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