
m_dst_sizes[3] = sizeof(double);
m_dst_sizes[4] = sizeof(double);
m_dst_sizes[5] = sizeof(double);
m_dst_sizes[6] = sizeof(uint);
m_dst_sizes[7] = 8;
m_fieldNames[0] = "timestamp";
m_fieldNames[1] = "timestring";
m_fieldNames[2] = "open";
m_fieldNames[3] = "high";
m_fieldNames[4] = "low";
m_fieldNames[5] = "close";
m_fieldNames[6] = "volume";
m_fieldNames[7] = "timeframe";
m_chunkSize = 10;
hid_t timeStringType;
hid_t timeFrameType;
m_fillData = NULL;
m_compress = 0;
timeStringType = H5Tcopy(H5T_C_S1);
H5Tset_size(timeStringType, 64);
timeFrameType = H5Tcopy(H5T_C_S1);
H5Tset_size(timeFrameType, 8);
m_fieldType[0] = H5T_NATIVE_UINT;
m_fieldType[1] = timeStringType;
m_fieldType[2] = H5T_NATIVE_DOUBLE;
m_fieldType[3] = H5T_NATIVE_DOUBLE;
m_fieldType[4] = H5T_NATIVE_DOUBLE;
m_fieldType[5] = H5T_NATIVE_DOUBLE;
m_fieldType[6] = H5T_NATIVE_UINT;
m_fieldType[7] = timeFrameType;
// CREATE OR OPEN THE FILE
// if (!QFileInfo::exists(m_filePath)) {
m_fid = H5Fcreate (m_filePath.toLatin1().constData(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// }
// else {
// m_fid = H5Fopen(m_filePath.toLatin1().data(), H5F_ACC_RDWR, H5P_DEFAULT);
// }
}
/**
@details
-# Set the file extension to ".h5"
-# Open the log file
-# Create the root directory in the HDF5 file
-# For each variable to be recorded
-# Create a fixed length packet table
-# Associate the packet table with the temporary memory buffer storing the simulation data
-# Declare the recording group to the memory manager so that the group can be checkpointed
and restored.
*/
int Trick::DRHDF5::format_specific_init() {
#ifdef HDF5
unsigned int ii ;
HDF5_INFO *hdf5_info ;
hsize_t chunk_size = 1024;
hid_t byte_id ;
hid_t file_names_id, param_types_id, param_units_id, param_names_id ;
hid_t datatype ;
herr_t ret_value ;
hid_t s256 ;
std::string buf;
file_name.append(".h5") ;
s256 = H5Tcopy(H5T_C_S1);
H5Tset_size(s256, 256);
// Create a new HDF5 file with the specified name; overwrite if it exists.
if ((file = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
message_publish(MSG_ERROR, "Can't open Data Record file %s.\n", file_name.c_str()) ;
record = false ;
return -1 ;
}
// All HDF5 objects live in the top-level "/" (root) group.
root_group = H5Gopen(file, "/", H5P_DEFAULT);
// Create a new group named "header" at the root ("/") level.
header_group = H5Gcreate(file, "/header", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// Create a packet table (PT) that stores byte order.
byte_id = H5PTcreate_fl(header_group, "byte_order", s256, chunk_size, 1) ;
// Add the byte order value to the byte packet table.
H5PTappend( byte_id, 1, byte_order.c_str() );
// Create a packet table (PT) that stores each parameter's file location.
file_names_id = H5PTcreate_fl(header_group, "file_names", s256, chunk_size, 1) ;
// Create a packet table (PT) that stores each parameter's type.
param_types_id = H5PTcreate_fl(header_group, "param_types", s256, chunk_size, 1) ;
// Create a packet table (PT) that stores each parameter's unit.
param_units_id = H5PTcreate_fl(header_group, "param_units", s256, chunk_size, 1) ;
// Create a packet table (PT) that stores each parameter's name.
param_names_id = H5PTcreate_fl(header_group, "param_names", s256, chunk_size, 1) ;
// Create a table for each requested parameter.
for (ii = 0; ii < rec_buffer.size(); ii++) {
hdf5_info = (HDF5_INFO *)malloc(sizeof(HDF5_INFO));
/* Case statements taken from "parameter_types.h."
* HDF5 Native types found in "H5Tpublic.h." */
switch (rec_buffer[ii]->ref->attr->type) {
case TRICK_CHARACTER:
datatype = H5T_NATIVE_CHAR;
break;
case TRICK_UNSIGNED_CHARACTER:
datatype = H5T_NATIVE_UCHAR;
break;
case TRICK_STRING:
datatype = s256;
break;
case TRICK_SHORT:
datatype = H5T_NATIVE_SHORT;
break;
case TRICK_UNSIGNED_SHORT:
datatype = H5T_NATIVE_USHORT;
break;
case TRICK_ENUMERATED:
case TRICK_INTEGER:
datatype = H5T_NATIVE_INT;
break;
case TRICK_UNSIGNED_INTEGER:
datatype = H5T_NATIVE_UINT;
break;
case TRICK_LONG:
datatype = H5T_NATIVE_LONG;
break;
case TRICK_UNSIGNED_LONG:
datatype = H5T_NATIVE_ULONG;
break;
case TRICK_FLOAT:
datatype = H5T_NATIVE_FLOAT;
break;
case TRICK_DOUBLE:
datatype = H5T_NATIVE_DOUBLE;
break;
case TRICK_BITFIELD:
if (rec_buffer[ii]->ref->attr->size == sizeof(int)) {
datatype = H5T_NATIVE_INT;
} else if (rec_buffer[ii]->ref->attr->size == sizeof(short)) {
datatype = H5T_NATIVE_SHORT;
} else {
datatype = H5T_NATIVE_CHAR;
}
break;
case TRICK_UNSIGNED_BITFIELD:
if (rec_buffer[ii]->ref->attr->size == sizeof(int)) {
datatype = H5T_NATIVE_UINT;
} else if (rec_buffer[ii]->ref->attr->size == sizeof(short)) {
datatype = H5T_NATIVE_USHORT;
} else {
datatype = H5T_NATIVE_UCHAR;
}
break;
case TRICK_LONG_LONG:
datatype = H5T_NATIVE_LLONG;
break;
case TRICK_UNSIGNED_LONG_LONG:
datatype = H5T_NATIVE_ULLONG;
break;
case TRICK_BOOLEAN:
#if ( __sun | __APPLE__ )
datatype = H5T_NATIVE_INT;
#else
datatype = H5T_NATIVE_UCHAR;
#endif
break;
default:
free(hdf5_info);
continue;
}
/* Create packet table(s) to store "fixed-length" packets.
* A separate packet table (PT) is created for each variable.
* PARAMETERS:
* IN: Identifier of the file or group to create the table within.
* IN: The name of the dataset (i.e. variable).
* IN: The datatype of a packet.
* IN: The packet table uses HDF5 chunked storage to allow it to
* grow. This value allows the user to set the size of a chunk.
* The chunk size affects performance.
* IN: Compression level, a value of 0 through 9. Level 0 is faster
* but offers the least compression; level 9 is slower but
* offers maximum compression. A setting of -1 indicates that
* no compression is desired.
* RETURN:
* Returns an identifier for the new packet table, or H5I_BADID on error.
*/
hdf5_info->dataset = H5PTcreate_fl(root_group, rec_buffer[ii]->ref->reference, datatype, chunk_size, 1) ;
hdf5_info->drb = rec_buffer[ii] ;
/* Add the new parameter element to the end of the vector.
* This effectively increases the vector size by one. */
parameters.push_back(hdf5_info);
// As a bonus, add a header entry for each parameter.
/* File Name */
buf = "log_" + group_name ;
H5PTappend( file_names_id, 1, buf.c_str() );
/* Param Type */
buf = type_string(rec_buffer[ii]->ref->attr->type, rec_buffer[ii]->ref->attr->size );
H5PTappend( param_types_id, 1, buf.c_str() );
/* Param Units */
H5PTappend( param_units_id, 1, rec_buffer[ii]->ref->attr->units );
/* Param Name */
H5PTappend( param_names_id, 1, rec_buffer[ii]->ref->reference );
}
ret_value = H5PTclose( byte_id );
ret_value = H5PTclose( file_names_id );
ret_value = H5PTclose( param_types_id );
ret_value = H5PTclose( param_units_id );
ret_value = H5PTclose( param_names_id );
ret_value = H5Gclose( header_group );
#endif
return(0);
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
/* Define a subset of Particle, with latitude and longitude fields */
typedef struct Position
{
int lati;
int longi;
} Position;
/* Calculate the type_size and the offsets of our struct members */
Particle dst_buf[NRECORDS];
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
size_t field_offset_pos[2] = { HOFFSET( Position, lati ),
HOFFSET( Position, longi )};
/* Initially no data */
Particle *p_data = NULL;
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} }; /* Fill value particle */
int compress = 0;
hsize_t nfields;
hsize_t start; /* Record to start reading/writing */
hsize_t nrecords; /* Number of records to read/write */
int i;
/* Define new values for the field "Pressure" */
float pressure_in [NRECORDS_ADD] =
{ 0.0f,1.0f,2.0f};
int field_index_pre[1] = { 3 };
int field_index_pos[2] = { 1,2 };
/* Define new values for the fields "Latitude,Longitude" */
Position position_in[NRECORDS_ADD] = { {0,0},
{10,10},
{20,20} };
size_t field_sizes_pos[2]=
{
sizeof(position_in[0].longi),
sizeof(position_in[0].lati)
};
size_t field_sizes_pre[1]=
{
sizeof(float)
};
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_05.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make the table */
H5TBmake_table( "Table Title", file_id, TABLE_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
/* Write the pressure field starting at record 2 */
nfields = 1;
start = 2;
nrecords = NRECORDS_ADD;
H5TBwrite_fields_index( file_id, TABLE_NAME, nfields, field_index_pre, start, nrecords,
sizeof( float ), 0, field_sizes_pre, pressure_in );
/* Write the new longitude and latitude information starting at record 2 */
nfields = 2;
start = 2;
nrecords = NRECORDS_ADD;
H5TBwrite_fields_index( file_id, TABLE_NAME, nfields, field_index_pos, start, nrecords,
sizeof( Position ), field_offset_pos, field_sizes_pos, position_in );
/* read the table */
H5TBread_table( file_id, TABLE_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* print it by rows */
for (i=0; i<NRECORDS; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
Particle dst_buf[NRECORDS];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
herr_t status;
int i;
/* Initialize field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "h5_table_01.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/*-------------------------------------------------------------------------
* H5TBmake_table
*-------------------------------------------------------------------------
*/
status=H5TBmake_table ("Table Title", /* Title of the table */
file_id, /* HDF5 object identifier to the file */
TABLE_NAME, /* Name of the table */
NFIELDS, /* Number of fields/columns */
NRECORDS, /* */
dst_size, /* Size of the struct/table row */
field_names, /* */
dst_offset, /* */
field_type, /* Type of the individual table fields */
chunk_size, /* Chunking size */
fill_data, /* */
compress, /* Enable/disable compression */
p_data /* Array with the table data */
);
/*-------------------------------------------------------------------------
* H5TBread_table
*-------------------------------------------------------------------------
*/
status = H5TBread_table (file_id, /* HDF5 object identifier */
TABLE_NAME, /* Name of the table */
dst_size, /* */
dst_offset, /* */
dst_sizes, /* */
dst_buf); /* Buffer to return the data */
/* print it by rows */
for (i=0; i<NRECORDS; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/*-------------------------------------------------------------------------
* end
*-------------------------------------------------------------------------
*/
/* Release object identifiers */
H5Tclose (string_type);
H5Fclose (file_id);
return 0;
}
/****************************************************************
**
** test_vlstring_type(): Test VL string type.
** Tests if VL string is treated as string.
**
****************************************************************/
static void test_vlstring_type(void)
{
hid_t fid; /* HDF5 File IDs */
hid_t tid_vlstr;
H5T_cset_t cset;
H5T_str_t pad;
htri_t vl_str; /* Whether string is VL */
herr_t ret;
/* Output message about test being performed */
MESSAGE(5, ("Testing VL String type\n"));
/* Open file */
fid = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
/* Create a datatype to refer to */
tid_vlstr = H5Tcopy(H5T_C_S1);
CHECK(tid_vlstr, FAIL, "H5Tcopy");
/* Change padding and verify it */
ret = H5Tset_strpad(tid_vlstr, H5T_STR_NULLPAD);
CHECK(ret, FAIL, "H5Tset_strpad");
pad = H5Tget_strpad(tid_vlstr);
VERIFY(pad, H5T_STR_NULLPAD, "H5Tget_strpad");
/* Convert to variable-length string */
ret = H5Tset_size(tid_vlstr, H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
/* Check if datatype is VL string */
ret = H5Tget_class(tid_vlstr);
VERIFY(ret, H5T_STRING, "H5Tget_class");
ret = H5Tis_variable_str(tid_vlstr);
VERIFY(ret, TRUE, "H5Tis_variable_str");
/* Verify that the class detects as a string */
vl_str = H5Tdetect_class(tid_vlstr, H5T_STRING);
CHECK(vl_str, FAIL, "H5Tdetect_class");
VERIFY(vl_str, TRUE, "H5Tdetect_class");
/* Check default character set and padding */
cset = H5Tget_cset(tid_vlstr);
VERIFY(cset, H5T_CSET_ASCII, "H5Tget_cset");
pad = H5Tget_strpad(tid_vlstr);
VERIFY(pad, H5T_STR_NULLPAD, "H5Tget_strpad");
/* Commit variable-length string datatype to storage */
ret = H5Tcommit2(fid, VLSTR_TYPE, tid_vlstr, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Tcommit2");
/* Close datatype */
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
tid_vlstr = H5Topen2(fid, VLSTR_TYPE, H5P_DEFAULT);
CHECK(tid_vlstr, FAIL, "H5Topen2");
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Fclose(fid);
CHECK(ret, FAIL, "H5Fclose");
fid = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
/* Open the variable-length string datatype just created */
tid_vlstr = H5Topen2(fid, VLSTR_TYPE, H5P_DEFAULT);
CHECK(tid_vlstr, FAIL, "H5Topen2");
/* Verify character set and padding */
cset = H5Tget_cset(tid_vlstr);
VERIFY(cset, H5T_CSET_ASCII, "H5Tget_cset");
pad = H5Tget_strpad(tid_vlstr);
VERIFY(pad, H5T_STR_NULLPAD, "H5Tget_strpad");
/* Close datatype and file */
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Fclose(fid);
CHECK(ret, FAIL, "H5Fclose");
} /* end test_vlstring_type() */
bool HDF5_IO::save_element_fits(std::string filename,
std::string path,
const data_struct::xrf::Fit_Count_Dict * const element_counts,
size_t row_idx_start,
int row_idx_end,
size_t col_idx_start,
int col_idx_end)
{
std::unique_lock<std::mutex> lock(_mutex);
//hid_t error_stack = H5Eget_current_stack();
//H5Eset_auto2(error_stack, NULL, NULL);
std::chrono::time_point<std::chrono::system_clock> start, end;
start = std::chrono::system_clock::now();
hid_t file_id, dset_id, memoryspace, filespace, dataspace_id, filetype, dataspace_ch_id, dataspace_ch_off_id, memtype, status, maps_grp_id, dset_ch_id, dcpl_id;
herr_t error;
dset_id = -1;
dset_ch_id = -1;
hsize_t dims_out[3];
hsize_t offset[3];
hsize_t count[3];
hsize_t chunk_dims[3];
file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
if (file_id < 1)
file_id = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if(file_id < 0)
{
std::cout<<"Error opening file "<<filename<<std::endl;
return false;
}
//get one element
data_struct::xrf::Fit_Counts_Array element;
//fix this
for(const auto& iter : *element_counts)
{
element = iter.second;
break;
}
//H5T_FLOAT
dims_out[0] = element_counts->size();
dims_out[1] = element.rows();
dims_out[2] = element.cols();
offset[0] = 0;
offset[1] = 0;
offset[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = dims_out[2];
chunk_dims[0] = 1;
chunk_dims[1] = 1;
chunk_dims[2] = dims_out[2];
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(dcpl_id, 3, chunk_dims);
H5Pset_deflate (dcpl_id, 7);
memoryspace = H5Screate_simple(3, count, NULL);
filespace = H5Screate_simple(3, dims_out, NULL);
dataspace_id = H5Screate_simple (3, dims_out, NULL);
dataspace_ch_id = H5Screate_simple (1, dims_out, NULL);
dataspace_ch_off_id = H5Screate_simple (1, dims_out, NULL);
H5Sselect_hyperslab (memoryspace, H5S_SELECT_SET, offset, NULL, count, NULL);
maps_grp_id = H5Gopen(file_id, "MAPS", H5P_DEFAULT);
if(maps_grp_id < 0)
maps_grp_id = H5Gcreate(file_id, "MAPS", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(maps_grp_id < 0)
{
std::cout<<"Error creating group 'MAPS'"<<std::endl;
return false;
}
//dset_id = H5Dopen (maps_grp_id, path.c_str(), H5P_DEFAULT);
if(dset_id < 0)
dset_id = H5Dcreate (maps_grp_id, path.c_str(), H5T_INTEL_F64, dataspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
if(dset_id < 0)
{
std::cout<<"Error creating dataset "<<path<<std::endl;
return false;
}
filetype = H5Tcopy (H5T_FORTRAN_S1);
H5Tset_size (filetype, 255);
memtype = H5Tcopy (H5T_C_S1);
status = H5Tset_size (memtype, 256);
dset_ch_id = H5Dopen (maps_grp_id, "channel_names", H5P_DEFAULT);
if(dset_ch_id < 0)
dset_ch_id = H5Dcreate (maps_grp_id, "channel_names", filetype, dataspace_ch_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dset_ch_id < 0)
{
std::cout<<"Error creating 'channel_names' dataset"<<std::endl;
return false;
}
/*
if (row_idx_end < row_idx_start || row_idx_end > spectra_volume->rows() -1)
{
row_idx_end = spectra_volume->rows();
}
if (col_idx_end < col_idx_start || col_idx_end > spectra_volume->cols() -1)
{
col_idx_end = spectra_volume->cols();
}
*/
//create save ordered vector by element Z number with K , L, M lines
std::vector<std::string> element_lines;
for (std::string el_name : data_struct::xrf::Element_Symbols)
{
element_lines.push_back(el_name);
}
for (std::string el_name : data_struct::xrf::Element_Symbols)
{
element_lines.push_back(el_name+"_L");
}
for (std::string el_name : data_struct::xrf::Element_Symbols)
{
element_lines.push_back(el_name+"_M");
}
int i=0;
//save by element Z order
//for(const auto& iter : *element_counts)
for (std::string el_name : element_lines)
{
if(element_counts->count(el_name) < 1 )
{
continue;
}
offset[0] = i;
element = element_counts->at(el_name);
H5Sselect_hyperslab (dataspace_ch_id, H5S_SELECT_SET, offset, NULL, count, NULL);
H5Sselect_hyperslab (dataspace_ch_off_id, H5S_SELECT_SET, &offset[2], NULL, count, NULL);
status = H5Dwrite (dset_ch_id, memtype, dataspace_ch_off_id, dataspace_ch_id, H5P_DEFAULT, (void*)(el_name.c_str()));
for(size_t row = 0; row < element.rows(); row++)
{
offset[1] = row;
H5Sselect_hyperslab (filespace, H5S_SELECT_SET, offset, NULL, count, NULL);
status = H5Dwrite (dset_id, H5T_NATIVE_DOUBLE, memoryspace, filespace, H5P_DEFAULT, (void*)&(element[row][0]));
}
i++;
}
H5Dclose(dset_id);
H5Dclose(dset_ch_id);
H5Sclose(memoryspace);
H5Sclose(filespace);
H5Sclose(dataspace_ch_off_id);
H5Sclose(dataspace_ch_id);
//h5Tclose(filetype);
//h5Tclose(memtype);
H5Pclose(dcpl_id);
H5Sclose(dataspace_id);
H5Gclose(maps_grp_id);
H5Fclose(file_id);
end = std::chrono::system_clock::now();
std::chrono::duration<double> elapsed_seconds = end-start;
std::cout << "\n\n save channels elapsed time: " << elapsed_seconds.count() << "s\n\n\n";
return true;
}
/****************************************************************
**
** test_compact_vlstring(): Test code for storing VL strings in
** compact datasets.
**
****************************************************************/
static void
test_compact_vlstring(void)
{
const char *wdata[SPACE1_DIM1] = {"one", "two", "three", "four"};
char *rdata[SPACE1_DIM1]; /* Information read in */
hid_t fid1; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hid_t plist; /* Dataset creation property list */
hsize_t dims1[] = {SPACE1_DIM1};
unsigned i; /* counting variable */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
MESSAGE(5, ("Testing VL Strings in compact dataset\n"));
/* Create file */
fid1 = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid1, FAIL, "H5Fcreate");
/* Create dataspace for datasets */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
CHECK(sid1, FAIL, "H5Screate_simple");
/* Create a datatype to refer to */
tid1 = H5Tcopy (H5T_C_S1);
CHECK(tid1, FAIL, "H5Tcopy");
ret = H5Tset_size (tid1,H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
plist = H5Pcreate(H5P_DATASET_CREATE);
CHECK(plist, FAIL, "H5Pcreate");
ret = H5Pset_layout(plist, H5D_COMPACT);
CHECK(ret, FAIL, "H5Pset_layout");
/* Create a dataset */
dataset = H5Dcreate2(fid1, "Dataset5", tid1, sid1, H5P_DEFAULT, plist, H5P_DEFAULT);
CHECK(dataset, FAIL, "H5Dcreate2");
/* Write dataset to disk */
ret = H5Dwrite(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
CHECK(ret, FAIL, "H5Dwrite");
/* Read dataset from disk */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Compare data read in */
for(i = 0; i < SPACE1_DIM1; i++) {
if(HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n",(int)i,(int)strlen(wdata[i]),(int)i,(int)strlen(rdata[i]));
continue;
} /* end if */
if(HDstrcmp(wdata[i], rdata[i]) != 0) {
TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n",(int)i,wdata[i],(int)i,rdata[i]);
continue;
} /* end if */
} /* end for */
/* Reclaim the read VL data */
ret = H5Dvlen_reclaim(tid1, sid1, H5P_DEFAULT, rdata);
CHECK(ret, FAIL, "H5Dvlen_reclaim");
/* Close Dataset */
ret = H5Dclose(dataset);
CHECK(ret, FAIL, "H5Dclose");
/* Close datatype */
ret = H5Tclose(tid1);
CHECK(ret, FAIL, "H5Tclose");
/* Close disk dataspace */
ret = H5Sclose(sid1);
CHECK(ret, FAIL, "H5Sclose");
/* Close dataset create property list */
ret = H5Pclose(plist);
CHECK(ret, FAIL, "H5Pclose");
/* Close file */
ret = H5Fclose(fid1);
CHECK(ret, FAIL, "H5Fclose");
} /*test_compact_vlstrings*/
op_map op_decl_map_hdf5(op_set from, op_set to, int dim, char const *file, char const *name)
{
//create new communicator
int my_rank, comm_size;
MPI_Comm_dup(MPI_COMM_WORLD, &OP_MPI_HDF5_WORLD);
MPI_Comm_rank(OP_MPI_HDF5_WORLD, &my_rank);
MPI_Comm_size(OP_MPI_HDF5_WORLD, &comm_size);
//MPI variables
MPI_Info info = MPI_INFO_NULL;
//HDF5 APIs definitions
hid_t file_id; //file identifier
hid_t plist_id; //property list identifier
hid_t dset_id; //dataset identifier
hid_t dataspace; //data space identifier
hid_t memspace; //memory space identifier
hsize_t count[2]; //hyperslab selection parameters
hsize_t offset[2];
//Set up file access property list with parallel I/O access
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, OP_MPI_HDF5_WORLD, info);
file_id = H5Fopen(file, H5F_ACC_RDONLY, plist_id );
H5Pclose(plist_id);
/*find total size of this map by reading attributes*/
int g_size;
//open existing data set
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//get OID of the attribute
hid_t attr = H5Aopen(dset_id, "size", H5P_DEFAULT);
//read attribute
H5Aread(attr,H5T_NATIVE_INT,&g_size);
H5Aclose(attr);
H5Dclose(dset_id);
//calculate local size of set for this mpi process
int l_size = compute_local_size (g_size, comm_size, my_rank);
//check if size is accurate
if(from->size != l_size)
{
printf("map from set size %d in file %s and size %d do not match on rank %d\n",
l_size,file,from->size, my_rank);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
/*find dim with available attributes*/
int map_dim = 0;
//open existing data set
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//get OID of the attribute
attr = H5Aopen(dset_id, "dim", H5P_DEFAULT);
//read attribute
H5Aread(attr,H5T_NATIVE_INT,&map_dim);
H5Aclose(attr);
H5Dclose(dset_id);
if(map_dim != dim)
{
printf("map.dim %d in file %s and dim %d do not match\n",map_dim,file,dim);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
/*find type with available attributes*/
dataspace= H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 10);
//open existing data set
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//get OID of the attribute
attr = H5Aopen(dset_id, "type", H5P_DEFAULT);
//read attribute
char typ[10];
H5Aread(attr,atype,typ);
H5Aclose(attr);
H5Sclose(dataspace);
H5Dclose(dset_id);
/*read in map in hyperslabs*/
//Create the dataset with default properties and close dataspace.
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//Each process defines dataset in memory and reads from a hyperslab in the file.
int disp = 0;
int* sizes = (int *)xmalloc(sizeof(int)*comm_size);
MPI_Allgather(&l_size, 1, MPI_INT, sizes, 1, MPI_INT, OP_MPI_HDF5_WORLD);
for(int i = 0; i<my_rank; i++)disp = disp + sizes[i];
free(sizes);
count[0] = l_size;
count[1] = dim;
offset[0] = disp;
offset[1] = 0;
memspace = H5Screate_simple(2, count, NULL);
//Select hyperslab in the file.
dataspace = H5Dget_space(dset_id);
H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
//Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
//initialize data buffer and read data
int* map = 0;
if(strcmp(typ,"int") == 0)
{
map = (int *)xmalloc(sizeof(int)*l_size*dim);
H5Dread(dset_id, H5T_NATIVE_INT, memspace, dataspace, plist_id, map);
}
else if (strcmp(typ,"long") == 0)
{
map = (int *)xmalloc(sizeof(long)*l_size*dim);
H5Dread(dset_id, H5T_NATIVE_LONG, memspace, dataspace, plist_id, map);
}
else if (strcmp(typ,"long long") == 0)
{
map = (int *)xmalloc(sizeof(long)*l_size*dim);
H5Dread(dset_id, H5T_NATIVE_LLONG, memspace, dataspace, plist_id, map);
}
else
{
printf("unknown type\n");
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
H5Pclose(plist_id);
H5Sclose(memspace);
H5Sclose(dataspace);
H5Dclose(dset_id);
H5Fclose(file_id);
MPI_Comm_free(&OP_MPI_HDF5_WORLD);
return op_decl_map(from, to, dim, map, name);
}
/****************************************************************
**
** test_read_vl_string_attribute(): Test basic VL string code.
** Tests reading VL strings from attributes
**
****************************************************************/
static void test_read_vl_string_attribute(void)
{
hid_t file, root, att;
hid_t type;
herr_t ret;
char *string_att_check = NULL;
/* Open file */
file = H5Fopen(DATAFILE, H5F_ACC_RDONLY, H5P_DEFAULT);
CHECK(file, FAIL, "H5Fopen");
/* Create a datatype to refer to. */
type = H5Tcopy (H5T_C_S1);
CHECK(type, FAIL, "H5Tcopy");
ret = H5Tset_size (type, H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
root = H5Gopen2(file, "/", H5P_DEFAULT);
CHECK(root, FAIL, "H5Gopen2");
/* Test reading "normal" sized string attribute */
att = H5Aopen(root, "test_scalar", H5P_DEFAULT);
CHECK(att, FAIL, "H5Aopen");
ret = H5Aread(att, type, &string_att_check);
CHECK(ret, FAIL, "H5Aread");
if(HDstrcmp(string_att_check,string_att) != 0)
TestErrPrintf("VL string attributes don't match!, string_att=%s, string_att_check=%s\n",string_att,string_att_check);
H5free_memory(string_att_check);
string_att_check = NULL;
ret = H5Aclose(att);
CHECK(ret, FAIL, "HAclose");
/* Test reading "large" sized string attribute */
att = H5Aopen(root, "test_scalar_large", H5P_DEFAULT);
CHECK(att, FAIL, "H5Aopen");
if(string_att_write) {
ret = H5Aread(att, type, &string_att_check);
CHECK(ret, FAIL, "H5Aread");
if(HDstrcmp(string_att_check,string_att_write) != 0)
TestErrPrintf("VL string attributes don't match!, string_att_write=%s, string_att_check=%s\n",string_att_write,string_att_check);
H5free_memory(string_att_check);
string_att_check = NULL;
}
/* Free string allocated in test_write_vl_string_attribute */
if(string_att_write)
HDfree(string_att_write);
ret = H5Aclose(att);
CHECK(ret, FAIL, "HAclose");
ret = H5Tclose(type);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Gclose(root);
CHECK(ret, FAIL, "H5Gclose");
ret = H5Fclose(file);
CHECK(ret, FAIL, "H5Fclose");
return;
}
op_dat op_decl_dat_hdf5(op_set set, int dim, char const *type, char const *file, char const *name)
{
//create new communicator
int my_rank, comm_size;
MPI_Comm_dup(MPI_COMM_WORLD, &OP_MPI_HDF5_WORLD);
MPI_Comm_rank(OP_MPI_HDF5_WORLD, &my_rank);
MPI_Comm_size(OP_MPI_HDF5_WORLD, &comm_size);
//MPI variables
MPI_Info info = MPI_INFO_NULL;
//HDF5 APIs definitions
hid_t file_id; //file identifier
hid_t plist_id; //property list identifier
hid_t dset_id; //dataset identifier
hid_t dataspace; //data space identifier
hid_t memspace; //memory space identifier
hsize_t count[2]; //hyperslab selection parameters
hsize_t offset[2];
hid_t attr; //attribute identifier
//Set up file access property list with parallel I/O access
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, OP_MPI_HDF5_WORLD, info);
file_id = H5Fopen(file, H5F_ACC_RDONLY, plist_id );
H5Pclose(plist_id);
/*find element size of this dat with available attributes*/
size_t dat_size = 0;
//open existing data set
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//get OID of the attribute
attr = H5Aopen(dset_id, "size", H5P_DEFAULT);
//read attribute
H5Aread(attr,H5T_NATIVE_INT,&dat_size);
H5Aclose(attr);
H5Dclose(dset_id);
/*find dim with available attributes*/
int dat_dim = 0;
//open existing data set
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//get OID of the attribute
attr = H5Aopen(dset_id, "dim", H5P_DEFAULT);
//read attribute
H5Aread(attr,H5T_NATIVE_INT,&dat_dim);
H5Aclose(attr);
H5Dclose(dset_id);
if(dat_dim != dim)
{
printf("dat.dim %d in file %s and dim %d do not match\n",dat_dim,file,dim);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
/*find type with available attributes*/
dataspace= H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 10);
//open existing data set
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//get OID of the attribute
attr = H5Aopen(dset_id, "type", H5P_DEFAULT);
//read attribute
char typ[10];
H5Aread(attr,atype,typ);
H5Aclose(attr);
H5Sclose(dataspace);
H5Dclose(dset_id);
if(strcmp(typ,type) != 0)
{
printf("dat.type %s in file %s and type %s do not match\n",typ,file,type);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
/*read in dat in hyperslabs*/
//Create the dataset with default properties and close dataspace.
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
//Each process defines dataset in memory and reads from a hyperslab in the file.
int disp = 0;
int* sizes = (int *)xmalloc(sizeof(int)*comm_size);
MPI_Allgather(&(set->size), 1, MPI_INT, sizes, 1, MPI_INT, OP_MPI_HDF5_WORLD);
for(int i = 0; i<my_rank; i++)disp = disp + sizes[i];
free(sizes);
count[0] = set->size;
count[1] = dim;
offset[0] = disp;
offset[1] = 0;
memspace = H5Screate_simple(2, count, NULL);
//Select hyperslab in the file.
dataspace = H5Dget_space(dset_id);
H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
//Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
//initialize data buffer and read in data
char* data = 0;
if(strcmp(type,"double") == 0)
{
data = (char *)xmalloc(set->size*dim*sizeof(double));
H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, dataspace, plist_id, data);
if(dat_size != dim*sizeof(double))
{
printf("dat.size %lu in file %s and %d*sizeof(double) do not match\n",dat_size,file,dim);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
else
dat_size = sizeof(double);
}else if(strcmp(type,"float") == 0)
{
data = (char *)xmalloc(set->size*dim*sizeof(float));
H5Dread(dset_id, H5T_NATIVE_FLOAT, memspace, dataspace, plist_id, data);
if(dat_size != dim*sizeof(float))
{
printf("dat.size %lu in file %s and %d*sizeof(float) do not match\n",dat_size,file,dim);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
else
dat_size = sizeof(float);
}else if(strcmp(type,"int") == 0)
{
data = (char *)xmalloc(set->size*dim*sizeof(int));
H5Dread(dset_id, H5T_NATIVE_INT, memspace, dataspace, plist_id, data);
if(dat_size != dim*sizeof(int))
{
printf("dat.size %lu in file %s and %d*sizeof(int) do not match\n",dat_size,file,dim);
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
else
dat_size = sizeof(int);
}else
{
printf("unknown type\n");
MPI_Abort(OP_MPI_HDF5_WORLD, 2);
}
H5Pclose(plist_id);
H5Sclose(memspace);
H5Sclose(dataspace);
H5Dclose(dset_id);
H5Fclose(file_id);
MPI_Comm_free(&OP_MPI_HDF5_WORLD);
return op_decl_dat(set, dim, type, dat_size, data, name );
}
int
main (void)
{
hid_t file, dataset; /* File and dataset identifiers */
hid_t fid; /* Dataspace identifier */
hid_t attr1, attr2, attr3; /* Attribute identifiers */
hid_t attr;
hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */
hid_t atype, atype_mem; /* Attribute type */
H5T_class_t type_class;
hsize_t fdim[] = {SIZE};
hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */
float matrix[ADIM1][ADIM2]; /* Attribute data */
herr_t ret; /* Return value */
H5O_info_t oinfo; /* Object info */
unsigned i, j; /* Counters */
char string_out[80]; /* Buffer to read string attribute back */
int point_out; /* Buffer to read scalar attribute back */
/*
* Data initialization.
*/
int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */
int point = 1; /* Value of the scalar attribute */
char string[] = "ABCD"; /* Value of the string attribute */
for (i=0; i < ADIM1; i++) { /* Values of the array attribute */
for (j=0; j < ADIM2; j++)
matrix[i][j] = -1.;
}
/*
* Create a file.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the dataspace for the dataset in the file.
*/
fid = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(fid, RANK, fdim, NULL);
/*
* Create the dataset in the file.
*/
dataset = H5Dcreate2(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector);
/*
* Create dataspace for the first attribute.
*/
aid1 = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL);
/*
* Create array attribute.
*/
attr1 = H5Acreate2(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write array attribute.
*/
ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix);
/*
* Create scalar attribute.
*/
aid2 = H5Screate(H5S_SCALAR);
attr2 = H5Acreate2(dataset, "Integer attribute", H5T_NATIVE_INT, aid2,
H5P_DEFAULT, H5P_DEFAULT);
/*
* Write scalar attribute.
*/
ret = H5Awrite(attr2, H5T_NATIVE_INT, &point);
/*
* Create string attribute.
*/
aid3 = H5Screate(H5S_SCALAR);
atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 5);
H5Tset_strpad(atype,H5T_STR_NULLTERM);
attr3 = H5Acreate2(dataset, ANAMES, atype, aid3, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write string attribute.
*/
ret = H5Awrite(attr3, atype, string);
/*
* Close attribute and file dataspaces, and datatype.
*/
ret = H5Sclose(aid1);
ret = H5Sclose(aid2);
ret = H5Sclose(aid3);
ret = H5Sclose(fid);
ret = H5Tclose(atype);
/*
* Close the attributes.
*/
ret = H5Aclose(attr1);
ret = H5Aclose(attr2);
ret = H5Aclose(attr3);
/*
* Close the dataset.
*/
ret = H5Dclose(dataset);
/*
* Close the file.
*/
ret = H5Fclose(file);
/*
* Reopen the file.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
/*
* Open the dataset.
*/
dataset = H5Dopen2(file, "Dataset", H5P_DEFAULT);
/*
* Attach to the scalar attribute using attribute name, then read and
* display its value.
*/
attr = H5Aopen(dataset, "Integer attribute", H5P_DEFAULT);
ret = H5Aread(attr, H5T_NATIVE_INT, &point_out);
printf("The value of the attribute \"Integer attribute\" is %d \n", point_out);
ret = H5Aclose(attr);
/*
* Find string attribute by iterating through all attributes
*/
ret = H5Oget_info(dataset, &oinfo);
for(i = 0; i < (unsigned)oinfo.num_attrs; i++) {
attr = H5Aopen_by_idx(dataset, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)i, H5P_DEFAULT, H5P_DEFAULT);
atype = H5Aget_type(attr);
type_class = H5Tget_class(atype);
if (type_class == H5T_STRING) {
atype_mem = H5Tget_native_type(atype, H5T_DIR_ASCEND);
ret = H5Aread(attr, atype_mem, string_out);
printf("Found string attribute; its index is %d , value = %s \n", i, string_out);
ret = H5Tclose(atype_mem);
}
ret = H5Aclose(attr);
ret = H5Tclose(atype);
}
/*
* Get attribute info using iteration function.
*/
ret = H5Aiterate2(dataset, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_info, NULL);
/*
* Close the dataset and the file.
*/
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
void op_write_hdf5(char const * file_name)
{
printf("Writing to %s\n",file_name);
//declare timers
double cpu_t1, cpu_t2, wall_t1, wall_t2;
double time;
double max_time;
op_timers(&cpu_t1, &wall_t1); //timer start for hdf5 file write
//create new communicator
int my_rank, comm_size;
MPI_Comm_dup(MPI_COMM_WORLD, &OP_MPI_HDF5_WORLD);
MPI_Comm_rank(OP_MPI_HDF5_WORLD, &my_rank);
MPI_Comm_size(OP_MPI_HDF5_WORLD, &comm_size);
//MPI variables
MPI_Info info = MPI_INFO_NULL;
//HDF5 APIs definitions
hid_t file_id; //file identifier
hid_t plist_id; //property list identifier
hid_t dset_id = 0; //dataset identifier
hid_t dataspace; //data space identifier
hid_t memspace; //memory space identifier
hsize_t dimsf[2]; // dataset dimensions
hsize_t count[2]; //hyperslab selection parameters
hsize_t offset[2];
//Set up file access property list with parallel I/O access
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, OP_MPI_HDF5_WORLD, info);
//Create a new file collectively and release property list identifier.
file_id = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
H5Pclose(plist_id);
/*loop over all the op_sets and write them to file*/
for(int s=0; s<OP_set_index; s++) {
op_set set=OP_set_list[s];
//Create the dataspace for the dataset.
hsize_t dimsf_set[] = {1};
dataspace = H5Screate_simple(1, dimsf_set, NULL);
//Create the dataset with default properties and close dataspace.
dset_id = H5Dcreate(file_id, set->name, H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
int size = 0;
int* sizes = (int *)xmalloc(sizeof(int)*comm_size);
MPI_Allgather(&set->size, 1, MPI_INT, sizes, 1, MPI_INT, OP_MPI_HDF5_WORLD);
for(int i = 0; i<comm_size; i++)size = size + sizes[i];
//write data
H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, plist_id, &size);
H5Sclose(dataspace);
H5Pclose(plist_id);
H5Dclose(dset_id);
}
/*loop over all the op_maps and write them to file*/
for(int m=0; m<OP_map_index; m++) {
op_map map=OP_map_list[m];
//find total size of map
int* sizes = (int *)xmalloc(sizeof(int)*comm_size);
int g_size = 0;
MPI_Allgather(&map->from->size, 1, MPI_INT, sizes, 1, MPI_INT, OP_MPI_HDF5_WORLD);
for(int i = 0; i<comm_size; i++)g_size = g_size + sizes[i];
//Create the dataspace for the dataset.
dimsf[0] = g_size;
dimsf[1] = map->dim;
dataspace = H5Screate_simple(2, dimsf, NULL);
//Create the dataset with default properties and close dataspace.
if(sizeof(map->map[0]) == sizeof(int))
dset_id = H5Dcreate(file_id, map->name, H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
else if(sizeof(map->map[0]) == sizeof(long))
dset_id = H5Dcreate(file_id, map->name, H5T_NATIVE_LONG, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
else if(sizeof(map->map[0]) == sizeof(long long))
dset_id = H5Dcreate(file_id, map->name, H5T_NATIVE_LLONG, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(dataspace);
//Each process defines dataset in memory and writes it to a hyperslab
//in the file.
int disp = 0;
for(int i = 0; i<my_rank; i++)disp = disp + sizes[i];
count[0] = map->from->size;
count[1] = dimsf[1];
offset[0] = disp;
offset[1] = 0;
memspace = H5Screate_simple(2, count, NULL);
//Select hyperslab in the file.
dataspace = H5Dget_space(dset_id);
H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
//Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
//write data
if(sizeof(map->map[0]) == sizeof(int))
H5Dwrite(dset_id, H5T_NATIVE_INT, memspace, dataspace, plist_id, map->map);
else if(sizeof(map->map[0]) == sizeof(long))
H5Dwrite(dset_id, H5T_NATIVE_LONG, memspace, dataspace, plist_id, map->map);
else if(sizeof(map->map[0]) == sizeof(long long))
H5Dwrite(dset_id, H5T_NATIVE_LLONG, memspace, dataspace, plist_id, map->map);
H5Pclose(plist_id);
H5Sclose(memspace);
H5Sclose(dataspace);
H5Dclose(dset_id);
free(sizes);
/*attach attributes to map*/
//open existing data set
dset_id = H5Dopen(file_id, map->name, H5P_DEFAULT);
//create the data space for the attribute
hsize_t dims = 1;
dataspace = H5Screate_simple(1, &dims, NULL);
//Create an int attribute - size
hid_t attribute = H5Acreate(dset_id, "size", H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT);
//Write the attribute data.
H5Awrite(attribute, H5T_NATIVE_INT, &g_size);
//Close the attribute.
H5Aclose(attribute);
//Create an int attribute - dimension
attribute = H5Acreate(dset_id, "dim", H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT);
//Write the attribute data.
H5Awrite(attribute, H5T_NATIVE_INT, &map->dim);
//Close the attribute.
H5Aclose(attribute);
H5Sclose(dataspace);
//Create an string attribute - type
dataspace= H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 10);
attribute = H5Acreate(dset_id, "type", atype, dataspace,
H5P_DEFAULT, H5P_DEFAULT);
if(sizeof(map->map[0]) == sizeof(int))
H5Awrite(attribute, atype, "int");
if(sizeof(map->map[0]) == sizeof(long))
H5Awrite(attribute, atype, "long");
if(sizeof(map->map[0]) == sizeof(long long))
H5Awrite(attribute, atype, "long long");
H5Aclose(attribute);
//Close the dataspace
H5Sclose(dataspace);
//Close to the dataset.
H5Dclose(dset_id);
}
/*loop over all the op_dats and write them to file*/
for(int d=0; d<OP_dat_index; d++) {
op_dat dat=OP_dat_list[d];
//find total size of map
int* sizes = (int *)xmalloc(sizeof(int)*comm_size);
int g_size = 0;
MPI_Allgather(&dat->set->size, 1, MPI_INT, sizes, 1, MPI_INT, OP_MPI_HDF5_WORLD);
for(int i = 0; i<comm_size; i++)g_size = g_size + sizes[i];
//Create the dataspace for the dataset.
dimsf[0] = g_size;
dimsf[1] = dat->dim;
dataspace = H5Screate_simple(2, dimsf, NULL);
//Create the dataset with default properties and close dataspace.
if(strcmp(dat->type,"double")==0)
dset_id = H5Dcreate(file_id, dat->name, H5T_NATIVE_DOUBLE, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
else if(strcmp(dat->type,"float")==0)
dset_id = H5Dcreate(file_id, dat->name, H5T_NATIVE_FLOAT, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
else if(strcmp(dat->type,"int")==0)
dset_id = H5Dcreate(file_id, dat->name, H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
else printf("Unknown type\n");
H5Sclose(dataspace);
//Each process defines dataset in memory and writes it to a hyperslab
//in the file.
int disp = 0;
for(int i = 0; i<my_rank; i++)disp = disp + sizes[i];
count[0] = dat->set->size;
count[1] = dimsf[1];
offset[0] = disp;
offset[1] = 0;
memspace = H5Screate_simple(2, count, NULL);
//Select hyperslab in the file.
dataspace = H5Dget_space(dset_id);
H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
//Create property list for collective dataset write.
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
//write data
if(strcmp(dat->type,"double") == 0)
H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, memspace, dataspace, plist_id, dat->data);
else if(strcmp(dat->type,"float") == 0)
H5Dwrite(dset_id, H5T_NATIVE_FLOAT, memspace, dataspace, plist_id, dat->data);
else if(strcmp(dat->type,"int") == 0)
H5Dwrite(dset_id, H5T_NATIVE_INT, memspace, dataspace, plist_id, dat->data);
else printf("Unknown type\n");
H5Pclose(plist_id);
H5Sclose(memspace);
H5Sclose(dataspace);
H5Dclose(dset_id);
free(sizes);
/*attach attributes to dat*/
//open existing data set
dset_id = H5Dopen(file_id, dat->name, H5P_DEFAULT);
//create the data space for the attribute
hsize_t dims = 1;
dataspace = H5Screate_simple(1, &dims, NULL);
//Create an int attribute - size
hid_t attribute = H5Acreate(dset_id, "size", H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT);
//Write the attribute data.
H5Awrite(attribute, H5T_NATIVE_INT, &dat->size);
//Close the attribute.
H5Aclose(attribute);
//Create an int attribute - dimension
attribute = H5Acreate(dset_id, "dim", H5T_NATIVE_INT, dataspace,
H5P_DEFAULT, H5P_DEFAULT);
//Write the attribute data.
H5Awrite(attribute, H5T_NATIVE_INT, &dat->dim);
H5Aclose(attribute);
H5Sclose(dataspace);
//Create an string attribute - type
dataspace= H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 10);
attribute = H5Acreate(dset_id, "type", atype, dataspace,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(attribute, atype, dat->type);
H5Aclose(attribute);
//Close the dataspace.
H5Sclose(dataspace);
H5Dclose(dset_id);
}
H5Fclose(file_id);
op_timers(&cpu_t2, &wall_t2); //timer stop for hdf5 file write
//compute import/export lists creation time
time = wall_t2-wall_t1;
MPI_Reduce(&time, &max_time, 1, MPI_DOUBLE, MPI_MAX, MPI_ROOT, OP_MPI_HDF5_WORLD);
//print performance results
if(my_rank == MPI_ROOT)
{
printf("Max hdf5 file write time = %lf\n\n",max_time);
}
MPI_Comm_free(&OP_MPI_HDF5_WORLD);
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
Particle dst_buf[ NRECORDS + NRECORDS_INS ];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int compress = 0;
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} }; /* Fill value particle */
hsize_t start1; /* Record to start reading from 1st table */
hsize_t nrecords; /* Number of records to insert */
hsize_t start2; /* Record to start writing in 2nd table */
herr_t status;
int i;
hsize_t nfields_out;
hsize_t nrecords_out;
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_09.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make 2 tables: TABLE2_NAME is empty */
status=H5TBmake_table( "Table Title",file_id,TABLE1_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
status=H5TBmake_table( "Table Title",file_id,TABLE2_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, NULL );
/* Add 2 records from TABLE1_NAME to TABLE2_NAME */
start1 = 3;
nrecords = NRECORDS_INS;
start2 = 6;
status=H5TBadd_records_from( file_id, TABLE1_NAME, start1, nrecords, TABLE2_NAME, start2 );
/* read TABLE2_NAME: it should have 2 more records now */
status=H5TBread_table( file_id, TABLE2_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* Get table info */
status=H5TBget_table_info (file_id,TABLE2_NAME, &nfields_out, &nrecords_out );
/* print */
printf ("Table has %d fields and %d records\n",(int)nfields_out,(int)nrecords_out);
/* print it by rows */
for (i=0; i<nrecords_out; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
med_err _MEDattributeStringWrByName(med_idt pid,
const char * const path,
const char * const attname,
const med_size attsize,
const char * const val)
{
med_access_mode MED_ACCESS_MODE;
med_idt _attid=0,aid=0;
med_err _ret=-1;
int type_hdf=0;
med_bool _attmustbecreated= MED_FALSE;
hsize_t _attsize=0;
med_size _valsize=0;
if ( (MED_ACCESS_MODE = _MEDmodeAcces(pid) ) == MED_ACC_UNDEF ) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ACCESSMODE, "MED_ACC_UNDEF" );
SSCRUTE(attname); SSCRUTE(path);goto ERROR;
}
_valsize=strlen(val);
if (_valsize > attsize) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ATTRIBUTE, attname );
ISCRUTE_size(_valsize);ISCRUTE_size(attsize);goto ERROR;
}
if ((aid = H5Screate(H5S_SCALAR)) < 0){
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_DATASPACE, attname );
ISCRUTE_id(aid);
}
if ( (type_hdf = H5Tcopy(H5T_C_S1)) < 0) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
SSCRUTE("H5T_C_S1"); goto ERROR;
}
if ( H5Tset_size(type_hdf,_valsize+1) < 0) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
SSCRUTE("H5T_C_S1"); goto ERROR;
}
if ( (_attid=H5Aopen_by_name( pid, path, attname, H5P_DEFAULT, H5P_DEFAULT )) >= 0 )
if ( MED_ACCESS_MODE == MED_ACC_RDEXT ) {
MED_ERR_(_ret,MED_ERR_INVALID,MED_ERR_ACCESSMODE, "MED_ACC_RDEXT" );
SSCRUTE(attname); SSCRUTE(path);goto ERROR;
}
if ( _attid > 0 ) {
if ( (_attsize=H5Aget_storage_size(_attid) ) < 0 ) goto ERROR;
if ( (_valsize+1) > _attsize ) {
if (H5Aclose(_attid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_ATTRIBUTE,"");
ISCRUTE_id(_attid);
goto ERROR;
}
if ( H5Adelete_by_name(pid,path,attname,H5P_DEFAULT) < 0 ) goto ERROR;
_attmustbecreated=MED_TRUE;
}
}
if ( (_attid < 0) || _attmustbecreated )
if ( (_attid=H5Acreate_by_name( pid, path, attname, type_hdf, aid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT )) < 0 ) {
MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_ATTRIBUTE, attname );
SSCRUTE(path);goto ERROR;
}
if ( H5Awrite(_attid,type_hdf,val) < 0) {
MED_ERR_(_ret,MED_ERR_WRITE,MED_ERR_ATTRIBUTE, attname );
SSCRUTE(path);goto ERROR;
}
_ret=0;
ERROR:
if (type_hdf > 0 ) if ( H5Tclose(type_hdf) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_HDFTYPE, MED_ERR_ID_MSG );
ISCRUTE_int(type_hdf);
}
if (aid > 0 ) if ( H5Sclose(aid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_DATASPACE, MED_ERR_ID_MSG );
ISCRUTE_id(aid);
}
if (_attid >0) if ( H5Aclose(_attid) < 0) {
MED_ERR_(_ret,MED_ERR_CLOSE,MED_ERR_ATTRIBUTE, MED_ERR_ID_MSG );
ISCRUTE_id(_attid);
}
return _ret;
}
int
main (void)
{
hid_t file, filetype, memtype, space, dset;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0};
char *wdata[DIM0] = {"Parting", "is such", "sweet", "sorrow."},
/* Write buffer */
**rdata; /* Read buffer */
int ndims,
i;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create file and memory datatypes. For this example we will save
* the strings as FORTRAN strings.
*/
filetype = H5Tcopy (H5T_FORTRAN_S1);
status = H5Tset_size (filetype, H5T_VARIABLE);
memtype = H5Tcopy (H5T_C_S1);
status = H5Tset_size (memtype, H5T_VARIABLE);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the dataset and write the variable-length string data to
* it.
*/
dset = H5Dcreate (file, DATASET, filetype, space, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Dwrite (dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
/*
* Close and release resources.
*/
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (filetype);
status = H5Tclose (memtype);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the dataset has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file and dataset.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET, H5P_DEFAULT);
/*
* Get the datatype.
*/
filetype = H5Dget_type (dset);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Dget_space (dset);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (char **) malloc (dims[0] * sizeof (char *));
/*
* Create the memory datatype.
*/
memtype = H5Tcopy (H5T_C_S1);
status = H5Tset_size (memtype, H5T_VARIABLE);
/*
* Read the data.
*/
status = H5Dread (dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++)
printf ("%s[%d]: %s\n", DATASET, i, rdata[i]);
/*
* Close and release resources. Note that H5Dvlen_reclaim works
* for variable-length strings as well as variable-length arrays.
* Also note that we must still free the array of pointers stored
* in rdata, as H5Tvlen_reclaim only frees the data these point to.
*/
status = H5Dvlen_reclaim (memtype, space, H5P_DEFAULT, rdata);
free (rdata);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (filetype);
status = H5Tclose (memtype);
status = H5Fclose (file);
return 0;
}
/****************************************************************
**
** test_vlstrings_basic(): Test basic VL string code.
** Tests simple VL string I/O
**
****************************************************************/
static void
test_vlstrings_basic(void)
{
const char *wdata[SPACE1_DIM1]= {
"Four score and seven years ago our forefathers brought forth on this continent a new nation,",
"conceived in liberty and dedicated to the proposition that all men are created equal.",
"Now we are engaged in a great civil war,",
"testing whether that nation or any nation so conceived and so dedicated can long endure."
}; /* Information to write */
char *rdata[SPACE1_DIM1]; /* Information read in */
char *wdata2;
hid_t dataspace, dataset2;
hid_t fid1; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hid_t xfer_pid; /* Dataset transfer property list ID */
hsize_t dims1[] = {SPACE1_DIM1};
hsize_t size; /* Number of bytes which will be used */
unsigned i; /* counting variable */
size_t str_used; /* String data in memory */
size_t mem_used=0; /* Memory used during allocation */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
MESSAGE(5, ("Testing Basic VL String Functionality\n"));
/* Create file */
fid1 = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid1, FAIL, "H5Fcreate");
/* Create dataspace for datasets */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
CHECK(sid1, FAIL, "H5Screate_simple");
/* Create a datatype to refer to */
tid1 = H5Tcopy(H5T_C_S1);
CHECK(tid1, FAIL, "H5Tcopy");
ret = H5Tset_size(tid1,H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
/* Create a dataset */
dataset = H5Dcreate2(fid1, "Dataset1", tid1, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(dataset, FAIL, "H5Dcreate2");
/* Write dataset to disk */
ret = H5Dwrite(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
CHECK(ret, FAIL, "H5Dwrite");
dataspace = H5Screate(H5S_SCALAR);
dataset2 = H5Dcreate2(fid1, "Dataset2", tid1, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(dataset, FAIL, "H5Dcreate2");
wdata2 = (char*)HDcalloc((size_t)65534, sizeof(char));
HDmemset(wdata2, 'A', (size_t)65533);
ret = H5Dwrite(dataset2, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, &wdata2);
CHECK(ret, FAIL, "H5Dwrite");
H5Sclose(dataspace);
H5Dclose(dataset2);
HDfree(wdata2);
/* Change to the custom memory allocation routines for reading VL string */
xfer_pid = H5Pcreate(H5P_DATASET_XFER);
CHECK(xfer_pid, FAIL, "H5Pcreate");
ret=H5Pset_vlen_mem_manager(xfer_pid,test_vlstr_alloc_custom,&mem_used,test_vlstr_free_custom,&mem_used);
CHECK(ret, FAIL, "H5Pset_vlen_mem_manager");
/* Make certain the correct amount of memory will be used */
ret=H5Dvlen_get_buf_size(dataset,tid1,sid1,&size);
CHECK(ret, FAIL, "H5Dvlen_get_buf_size");
/* Count the actual number of bytes used by the strings */
for(i=0,str_used=0; i<SPACE1_DIM1; i++)
str_used+=HDstrlen(wdata[i])+1;
/* Compare against the strings actually written */
VERIFY(size,(hsize_t)str_used,"H5Dvlen_get_buf_size");
/* Read dataset from disk */
ret = H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, xfer_pid, rdata);
CHECK(ret, FAIL, "H5Dread");
/* Make certain the correct amount of memory has been used */
VERIFY(mem_used,str_used,"H5Dread");
/* Compare data read in */
for(i = 0; i < SPACE1_DIM1; i++) {
if(HDstrlen(wdata[i]) != HDstrlen(rdata[i])) {
TestErrPrintf("VL data length don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n",(int)i,(int)strlen(wdata[i]),(int)i,(int)strlen(rdata[i]));
continue;
} /* end if */
if(HDstrcmp(wdata[i], rdata[i]) != 0 ) {
TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n",(int)i,wdata[i],(int)i,rdata[i]);
continue;
} /* end if */
} /* end for */
/* Reclaim the read VL data */
ret = H5Dvlen_reclaim(tid1,sid1,xfer_pid,rdata);
CHECK(ret, FAIL, "H5Dvlen_reclaim");
/* Make certain the VL memory has been freed */
VERIFY(mem_used,0,"H5Dvlen_reclaim");
/* Close Dataset */
ret = H5Dclose(dataset);
CHECK(ret, FAIL, "H5Dclose");
/* Close datatype */
ret = H5Tclose(tid1);
CHECK(ret, FAIL, "H5Tclose");
/* Close disk dataspace */
ret = H5Sclose(sid1);
CHECK(ret, FAIL, "H5Sclose");
/* Close dataset transfer property list */
ret = H5Pclose(xfer_pid);
CHECK(ret, FAIL, "H5Pclose");
/* Close file */
ret = H5Fclose(fid1);
CHECK(ret, FAIL, "H5Fclose");
} /* end test_vlstrings_basic() */
int
main (void)
{
hid_t sourcetype, desttype, strtype, space;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0};
reading_t *reading; /* Conversion buffer */
sensor_t *sensor, /* Conversion buffer */
bkgrd[DIM0]; /* Background buffer */
int i;
/*
* Allocate memory for conversion buffer. We will allocate space
* for it to hold DIM0 elements of the destination type, as the
* type conversion is performed in place. Of course, if the
* destination type were smaller than the source type, we would
* allocate space to hold DIM0 elements of the source type.
*/
reading = (reading_t *) malloc (DIM0 * sizeof (sensor_t));
/*
* Assign the allocated space to a pointer of the destination type,
* to allow the buffer to be accessed correctly after the
* conversion has taken place.
*/
sensor = (sensor_t *) reading;
/*
* Initialize data.
*/
bkgrd[0].serial_no = 1153;
bkgrd[0].location = "Exterior (static)";
bkgrd[0].temperature = 53.23;
bkgrd[0].pressure = 24.57;
bkgrd[1].serial_no = 1184;
bkgrd[1].location = "Intake";
bkgrd[1].temperature = 55.12;
bkgrd[1].pressure = 22.95;
bkgrd[2].serial_no = 1027;
bkgrd[2].location = "Intake manifold";
bkgrd[2].temperature = 103.55;
bkgrd[2].pressure = 31.23;
bkgrd[3].serial_no = 1313;
bkgrd[3].location = "Exhaust manifold";
bkgrd[3].temperature = 1252.89;
bkgrd[3].pressure = 84.11;
reading[0].temperature = 54.84;
reading[0].pressure = 24.76;
reading[1].temperature = 56.63;
reading[1].pressure = 23.10;
reading[2].temperature = 102.69;
reading[2].pressure = 30.97;
reading[3].temperature = 1238.27;
reading[3].pressure = 82.15;
/*
* Create variable-length string datatype.
*/
strtype = H5Tcopy (H5T_C_S1);
status = H5Tset_size (strtype, H5T_VARIABLE);
/*
* Create the compound datatype for memory.
*/
sourcetype = H5Tcreate (H5T_COMPOUND, sizeof (reading_t));
status = H5Tinsert (sourcetype, "Temperature (F)",
HOFFSET (reading_t, temperature), H5T_NATIVE_DOUBLE);
status = H5Tinsert (sourcetype, "Pressure (inHg)",
HOFFSET (reading_t, pressure), H5T_NATIVE_DOUBLE);
desttype = H5Tcreate (H5T_COMPOUND, sizeof (sensor_t));
status = H5Tinsert (desttype, "Serial number",
HOFFSET (sensor_t, serial_no), H5T_NATIVE_INT);
status = H5Tinsert (desttype, "Location", HOFFSET (sensor_t, location),
strtype);
status = H5Tinsert (desttype, "Temperature (F)",
HOFFSET (sensor_t, temperature), H5T_NATIVE_DOUBLE);
status = H5Tinsert (desttype, "Pressure (inHg)",
HOFFSET (sensor_t, pressure), H5T_NATIVE_DOUBLE);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Convert the buffer in reading from sourcetype to desttype.
* After this conversion we will use sensor to access the buffer,
* as the buffer now matches its type.
*/
status = H5Tconvert (sourcetype, desttype, DIM0, reading, bkgrd,
H5P_DEFAULT);
/*
* Output the data to the screen.
*/
for (i=0; i<DIM0; i++) {
printf ("sensor[%d]:\n", i);
printf ("Serial number : %d\n", sensor[i].serial_no);
printf ("Location : %s\n", sensor[i].location);
printf ("Temperature (F) : %f\n", sensor[i].temperature);
printf ("Pressure (inHg) : %f\n\n", sensor[i].pressure);
}
/*
* Close and release resources. In this case H5Tconvert preserves
* the memory locations of the variable-length strings in
* "location", so we do not need to free those strings as they were
* initialized as string constants.
*/
free (sensor);
status = H5Sclose (space);
status = H5Tclose (sourcetype);
status = H5Tclose (desttype);
status = H5Tclose (strtype);
return 0;
}
/*
** WARNING : this function returns an allocated value that must be freed.
*/
static char* readAttribute(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
hid_t iFileType, memtype, iSpace;
herr_t status;
hsize_t dims[1];
size_t iDim;
hsize_t n = 0;
char *pstValue = NULL;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen(_iDatasetId, _pstName, H5P_DEFAULT);
if (iAttributeId < 0)
{
return NULL;
}
/*
* Get the datatype and its size.
*/
iFileType = H5Aget_type(iAttributeId);
iDim = H5Tget_size(iFileType);
iDim++; /* Make room for null terminator */
/*
* Get dataspace and allocate memory for read buffer. This is a
* two dimensional attribute so the dynamic allocation must be done
* in steps.
*/
iSpace = H5Aget_space(iAttributeId);
if (iSpace < 0)
{
return NULL;
}
status = H5Sget_simple_extent_dims(iSpace, dims, NULL);
if (status < 0)
{
return NULL;
}
/*
* Allocate space for string data.
*/
pstValue = (char *)MALLOC((size_t) ((dims[0] * iDim + 1) * sizeof(char)));
/*
* Create the memory datatype.
*/
memtype = H5Tcopy(H5T_C_S1);
status = H5Tset_size(memtype, iDim);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
/*
* Read the data.
*/
status = H5Aread(iAttributeId, memtype, pstValue);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Tclose(memtype);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Sclose(iSpace);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Tclose(iFileType);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Aclose(iAttributeId);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
}
return pstValue;
}