16 #include "nc4internal.h" 17 #include "nc4dispatch.h" 20 #include <H5DSpublic.h> 21 #include <H5Fpublic.h> 38 extern int num_plists;
39 extern int num_spaces;
42 #define MIN_DEFLATE_LEVEL 0 43 #define MAX_DEFLATE_LEVEL 9 50 extern void reportopenobjects(
int log, hid_t);
57 typedef struct NC4_rec_read_metadata_obj_info
62 struct NC4_rec_read_metadata_obj_info *next;
71 typedef struct NC4_rec_read_metadata_ud
78 static int NC4_enddef(
int ncid);
79 static int nc4_rec_read_metadata(NC_GRP_INFO_T *grp);
80 static int close_netcdf4_file(NC_HDF5_FILE_INFO_T *h5,
int abort);
87 const char* NC_RESERVED_VARATT_LIST[] = {
88 NC_ATT_REFERENCE_LIST,
90 NC_ATT_DIMENSION_LIST,
101 const char* NC_RESERVED_ATT_LIST[] = {
111 const char* NC_RESERVED_SPECIAL_LIST[] = {
120 size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE;
121 size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS;
122 float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION;
127 static hid_t h5_native_type_constant_g[NUM_TYPES];
128 static const char nc_type_name_g[NUM_TYPES][
NC_MAX_NAME + 1] = {
"char",
"byte",
"short",
129 "int",
"float",
"double",
"ubyte",
130 "ushort",
"uint",
"int64",
136 static const int nc_type_size_g[NUM_TYPES] = {
sizeof(char),
sizeof(
char),
sizeof(short),
137 sizeof(
int),
sizeof(float),
sizeof(
double),
sizeof(
unsigned char),
138 sizeof(
unsigned short),
sizeof(
unsigned int),
sizeof(
long long),
139 sizeof(
unsigned long long),
sizeof(
char *)};
144 nc_set_chunk_cache(
size_t size,
size_t nelems,
float preemption)
146 if (preemption < 0 || preemption > 1)
148 nc4_chunk_cache_size = size;
149 nc4_chunk_cache_nelems = nelems;
150 nc4_chunk_cache_preemption = preemption;
157 nc_get_chunk_cache(
size_t *sizep,
size_t *nelemsp,
float *preemptionp)
160 *sizep = nc4_chunk_cache_size;
163 *nelemsp = nc4_chunk_cache_nelems;
166 *preemptionp = nc4_chunk_cache_preemption;
172 nc_set_chunk_cache_ints(
int size,
int nelems,
int preemption)
174 if (size <= 0 || nelems <= 0 || preemption < 0 || preemption > 100)
176 nc4_chunk_cache_size = size;
177 nc4_chunk_cache_nelems = nelems;
178 nc4_chunk_cache_preemption = (float)preemption / 100;
183 nc_get_chunk_cache_ints(
int *sizep,
int *nelemsp,
int *preemptionp)
186 *sizep = (int)nc4_chunk_cache_size;
188 *nelemsp = (int)nc4_chunk_cache_nelems;
190 *preemptionp = (int)(nc4_chunk_cache_preemption * 100);
220 #define MAGIC_NUMBER_LEN 4 221 #define NC_HDF5_FILE 1 222 #define NC_HDF4_FILE 2 224 nc_check_for_hdf(
const char *path,
int flags,
void* parameters,
int *hdf_file)
226 char blob[MAGIC_NUMBER_LEN];
229 NC_MPI_INFO* mpiinfo = (NC_MPI_INFO*)parameters;
230 MPI_Comm comm = MPI_COMM_WORLD;
231 MPI_Info info = MPI_INFO_NULL;
235 NC_MEM_INFO* meminfo = (NC_MEM_INFO*)parameters;
240 comm = mpiinfo->comm;
241 info = mpiinfo->info;
246 LOG((3,
"%s: path %s", __func__, path));
249 if(!inmemory && H5Fis_hdf5(path))
251 *hdf_file = NC_HDF5_FILE;
257 if (!inmemory && use_parallel)
262 if ((retval = MPI_File_open(comm, (
char *)path, MPI_MODE_RDONLY,
263 info, &fh)) != MPI_SUCCESS)
265 if ((retval = MPI_File_read(fh, blob, MAGIC_NUMBER_LEN, MPI_CHAR,
266 &status)) != MPI_SUCCESS)
268 if ((retval = MPI_File_close(&fh)) != MPI_SUCCESS)
275 if (!(fp = fopen(path,
"r")) ||
276 fread(blob, MAGIC_NUMBER_LEN, 1, fp) != 1) {
283 if(meminfo->size < MAGIC_NUMBER_LEN)
285 memcpy(blob,meminfo->memory,MAGIC_NUMBER_LEN);
289 if (memcmp(blob,
"\016\003\023\001", 4)==0)
290 *hdf_file = NC_HDF4_FILE;
291 else if (memcmp(blob,
"HDF", 3)==0)
292 *hdf_file = NC_HDF5_FILE;
302 nc4_create_file(
const char *path,
int cmode, MPI_Comm comm, MPI_Info info,
305 hid_t fcpl_id, fapl_id = -1;
309 NC_HDF5_FILE_INFO_T* nc4_info = NULL;
320 flags = H5F_ACC_TRUNC;
322 flags = H5F_ACC_EXCL;
324 flags = H5F_ACC_TRUNC;
326 LOG((3,
"%s: path %s mode 0x%x", __func__, path, cmode));
331 if (cmode & NC_DISKLESS) {
332 #ifndef USE_PARALLEL4 336 }
else if ((cmode & NC_NOCLOBBER) && (fp = fopen(path,
"r"))) {
342 if ((retval = nc4_nc4f_list_add(nc, path, (
NC_WRITE | cmode))))
344 nc4_info = NC4_DATA(nc);
345 assert(nc4_info && nc4_info->root_grp);
350 if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
356 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
359 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG))
368 nc4_info->parallel = NC_TRUE;
369 if (cmode & NC_MPIIO)
371 LOG((4,
"creating parallel file with MPI/IO"));
372 if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
375 #ifdef USE_PARALLEL_POSIX 378 LOG((4,
"creating parallel file with MPI/posix"));
379 if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
392 if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
395 if (MPI_INFO_NULL != info)
397 if (MPI_SUCCESS != MPI_Info_dup(info, &nc4_info->info))
404 nc4_info->info = info;
408 if(cmode & NC_DISKLESS) {
409 if (H5Pset_fapl_core(fapl_id, 4096, persist))
412 if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
413 nc4_chunk_cache_preemption) < 0)
415 LOG((4,
"%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
416 __func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
419 #ifdef HDF5_HAS_LIBVER_BOUNDS 420 if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST) < 0)
425 if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0)
432 if (H5Pset_obj_track_times(fcpl_id,0)<0)
438 if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
439 H5P_CRT_ORDER_INDEXED)) < 0)
441 if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
442 H5P_CRT_ORDER_INDEXED)) < 0)
446 if ((nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0)
452 if ((nc4_info->root_grp->hdf_grpid = H5Gopen2(nc4_info->hdfid,
"/",
457 if (H5Pclose(fapl_id) < 0 || H5Pclose(fcpl_id) < 0)
465 nc4_info->flags |= NC_INDEF;
467 NC4_get_fileinfo(nc4_info,&globalpropinfo);
468 NC4_put_propattr(nc4_info);
474 if (comm_duped) MPI_Comm_free(&nc4_info->comm);
475 if (info_duped) MPI_Info_free(&nc4_info->info);
480 if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
481 if(!nc4_info)
return retval;
482 close_netcdf4_file(nc4_info,1);
502 NC4_create(
const char* path,
int cmode,
size_t initialsz,
int basepe,
503 size_t *chunksizehintp,
int use_parallel,
void *parameters,
504 NC_Dispatch *dispatch, NC* nc_file)
506 MPI_Comm comm = MPI_COMM_WORLD;
507 MPI_Info info = MPI_INFO_NULL;
511 assert(nc_file && path);
513 LOG((1,
"%s: path %s cmode 0x%x comm %d info %d",
514 __func__, path, cmode, comm, info));
519 comm = ((NC_MPI_INFO *)parameters)->comm;
520 info = ((NC_MPI_INFO *)parameters)->info;
525 if (!nc4_hdf5_initialized)
526 nc4_hdf5_initialize();
529 if((cmode & ILLEGAL_CREATE_FLAGS) != 0)
533 if((cmode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
537 if((cmode & (NC_MPIIO | NC_MPIPOSIX)) && (cmode & NC_DISKLESS))
540 #ifndef USE_PARALLEL_POSIX 544 if(cmode & NC_MPIPOSIX)
546 cmode &= ~NC_MPIPOSIX;
561 LOG((2,
"cmode after applying default format: 0x%x", cmode));
563 nc_file->int_ncid = nc_file->ext_ncid;
564 res = nc4_create_file(path, cmode, comm, info, nc_file);
575 read_scale(NC_GRP_INFO_T *grp, hid_t datasetid,
const char *obj_name,
576 const H5G_stat_t *statbuf, hsize_t scale_size, hsize_t max_scale_size,
579 NC_DIM_INFO_T *new_dim;
581 htri_t attr_exists = -1;
583 int dimscale_created = 0;
584 int initial_grp_ndims = grp->ndims;
585 short initial_next_dimid = grp->nc4_info->next_dimid;
589 if ((retval = nc4_dim_list_add(&grp->dim, &new_dim)))
595 if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
599 if ((attid = H5Aopen_name(datasetid, NC_DIMID_ATT_NAME)) < 0)
602 if (H5Aread(attid, H5T_NATIVE_INT, &new_dim->dimid) < 0)
606 if (new_dim->dimid >= grp->nc4_info->next_dimid)
607 grp->nc4_info->next_dimid = new_dim->dimid + 1;
612 new_dim->dimid = grp->nc4_info->next_dimid++;
618 if (!(new_dim->name = strdup(obj_name)))
623 new_dim->too_long = NC_TRUE;
626 new_dim->len = scale_size;
627 new_dim->hdf5_objid.fileno[0] = statbuf->fileno[0];
628 new_dim->hdf5_objid.fileno[1] = statbuf->fileno[1];
629 new_dim->hdf5_objid.objno[0] = statbuf->objno[0];
630 new_dim->hdf5_objid.objno[1] = statbuf->objno[1];
631 new_dim->hash = hash_fast(obj_name, strlen(obj_name));
635 if (max_scale_size == H5S_UNLIMITED)
636 new_dim->unlimited = NC_TRUE;
641 if (H5DSget_scale_name(datasetid, dimscale_name_att,
NC_MAX_NAME) >= 0)
643 if (!strncmp(dimscale_name_att, DIM_WITHOUT_VARIABLE,
644 strlen(DIM_WITHOUT_VARIABLE)))
646 if (new_dim->unlimited)
648 size_t len = 0, *lenp = &len;
650 if ((retval = nc4_find_dim_len(grp, new_dim->dimid, &lenp)))
652 new_dim->len = *lenp;
656 new_dim->hdf_dimscaleid = datasetid;
657 H5Iinc_ref(new_dim->hdf_dimscaleid);
666 if (attid > 0 && H5Aclose(attid) < 0)
670 if (retval < 0 && dimscale_created)
673 if ((retval = nc4_dim_list_del(&grp->dim, new_dim)))
677 grp->ndims = initial_grp_ndims;
678 grp->nc4_info->next_dimid = initial_next_dimid;
687 read_coord_dimids(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
689 hid_t coord_att_typeid = -1, coord_attid = -1, spaceid = -1;
697 if ((coord_attid = H5Aopen_name(var->hdf_datasetid, COORDINATES)) < 0) ret++;
698 if (!ret && (coord_att_typeid = H5Aget_type(coord_attid)) < 0) ret++;
701 if (!ret && (spaceid = H5Aget_space(coord_attid)) < 0) ret++;
705 if (!ret && (npoints = H5Sget_simple_extent_npoints(spaceid)) < 0) ret++;
709 if (!ret && npoints != var->ndims) ret++;
711 if (!ret && H5Aread(coord_attid, coord_att_typeid, var->dimids) < 0) ret++;
712 LOG((4,
"dimscale %s is multidimensional and has coords", var->name));
715 for (d = 0; d < var->ndims; d++) {
717 nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
721 if (spaceid >= 0 && H5Sclose(spaceid) < 0) ret++;
725 if (coord_att_typeid >= 0 && H5Tclose(coord_att_typeid) < 0) ret++;
726 if (coord_attid >= 0 && H5Aclose(coord_attid) < 0) ret++;
733 dimscale_visitor(hid_t did,
unsigned dim, hid_t dsid,
734 void *dimscale_hdf5_objids)
739 if (H5Gget_objinfo(dsid,
".", 1, &statbuf) < 0)
743 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[0] = statbuf.fileno[0];
744 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[1] = statbuf.fileno[1];
745 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[0] = statbuf.objno[0];
746 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[1] = statbuf.objno[1];
752 get_netcdf_type(NC_HDF5_FILE_INFO_T *h5, hid_t native_typeid,
755 NC_TYPE_INFO_T *type;
757 htri_t is_str, equal = 0;
761 if ((
class = H5Tget_class(native_typeid)) < 0)
766 if (
class == H5T_STRING)
768 if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
776 else if (
class == H5T_INTEGER ||
class == H5T_FLOAT)
780 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SCHAR)) < 0)
787 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SHORT)) < 0)
794 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_INT)) < 0)
801 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_FLOAT)) < 0)
808 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_DOUBLE)) < 0)
815 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UCHAR)) < 0)
822 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_USHORT)) < 0)
829 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UINT)) < 0)
836 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_LLONG)) < 0)
843 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_ULLONG)) < 0)
854 if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
856 *xtype = type->nc_typeid;
868 get_type_info2(NC_HDF5_FILE_INFO_T *h5, hid_t datasetid,
869 NC_TYPE_INFO_T **type_info)
871 htri_t is_str, equal = 0;
873 hid_t native_typeid, hdf_typeid;
877 assert(h5 && type_info);
885 if (!h5_native_type_constant_g[1])
887 h5_native_type_constant_g[1] = H5T_NATIVE_SCHAR;
888 h5_native_type_constant_g[2] = H5T_NATIVE_SHORT;
889 h5_native_type_constant_g[3] = H5T_NATIVE_INT;
890 h5_native_type_constant_g[4] = H5T_NATIVE_FLOAT;
891 h5_native_type_constant_g[5] = H5T_NATIVE_DOUBLE;
892 h5_native_type_constant_g[6] = H5T_NATIVE_UCHAR;
893 h5_native_type_constant_g[7] = H5T_NATIVE_USHORT;
894 h5_native_type_constant_g[8] = H5T_NATIVE_UINT;
895 h5_native_type_constant_g[9] = H5T_NATIVE_LLONG;
896 h5_native_type_constant_g[10] = H5T_NATIVE_ULLONG;
900 if ((hdf_typeid = H5Dget_type(datasetid)) < 0)
905 if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
909 if ((
class = H5Tget_class(native_typeid)) < 0)
913 if (
class == H5T_STRING ||
class == H5T_INTEGER ||
class == H5T_FLOAT)
916 if (!(*type_info = calloc(1,
sizeof(NC_TYPE_INFO_T))))
921 if (
class == H5T_STRING)
923 if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
926 if (is_str || H5Tget_size(hdf_typeid) > 1)
936 (*type_info)->nc_type_class =
NC_CHAR;
939 else if (
class == H5T_INTEGER ||
class == H5T_FLOAT)
941 for (t = 1; t < NUM_TYPES - 1; t++)
943 if ((equal = H5Tequal(native_typeid, h5_native_type_constant_g[t])) < 0)
955 if((order = H5Tget_order(hdf_typeid)) < 0)
958 if(order == H5T_ORDER_LE)
960 else if(order == H5T_ORDER_BE)
965 if(
class == H5T_INTEGER)
966 (*type_info)->nc_type_class =
NC_INT;
968 (*type_info)->nc_type_class =
NC_FLOAT;
970 (*type_info)->nc_typeid = nc_type_constant_g[t];
971 (*type_info)->size = nc_type_size_g[t];
972 if (!((*type_info)->name = strdup(nc_type_name_g[t])))
974 (*type_info)->hdf_typeid = hdf_typeid;
975 (*type_info)->native_hdf_typeid = native_typeid;
980 NC_TYPE_INFO_T *type;
983 if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
989 if (H5Tclose(native_typeid) < 0)
991 if (H5Tclose(hdf_typeid) < 0)
1003 read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
1005 hid_t spaceid = 0, file_typeid = 0;
1006 hsize_t dims[1] = {0};
1010 hssize_t att_npoints;
1011 H5T_class_t att_class;
1012 int fixed_len_string = 0;
1013 size_t fixed_size = 0;
1016 LOG((5,
"%s: att->attnum %d att->name %s att->nc_typeid %d att->len %d",
1017 __func__, att->attnum, att->name, (
int)att->nc_typeid, att->len));
1020 if ((file_typeid = H5Aget_type(attid)) < 0)
1022 if ((att->native_hdf_typeid = H5Tget_native_type(file_typeid, H5T_DIR_DEFAULT)) < 0)
1024 if ((att_class = H5Tget_class(att->native_hdf_typeid)) < 0)
1026 if (att_class == H5T_STRING && !H5Tis_variable_str(att->native_hdf_typeid))
1029 if (!(fixed_size = H5Tget_size(att->native_hdf_typeid)))
1032 if ((retval = get_netcdf_type(grp->nc4_info, att->native_hdf_typeid, &(att->nc_typeid))))
1037 if ((spaceid = H5Aget_space(attid)) < 0)
1042 if ((att_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
1044 if ((att_npoints = H5Sget_simple_extent_npoints(spaceid)) < 0)
1049 if (att_ndims == 0 && att_npoints == 0)
1052 dims[0] = att_npoints;
1053 else if (att->nc_typeid ==
NC_CHAR)
1059 if (!(dims[0] = H5Tget_size(file_typeid)))
1066 dims[0] = att_npoints;
1071 H5S_class_t space_class;
1078 if ((space_class = H5Sget_simple_extent_type(spaceid)) < 0)
1082 if (H5S_NULL == space_class)
1086 if (H5S_SCALAR == space_class)
1091 if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0)
1103 if ((retval = nc4_get_typelen_mem(grp->nc4_info, att->nc_typeid, 0,
1106 if (att_class == H5T_VLEN)
1108 if (!(att->vldata = malloc((
unsigned int)(att->len *
sizeof(hvl_t)))))
1110 if (H5Aread(attid, att->native_hdf_typeid, att->vldata) < 0)
1115 if (!(att->stdata = calloc(att->len,
sizeof(
char *))))
1128 if (fixed_len_string)
1131 char *contig_buf, *cur;
1134 if (!(contig_buf = malloc(att->len * fixed_size *
sizeof(
char))))
1138 if (H5Aread(attid, att->native_hdf_typeid, contig_buf) < 0) {
1147 for (i = 0; i < att->len; i++)
1149 if (!(att->stdata[i] = malloc(fixed_size))) {
1153 strncpy(att->stdata[i], cur, fixed_size);
1163 if (H5Aread(attid, att->native_hdf_typeid, att->stdata) < 0)
1169 if (!(att->data = malloc((
unsigned int)(att->len * type_size))))
1171 if (H5Aread(attid, att->native_hdf_typeid, att->data) < 0)
1176 if (H5Tclose(file_typeid) < 0)
1178 if (H5Sclose(spaceid) < 0)
1187 if (H5Tclose(file_typeid) < 0)
1189 if (spaceid > 0 && H5Sclose(spaceid) < 0)
1200 read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid,
char *type_name)
1202 NC_TYPE_INFO_T *type;
1204 hid_t native_typeid;
1208 assert(grp && type_name);
1210 LOG((4,
"%s: type_name %s grp->name %s", __func__, type_name, grp->name));
1213 if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
1217 if (!(type_size = H5Tget_size(native_typeid)))
1219 LOG((5,
"type_size %d", type_size));
1222 if ((retval = nc4_type_list_add(grp, type_size, type_name, &type)))
1226 type->committed = NC_TRUE;
1227 type->hdf_typeid = hdf_typeid;
1228 H5Iinc_ref(type->hdf_typeid);
1229 type->native_hdf_typeid = native_typeid;
1232 if ((
class = H5Tget_class(hdf_typeid)) < 0)
1244 char* member_name = NULL;
1251 if ((nmembers = H5Tget_nmembers(hdf_typeid)) < 0)
1253 LOG((5,
"compound type has %d members", nmembers));
1254 for (m = 0; m < nmembers; m++)
1256 hid_t member_hdf_typeid;
1257 hid_t member_native_typeid;
1258 size_t member_offset;
1259 H5T_class_t mem_class;
1265 if ((member_hdf_typeid = H5Tget_member_type(type->native_hdf_typeid, m)) < 0)
1268 if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid, H5T_DIR_DEFAULT)) < 0)
1272 member_name = H5Tget_member_name(type->native_hdf_typeid, m);
1273 if (!member_name || strlen(member_name) >
NC_MAX_NAME) {
1279 strncpy(jna,member_name,1000);
1285 member_offset = H5Tget_member_offset(type->native_hdf_typeid, m);
1288 if ((mem_class = H5Tget_class(member_hdf_typeid)) < 0)
1290 if (mem_class == H5T_ARRAY)
1296 if ((ndims = H5Tget_array_ndims(member_hdf_typeid)) < 0) {
1300 if (H5Tget_array_dims(member_hdf_typeid, dims, NULL) != ndims) {
1304 for (d = 0; d < ndims; d++)
1305 dim_size[d] = dims[d];
1308 if ((retval = get_netcdf_type(grp->nc4_info, H5Tget_super(member_hdf_typeid),
1313 if ((retval = nc4_field_list_add(&type->u.c.field, type->u.c.num_fields++, member_name,
1314 member_offset, H5Tget_super(member_hdf_typeid),
1315 H5Tget_super(member_native_typeid),
1316 member_xtype, ndims, dim_size)))
1322 if ((retval = get_netcdf_type(grp->nc4_info, member_native_typeid,
1327 if ((retval = nc4_field_list_add(&type->u.c.field, type->u.c.num_fields++, member_name,
1328 member_offset, member_hdf_typeid, member_native_typeid,
1329 member_xtype, 0, NULL)))
1340 #ifdef HDF5_HAS_H5FREE 1341 if(member_name != NULL) H5free_memory(member_name);
1344 if(member_name != NULL) free(member_name);
1351 if(member_name != NULL)
1367 if ((ret = H5Tis_variable_str(hdf_typeid)) < 0)
1373 hid_t base_hdf_typeid;
1376 type->nc_type_class =
NC_VLEN;
1380 if (!(base_hdf_typeid = H5Tget_super(native_typeid)))
1384 if (!(type_size = H5Tget_size(base_hdf_typeid)))
1388 if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
1391 LOG((5,
"base_hdf_typeid 0x%x type_size %d base_nc_type %d",
1392 base_hdf_typeid, type_size, base_nc_type));
1395 type->u.v.base_nc_typeid = base_nc_type;
1396 type->u.v.base_hdf_typeid = base_hdf_typeid;
1407 hid_t base_hdf_typeid;
1411 char *member_name = NULL;
1416 type->nc_type_class =
NC_ENUM;
1420 if (!(base_hdf_typeid = H5Tget_super(hdf_typeid)))
1423 if (!(type_size = H5Tget_size(base_hdf_typeid)))
1426 if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
1429 LOG((5,
"base_hdf_typeid 0x%x type_size %d base_nc_type %d",
1430 base_hdf_typeid, type_size, base_nc_type));
1433 type->u.e.base_nc_typeid = base_nc_type;
1434 type->u.e.base_hdf_typeid = base_hdf_typeid;
1437 if ((type->u.e.num_members = H5Tget_nmembers(hdf_typeid)) < 0)
1441 if (!(value = calloc(1, type_size)))
1445 for (i = 0; i < type->u.e.num_members; i++)
1449 if (!(member_name = H5Tget_member_name(hdf_typeid, i)))
1455 strncpy(jna,member_name,1000);
1464 if (H5Tget_member_value(hdf_typeid, i, value) < 0)
1471 if ((retval = nc4_enum_member_add(&type->u.e.enum_member, type->size,
1472 member_name, value)))
1479 if(member_name != NULL) free(member_name);
1485 if(member_name != NULL)
1488 if(value) free(value);
1495 LOG((0,
"unknown class"));
1506 read_var(NC_GRP_INFO_T *grp, hid_t datasetid,
const char *obj_name,
1507 size_t ndims, NC_DIM_INFO_T *dim)
1509 NC_VAR_INFO_T *var = NULL;
1510 hid_t access_pid = 0;
1513 const char** reserved;
1517 char att_name[NC_MAX_HDF5_NAME + 1];
1519 #define CD_NELEMS_ZLIB 1 1520 #define CD_NELEMS_SZIP 4 1521 H5Z_filter_t filter;
1523 unsigned int cd_values[CD_NELEMS_SZIP];
1524 size_t cd_nelems = CD_NELEMS_SZIP;
1526 H5D_fill_value_t fill_status;
1527 H5D_layout_t layout;
1533 assert(obj_name && grp);
1534 LOG((4,
"%s: obj_name %s", __func__, obj_name));
1537 if ((retval = nc4_var_list_add(&grp->var, &var)))
1541 var->hdf_datasetid = datasetid;
1542 H5Iinc_ref(var->hdf_datasetid);
1544 var->varid = grp->nvars++;
1545 var->created = NC_TRUE;
1552 if (!(var->dim = calloc(var->ndims,
sizeof(NC_DIM_INFO_T *))))
1554 if (!(var->dimids = calloc(var->ndims,
sizeof(
int))))
1559 if ((access_pid = H5Dget_access_plist(datasetid)) < 0)
1566 if ((H5Pget_chunk_cache(access_pid, &(var->chunk_cache_nelems),
1567 &(var->chunk_cache_size), &rdcc_w0)) < 0)
1569 var->chunk_cache_preemption = rdcc_w0;
1574 if (strlen(obj_name) > strlen(NON_COORD_PREPEND) &&
1575 !strncmp(obj_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)))
1578 if (!(var->name = malloc(((strlen(obj_name) - strlen(NON_COORD_PREPEND))+ 1) *
sizeof(
char))))
1581 strcpy(var->name, &obj_name[strlen(NON_COORD_PREPEND)]);
1584 if (!(var->hdf5_name = malloc((strlen(obj_name) + 1) *
sizeof(
char))))
1587 strcpy(var->hdf5_name, obj_name);
1592 if (!(var->name = malloc((strlen(obj_name) + 1) *
sizeof(
char))))
1595 strcpy(var->name, obj_name);
1598 var->hash = hash_fast(var->name, strlen(var->name));
1602 if ((propid = H5Dget_create_plist(datasetid)) < 0)
1609 if ((layout = H5Pget_layout(propid)) < -1)
1611 if (layout == H5D_CHUNKED)
1615 if (!(var->chunksizes = malloc(var->ndims *
sizeof(
size_t))))
1617 for (d = 0; d < var->ndims; d++)
1618 var->chunksizes[d] = chunksize[d];
1620 else if (layout == H5D_CONTIGUOUS || layout == H5D_COMPACT)
1621 var->contiguous = NC_TRUE;
1625 if ((num_filters = H5Pget_nfilters(propid)) < 0)
1627 for (f = 0; f < num_filters; f++)
1629 if ((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems,
1630 cd_values, 0, NULL, NULL)) < 0)
1634 case H5Z_FILTER_SHUFFLE:
1635 var->shuffle = NC_TRUE;
1638 case H5Z_FILTER_FLETCHER32:
1639 var->fletcher32 = NC_TRUE;
1642 case H5Z_FILTER_DEFLATE:
1643 var->deflate = NC_TRUE;
1644 if (cd_nelems != CD_NELEMS_ZLIB || cd_values[0] > MAX_DEFLATE_LEVEL)
1646 var->deflate_level = cd_values[0];
1649 case H5Z_FILTER_SZIP:
1650 var->szip = NC_TRUE;
1651 if (cd_nelems != CD_NELEMS_SZIP)
1653 var->options_mask = cd_values[0];
1654 var->pixels_per_block = cd_values[1];
1658 LOG((1,
"Yikes! Unknown filter type found on dataset!"));
1664 if ((retval = get_type_info2(grp->nc4_info, datasetid,
1669 var->type_info->rc++;
1672 if (H5Pfill_value_defined(propid, &fill_status) < 0)
1676 if (fill_status == H5D_FILL_VALUE_USER_DEFINED)
1679 if (!var->fill_value)
1681 if (var->type_info->nc_type_class ==
NC_VLEN)
1683 if (!(var->fill_value = malloc(
sizeof(
nc_vlen_t))))
1686 else if (var->type_info->nc_type_class ==
NC_STRING)
1688 if (!(var->fill_value = malloc(
sizeof(
char *))))
1693 assert(var->type_info->size);
1694 if (!(var->fill_value = malloc(var->type_info->size)))
1700 if (H5Pget_fill_value(propid, var->type_info->native_hdf_typeid,
1701 var->fill_value) < 0)
1705 var->no_fill = NC_TRUE;
1711 var->dimscale = NC_TRUE;
1714 if ((retval = read_coord_dimids(grp, var)))
1720 assert(0 == strcmp(var->name, dim->name));
1722 var->dimids[0] = dim->dimid;
1725 dim->coord_var = var;
1737 num_scales = H5DSget_num_scales(datasetid, 0);
1741 if (num_scales && ndims)
1745 if (NULL == (var->dimscale_attached = calloc(ndims,
sizeof(nc_bool_t))))
1750 if (NULL == (var->dimscale_hdf5_objids = malloc(ndims *
sizeof(
struct hdf5_objid))))
1752 for (d = 0; d < var->ndims; d++)
1754 if (H5DSiterate_scales(var->hdf_datasetid, d, NULL, dimscale_visitor,
1755 &(var->dimscale_hdf5_objids[d])) < 0)
1757 var->dimscale_attached[d] = NC_TRUE;
1764 if ((natts = H5Aget_num_attrs(var->hdf_datasetid)) < 0)
1766 for (a = 0; a < natts; a++)
1771 if (attid && H5Aclose(attid) < 0)
1775 if ((attid = H5Aopen_idx(var->hdf_datasetid, (
unsigned int)a)) < 0)
1777 if (H5Aget_name(attid, NC_MAX_HDF5_NAME, att_name) < 0)
1779 LOG((4,
"%s:: a %d att_name %s", __func__, a, att_name));
1782 for(reserved=NC_RESERVED_VARATT_LIST;*reserved;reserved++) {
1783 if (strcmp(att_name, *reserved)==0)
break;
1785 if(*reserved == NULL) {
1787 if ((retval = nc4_att_list_add(&var->att, &att)))
1791 att->attnum = var->natts++;
1792 if (!(att->name = strdup(att_name)))
1797 if ((retval = read_hdf5_att(grp, attid, att)))
1801 if ((retval = nc4_att_list_del(&var->att, att)))
1809 att->created = NC_TRUE;
1815 if ((retval = nc4_adjust_var_cache(grp, var)))
1821 if (incr_id_rc && H5Idec_ref(datasetid) < 0)
1823 if (var && nc4_var_list_del(&grp->var, var))
1826 if (access_pid && H5Pclose(access_pid) < 0)
1831 if (propid > 0 && H5Pclose(propid) < 0)
1836 if (attid > 0 && H5Aclose(attid) < 0)
1844 read_grp_atts(NC_GRP_INFO_T *grp)
1849 NC_TYPE_INFO_T *type;
1850 char obj_name[NC_MAX_HDF5_NAME + 1];
1855 num_obj = H5Aget_num_attrs(grp->hdf_grpid);
1856 for (i = 0; i < num_obj; i++)
1858 if ((attid = H5Aopen_idx(grp->hdf_grpid, (
unsigned int)i)) < 0)
1860 if (H5Aget_name(attid,
NC_MAX_NAME + 1, obj_name) < 0)
1862 LOG((3,
"reading attribute of _netCDF group, named %s", obj_name));
1865 if(grp->nc4_info->root_grp == grp) {
1866 const char** reserved = NC_RESERVED_ATT_LIST;
1868 for(;*reserved;reserved++) {
1869 if(strcmp(*reserved,obj_name)==0) {
1880 if(strcmp(obj_name, NC3_STRICT_ATT_NAME)==0)
1884 if ((retval = nc4_att_list_add(&grp->att, &att)))
1889 if (!(att->name = malloc((max_len + 1) *
sizeof(
char))))
1891 strncpy(att->name, obj_name, max_len);
1892 att->name[max_len] = 0;
1893 att->attnum = grp->natts++;
1894 retval = read_hdf5_att(grp, attid, att);
1896 if((retval = nc4_att_list_del(&grp->att, att)))
1901 att->created = NC_TRUE;
1902 if ((retval = nc4_find_type(grp->nc4_info, att->nc_typeid, &type)))
1913 if(H5Aclose(attid) < 0)
1922 read_dataset(NC_GRP_INFO_T *grp, hid_t datasetid,
const char *obj_name,
1923 const H5G_stat_t *statbuf)
1925 NC_DIM_INFO_T *dim = NULL;
1932 if ((spaceid = H5Dget_space(datasetid)) < 0)
1937 if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
1941 if ((is_scale = H5DSis_scale(datasetid)) < 0)
1945 hsize_t dims[H5S_MAX_RANK];
1946 hsize_t max_dims[H5S_MAX_RANK];
1949 if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0)
1953 if ((retval = read_scale(grp, datasetid, obj_name, statbuf, dims[0],
1954 max_dims[0], &dim)))
1961 if (NULL == dim || (dim && !dim->hdf_dimscaleid))
1962 if ((retval = read_var(grp, datasetid, obj_name, ndims, dim)))
1966 if (spaceid && H5Sclose(spaceid) <0)
1983 if (!(new_oinfo = calloc(1,
sizeof(*new_oinfo))))
1987 memcpy(new_oinfo, oinfo,
sizeof(*oinfo));
1992 (*tail)->next = new_oinfo;
1997 assert(NULL == *head);
1998 *head = *tail = new_oinfo;
2005 nc4_rec_read_metadata_cb(hid_t grpid,
const char *name,
const H5L_info_t *info,
2010 int retval = H5_ITER_CONT;
2013 memset(&oinfo, 0,
sizeof(oinfo));
2016 if ((oinfo.oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0)
2017 BAIL(H5_ITER_ERROR);
2020 if (H5Gget_objinfo(oinfo.oid,
".", 1, &oinfo.statbuf) < 0)
2021 BAIL(H5_ITER_ERROR);
2026 switch(oinfo.statbuf.type)
2029 LOG((3,
"found group %s", oinfo.oname));
2035 if (nc4_rec_read_metadata_cb_list_add(&udata->grps_head, &udata->grps_tail, &oinfo))
2036 BAIL(H5_ITER_ERROR);
2040 LOG((3,
"found dataset %s", oinfo.oname));
2044 if ((retval = read_dataset(udata->grp, oinfo.oid, oinfo.oname, &oinfo.statbuf)))
2052 BAIL(H5_ITER_ERROR);
2054 retval = H5_ITER_CONT;
2058 if (H5Oclose(oinfo.oid) < 0)
2059 BAIL(H5_ITER_ERROR);
2063 LOG((3,
"found datatype %s", oinfo.oname));
2066 if (read_type(udata->grp, oinfo.oid, oinfo.oname))
2067 BAIL(H5_ITER_ERROR);
2070 if (H5Oclose(oinfo.oid) < 0)
2071 BAIL(H5_ITER_ERROR);
2075 LOG((0,
"Unknown object class %d in %s!", oinfo.statbuf.type, __func__));
2076 BAIL(H5_ITER_ERROR);
2082 if (oinfo.oid > 0 && H5Oclose(oinfo.oid) < 0)
2083 BAIL2(H5_ITER_ERROR);
2097 nc4_rec_read_metadata(NC_GRP_INFO_T *grp)
2103 unsigned crt_order_flags = 0;
2104 H5_index_t iter_index;
2107 assert(grp && grp->name);
2108 LOG((3,
"%s: grp->name %s", __func__, grp->name));
2111 memset(&udata, 0,
sizeof(udata));
2115 if (!grp->hdf_grpid)
2119 if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid,
2120 grp->name, H5P_DEFAULT)) < 0)
2125 if ((grp->hdf_grpid = H5Gopen2(grp->nc4_info->hdfid,
2126 "/", H5P_DEFAULT)) < 0)
2130 assert(grp->hdf_grpid > 0);
2133 pid = H5Gget_create_plist(grp->hdf_grpid);
2134 H5Pget_link_creation_order(pid, &crt_order_flags);
2135 if (H5Pclose(pid) < 0)
2139 if (crt_order_flags & H5P_CRT_ORDER_TRACKED)
2140 iter_index = H5_INDEX_CRT_ORDER;
2143 NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
2149 iter_index = H5_INDEX_NAME;
2158 if (H5Literate(grp->hdf_grpid, iter_index, H5_ITER_INC, &idx,
2159 nc4_rec_read_metadata_cb, (
void *)&udata) < 0)
2166 for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
2168 NC_GRP_INFO_T *child_grp;
2169 NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
2172 if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++,
2173 grp, grp->nc4_info->controller, oinfo->oname, &child_grp)))
2177 if ((retval = nc4_rec_read_metadata(child_grp)))
2181 if (H5Oclose(oinfo->oid) < 0)
2185 udata.grps_head = oinfo->next;
2190 if ((retval = read_grp_atts(grp)))
2197 for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
2200 if (H5Oclose(oinfo->oid) < 0)
2204 udata.grps_head = oinfo->next;
2216 nc4_open_file(
const char *path,
int mode,
void* parameters, NC *nc)
2218 hid_t fapl_id = H5P_DEFAULT;
2219 unsigned flags = (mode &
NC_WRITE) ?
2220 H5F_ACC_RDWR : H5F_ACC_RDONLY;
2222 NC_HDF5_FILE_INFO_T* nc4_info = NULL;
2225 NC_MEM_INFO* meminfo = (NC_MEM_INFO*)parameters;
2227 #ifdef USE_PARALLEL4 2228 NC_MPI_INFO* mpiinfo = (NC_MPI_INFO*)parameters;
2233 LOG((3,
"%s: path %s mode %d", __func__, path, mode));
2237 if ((retval = nc4_nc4f_list_add(nc, path, mode)))
2239 nc4_info = NC4_DATA(nc);
2240 assert(nc4_info && nc4_info->root_grp);
2245 if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
2252 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
2255 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG))
2259 #ifdef USE_PARALLEL4 2262 if (mode & NC_MPIIO || mode & NC_MPIPOSIX)
2264 nc4_info->parallel = NC_TRUE;
2265 if (mode & NC_MPIIO)
2267 LOG((4,
"opening parallel file with MPI/IO"));
2268 if (H5Pset_fapl_mpio(fapl_id, mpiinfo->comm, mpiinfo->info) < 0)
2271 #ifdef USE_PARALLEL_POSIX 2274 LOG((4,
"opening parallel file with MPI/posix"));
2275 if (H5Pset_fapl_mpiposix(fapl_id, mpiinfo->comm, 0) < 0)
2288 if (MPI_SUCCESS != MPI_Comm_dup(mpiinfo->comm, &nc4_info->comm))
2291 if (MPI_INFO_NULL != mpiinfo->info)
2293 if (MPI_SUCCESS != MPI_Info_dup(mpiinfo->info, &nc4_info->info))
2300 nc4_info->info = mpiinfo->info;
2304 if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
2305 nc4_chunk_cache_preemption) < 0)
2307 LOG((4,
"%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
2308 __func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
2315 if((nc4_info->hdfid = H5LTopen_file_image(meminfo->memory,meminfo->size,
2316 H5LT_FILE_IMAGE_DONT_COPY|H5LT_FILE_IMAGE_DONT_RELEASE
2319 nc4_info->no_write = NC_TRUE;
2320 }
else if ((nc4_info->hdfid = H5Fopen(path, flags, fapl_id)) < 0)
2325 nc4_info->no_write = NC_TRUE;
2331 if ((retval = nc4_rec_read_metadata(nc4_info->root_grp)))
2336 if ((retval = nc4_rec_match_dimscales(nc4_info->root_grp)))
2342 log_metadata_nc(nc);
2346 if (H5Pclose(fapl_id) < 0)
2352 NC4_get_fileinfo(nc4_info,NULL);
2357 #ifdef USE_PARALLEL4 2358 if (comm_duped) MPI_Comm_free(&nc4_info->comm);
2359 if (info_duped) MPI_Info_free(&nc4_info->info);
2364 if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
2365 if (!nc4_info)
return retval;
2366 close_netcdf4_file(nc4_info,1);
2385 get_netcdf_type_from_hdf4(NC_HDF5_FILE_INFO_T *h5, int32 hdf4_typeid,
2386 nc_type *xtype, NC_TYPE_INFO_T *type_info)
2398 assert(h5 && xtype);
2486 if (hdf4_typeid == DFNT_FLOAT32)
2487 type_info->nc_type_class =
NC_FLOAT;
2488 else if (hdf4_typeid == DFNT_FLOAT64)
2490 else if (hdf4_typeid == DFNT_CHAR)
2493 type_info->nc_type_class =
NC_INT;
2494 type_info->endianness = endianness;
2495 type_info->nc_typeid = *xtype;
2496 type_info->size = nc_type_size_g[t];
2497 if (!(type_info->name = strdup(nc_type_name_g[t])))
2507 nc4_open_hdf4_file(
const char *path,
int mode, NC *nc)
2509 NC_HDF5_FILE_INFO_T *h5;
2512 int32 num_datasets, num_gatts;
2516 NC_HDF5_FILE_INFO_T* nc4_info = NULL;
2518 LOG((3,
"%s: path %s mode %d", __func__, path, mode));
2526 if ((retval = nc4_nc4f_list_add(nc, path, mode)))
2528 nc4_info = NC4_DATA(nc);
2529 assert(nc4_info && nc4_info->root_grp);
2533 h5->no_write = NC_TRUE;
2536 if ((h5->sdid = SDstart(path, DFACC_READ)) == FAIL)
2540 if (SDfileinfo(h5->sdid, &num_datasets, &num_gatts))
2544 for (a = 0; a < num_gatts; a++)
2546 int32 att_data_type, att_count;
2547 size_t att_type_size;
2550 if ((retval = nc4_att_list_add(&h5->root_grp->att, &att)))
2552 att->attnum = grp->natts++;
2553 att->created = NC_TRUE;
2558 if (SDattrinfo(h5->sdid, a, att->name, &att_data_type, &att_count))
2560 if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type,
2561 &att->nc_typeid, NULL)))
2563 att->len = att_count;
2566 if ((retval = nc4_get_typelen_mem(h5, att->nc_typeid, 0, &att_type_size)))
2568 if (!(att->data = malloc(att_type_size * att->len)))
2572 if (SDreadattr(h5->sdid, a, att->data))
2577 for (v = 0; v < num_datasets; v++)
2580 int32 data_type, num_atts;
2589 int32 *dimsize = NULL;
2590 size_t var_type_size;
2594 if ((retval = nc4_var_list_add(&grp->var, &var)))
2597 var->varid = grp->nvars++;
2598 var->created = NC_TRUE;
2599 var->written_to = NC_TRUE;
2602 if ((var->sdsid = SDselect(h5->sdid, v)) == FAIL)
2610 if (SDgetinfo(var->sdsid, var->name, &rank, NULL, &data_type, &num_atts))
2613 var->hash = hash_fast(var->name, strlen(var->name));
2615 if(!(dimsize = (int32*)malloc(
sizeof(int32)*rank)))
2618 if (SDgetinfo(var->sdsid, var->name, &rank, dimsize, &data_type, &num_atts)) {
2619 if(dimsize) free(dimsize);
2624 var->hdf4_data_type = data_type;
2627 if (!(var->type_info = calloc(1,
sizeof(NC_TYPE_INFO_T)))) {
2628 if(dimsize) free(dimsize);
2632 if ((retval = get_netcdf_type_from_hdf4(h5, data_type, &var->type_info->nc_typeid, var->type_info))) {
2633 if(dimsize) free(dimsize);
2638 var->type_info->rc++;
2640 if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0, &var_type_size))) {
2641 if(dimsize) free(dimsize);
2645 var->type_info->size = var_type_size;
2646 LOG((3,
"reading HDF4 dataset %s, rank %d netCDF type %d", var->name,
2647 rank, var->type_info->nc_typeid));
2650 if (!(var->fill_value = malloc(var_type_size))) {
2651 if(dimsize) free(dimsize);
2655 if (SDgetfillvalue(var->sdsid, var->fill_value))
2658 free(var->fill_value);
2659 var->fill_value = NULL;
2665 if (!(var->dim = malloc(
sizeof(NC_DIM_INFO_T *) * var->ndims))) {
2666 if(dimsize) free(dimsize);
2670 if (!(var->dimids = malloc(
sizeof(
int) * var->ndims))) {
2671 if(dimsize) free(dimsize);
2678 for (d = 0; d < var->ndims; d++)
2680 int32 dimid, dim_len, dim_data_type, dim_num_attrs;
2684 if ((dimid = SDgetdimid(var->sdsid, d)) == FAIL) {
2685 if(dimsize) free(dimsize);
2688 if (SDdiminfo(dimid, dim_name, &dim_len, &dim_data_type,
2691 if(dimsize) free(dimsize);
2697 for (dim = grp->dim; dim; dim = dim->l.next)
2698 if (!strcmp(dim->name, dim_name))
2704 LOG((4,
"adding dimension %s for HDF4 dataset %s",
2705 dim_name, var->name));
2706 if ((retval = nc4_dim_list_add(&grp->dim, &dim)))
2709 dim->dimid = grp->nc4_info->next_dimid++;
2712 if (!(dim->name = strdup(dim_name)))
2717 dim->len = *dimsize;
2718 dim->hash = hash_fast(dim_name, strlen(dim_name));
2722 var->dimids[d] = dim->dimid;
2727 for (a = 0; a < num_atts; a++)
2729 int32 att_data_type, att_count;
2730 size_t att_type_size;
2733 if ((retval = nc4_att_list_add(&var->att, &att))) {
2734 if(dimsize) free(dimsize);
2737 att->attnum = var->natts++;
2738 att->created = NC_TRUE;
2742 if(dimsize) free(dimsize);
2745 if (SDattrinfo(var->sdsid, a, att->name, &att_data_type, &att_count)) {
2746 if(dimsize) free(dimsize);
2749 if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type,
2750 &att->nc_typeid, NULL))) {
2751 if(dimsize) free(dimsize);
2755 att->len = att_count;
2758 if ((retval = nc4_get_typelen_mem(h5, att->nc_typeid, 0, &att_type_size))) {
2759 if(dimsize) free(dimsize);
2762 if (!(att->data = malloc(att_type_size * att->len))) {
2763 if(dimsize) free(dimsize);
2768 if (SDreadattr(var->sdsid, a, att->data)) {
2769 if(dimsize) free(dimsize);
2773 if(dimsize) free(dimsize);
2777 HDF_CHUNK_DEF chunkdefs;
2779 if(!SDgetchunkinfo(var->sdsid, &chunkdefs, &flag)) {
2780 if(flag == HDF_NONE)
2781 var->contiguous = NC_TRUE;
2782 else if((flag & HDF_CHUNK) != 0) {
2783 var->contiguous = NC_FALSE;
2784 if (!(var->chunksizes = malloc(var->ndims *
sizeof(
size_t))))
2786 for (d = 0; d < var->ndims; d++) {
2787 var->chunksizes[d] = chunkdefs.chunk_lengths[d];
2798 log_metadata_nc(h5->root_grp->nc4_info->controller);
2806 NC4_open(
const char *path,
int mode,
int basepe,
size_t *chunksizehintp,
2807 int use_parallel,
void *parameters, NC_Dispatch *dispatch, NC *nc_file)
2811 #ifdef USE_PARALLEL4 2812 NC_MPI_INFO mpidfalt = {MPI_COMM_WORLD, MPI_INFO_NULL};
2814 #if defined USE_PARALLEL4 || defined USE_HDF4 2818 assert(nc_file && path);
2820 LOG((1,
"%s: path %s mode %d params %x",
2821 __func__, path, mode, parameters));
2823 #ifdef USE_PARALLEL4 2824 if (!inmemory && use_parallel && parameters == NULL)
2825 parameters = &mpidfalt;
2829 if (!nc4_hdf5_initialized)
2830 nc4_hdf5_initialize();
2833 if((mode & ILLEGAL_OPEN_FLAGS) != 0)
2837 if((mode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
2840 #ifndef USE_PARALLEL_POSIX 2844 if(mode & NC_MPIPOSIX)
2846 mode &= ~NC_MPIPOSIX;
2852 if ((res = nc_check_for_hdf(path, use_parallel, parameters, &hdf_file)))
2856 nc_file->int_ncid = nc_file->ext_ncid;
2857 if (hdf_file == NC_HDF5_FILE)
2858 res = nc4_open_file(path, mode, parameters, nc_file);
2860 else if (hdf_file == NC_HDF4_FILE && inmemory)
2862 else if (hdf_file == NC_HDF4_FILE)
2863 res = nc4_open_hdf4_file(path, mode, nc_file);
2877 NC4_set_fill(
int ncid,
int fillmode,
int *old_modep)
2880 NC_HDF5_FILE_INFO_T* nc4_info;
2882 LOG((2,
"%s: ncid 0x%x fillmode %d", __func__, ncid, fillmode));
2884 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
2889 if (nc4_info->no_write)
2898 *old_modep = nc4_info->fill_mode;
2900 nc4_info->fill_mode = fillmode;
2911 NC_HDF5_FILE_INFO_T* nc4_info;
2913 LOG((1,
"%s: ncid 0x%x", __func__, ncid));
2916 if (!(nc4_find_nc_file(ncid,&nc4_info)))
2921 if (nc4_info->flags & NC_INDEF)
2925 if (nc4_info->no_write)
2929 nc4_info->flags |= NC_INDEF;
2933 nc4_info->redef = NC_TRUE;
2941 NC4__enddef(
int ncid,
size_t h_minfree,
size_t v_align,
2942 size_t v_minfree,
size_t r_align)
2944 if (nc4_find_nc_file(ncid,NULL) == NULL)
2947 return NC4_enddef(ncid);
2952 static int NC4_enddef(
int ncid)
2955 NC_HDF5_FILE_INFO_T* nc4_info;
2957 LOG((1,
"%s: ncid 0x%x", __func__, ncid));
2959 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
2963 return nc4_enddef_netcdf4_file(nc4_info);
2969 sync_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
2974 LOG((3,
"%s", __func__));
2978 if (h5->flags & NC_INDEF)
2984 h5->flags ^= NC_INDEF;
2987 h5->redef = NC_FALSE;
2993 log_metadata_nc(h5->root_grp->nc4_info->controller);
2999 nc_bool_t bad_coord_order = NC_FALSE;
3001 if ((retval = nc4_rec_write_groups_types(h5->root_grp)))
3003 if ((retval = nc4_rec_detect_need_to_preserve_dimids(h5->root_grp, &bad_coord_order)))
3005 if ((retval = nc4_rec_write_metadata(h5->root_grp, bad_coord_order)))
3009 if (H5Fflush(h5->hdfid, H5F_SCOPE_GLOBAL) < 0)
3022 NC_HDF5_FILE_INFO_T* nc4_info;
3024 LOG((2,
"%s: ncid 0x%x", __func__, ncid));
3026 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
3031 if (nc4_info && nc4_info->flags & NC_INDEF)
3035 if ((retval = NC4_enddef(ncid)))
3039 return sync_netcdf4_file(nc4_info);
3046 close_netcdf4_file(NC_HDF5_FILE_INFO_T *h5,
int abort)
3050 assert(h5 && h5->root_grp);
3051 LOG((3,
"%s: h5->path %s abort %d", __func__, h5->controller->path, abort));
3054 if (h5->flags & NC_INDEF)
3055 h5->flags ^= NC_INDEF;
3059 if (!h5->no_write && !abort)
3060 if ((retval = sync_netcdf4_file(h5)))
3065 if ((retval = nc4_rec_grp_del(&h5->root_grp, h5->root_grp)))
3072 if (SDend(h5->sdid))
3078 #ifdef USE_PARALLEL4 3082 if(MPI_COMM_NULL != h5->comm)
3083 MPI_Comm_free(&h5->comm);
3084 if(MPI_INFO_NULL != h5->info)
3085 MPI_Info_free(&h5->info);
3089 if(h5->fileinfo) free(h5->fileinfo);
3091 if (H5Fclose(h5->hdfid) < 0)
3095 nobjs = H5Fget_obj_count(h5->hdfid, H5F_OBJ_ALL);
3099 }
else if(nobjs > 0) {
3107 snprintf(msg,
sizeof(msg),
"There are %d HDF5 objects open!", nobjs);
3111 fprintf(stdout,msg);
3114 reportopenobjects(logit,h5->hdfid);
3137 int delete_file = 0;
3140 NC_HDF5_FILE_INFO_T* nc4_info;
3142 LOG((2,
"%s: ncid 0x%x", __func__, ncid));
3145 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
3151 if (nc4_info->flags & NC_INDEF && !nc4_info->redef)
3159 if ((retval = close_netcdf4_file(nc4_info, 1)))
3164 if (
remove(path) < 0)
3176 NC_HDF5_FILE_INFO_T *h5;
3179 LOG((1,
"%s: ncid 0x%x", __func__, ncid));
3182 if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
3185 assert(nc && h5 && grp);
3192 if ((retval = close_netcdf4_file(grp->nc4_info, 0)))
3201 NC4_inq(
int ncid,
int *ndimsp,
int *nvarsp,
int *nattsp,
int *unlimdimidp)
3204 NC_HDF5_FILE_INFO_T *h5;
3211 LOG((2,
"%s: ncid 0x%x", __func__, ncid));
3214 if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
3217 assert(h5 && grp && nc);
3223 for (dim = grp->dim; dim; dim = dim->l.next)
3229 for (var = grp->var; var; var= var->l.next)
3235 for (att = grp->att; att; att = att->l.next)
3248 for (dim = grp->dim; dim; dim = dim->l.next)
3251 *unlimdimidp = dim->dimid;
3261 nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
3264 LOG((3,
"%s", __func__));
3267 if (!(h5->flags & NC_INDEF))
3271 h5->flags ^= NC_INDEF;
3274 h5->redef = NC_FALSE;
3276 return sync_netcdf4_file(h5);
3283 if (num_plists || num_spaces)
3290 #ifdef USE_PARALLEL4 3292 nc_use_parallel_enabled()
#define NC_ENOMEM
Memory allocation (malloc) failure.
#define NC_CHAR
ISO/ASCII character.
#define NC_ECANTWRITE
Can't write.
int NC4_create(const char *path, int cmode, size_t initialsz, int basepe, size_t *chunksizehintp, int use_parallel, void *parameters, NC_Dispatch *dispatch, NC *nc_file)
Create a netCDF-4/HDF5 file.
#define NC_UBYTE
unsigned 1 byte int
#define NC_CLASSIC_MODEL
Enforce classic model on netCDF-4.
#define NC_MAX_VAR_DIMS
max per variable dimensions
#define NC_UINT
unsigned 4-byte int
#define NC_NOCLOBBER
Don't destroy existing file.
#define NC_INMEMORY
Read from memory.
#define NC_EHDFERR
Error at HDF5 layer.
#define NC_OPAQUE
opaque types
#define NC_MPIIO
Turn on MPI I/O.
#define NC_INT64
signed 8-byte int
#define NC_ENOTINDEFINE
Operation not allowed in data mode.
#define NC_DOUBLE
double precision floating point number
#define NC_EBADCLASS
Bad class.
int nc_type
The nc_type type is just an int.
#define NC_64BIT_OFFSET
Use large (64-bit) file offsets.
#define NC_NOWRITE
Set read-only access for nc_open().
#define NC_BYTE
signed 1 byte integer
#define NC_EINDEFINE
Operation not allowed in define mode.
#define NC_ENOTNC
Not a netcdf file.
#define NC_FORMAT_CDF5
Format specifier for nc_set_default_format() and returned by nc_inq_format.
#define NC_ENOTBUILT
Attempt to use feature that was not turned on when netCDF was built.
#define NC_ENDIAN_LITTLE
In HDF5 files you can set the endianness of variables with nc_def_var_endian().
#define NC_EATTMETA
Problem with attribute metadata.
#define NC_VLEN
vlen (variable-length) types
#define NC_EMPI
MPI operation failed.
#define NC_EDISKLESS
Error in using diskless access.
#define NC_EFILEMETA
Problem with file metadata.
#define NC_EBADTYPE
Not a netcdf data type.
#define NC_EBADNAME
Attribute or variable name contains illegal characters.
#define NC_EDIMMETA
Problem with dimension metadata.
#define NC_EINVAL
Invalid Argument.
#define NC_INT
signed 4 byte integer
#define NC_EBADGRPID
Bad group ID.
#define NC_NOFILL
Argument to nc_set_fill() to turn off filling of data.
#define NC_ENDIAN_BIG
In HDF5 files you can set the endianness of variables with nc_def_var_endian().
#define NC_MAX_NAME
Maximum for classic library.
#define NC_ECANTREMOVE
Can't remove file.
#define NC_NAT
Not A Type.
#define NC_EBADTYPID
Bad type ID.
#define NC_USHORT
unsigned 2-byte int
#define NC_EPARINIT
Error initializing for parallel access.
#define NC_NETCDF4
Use netCDF-4/HDF5 format.
#define NC_EEXIST
netcdf file exists && NC_NOCLOBBER
#define NC_FORMAT_NETCDF4_CLASSIC
Format specifier for nc_set_default_format() and returned by nc_inq_format.
#define NC_EBADID
Not a netcdf id.
#define NC_EVARMETA
Problem with variable metadata.
This is the type of arrays of vlens.
struct NC4_rec_read_metadata_ud NC4_rec_read_metadata_ud_t
User data struct for call to H5Literate() in nc4_rec_read_metadata()
#define NC_MAX_UINT
Max or min values for a type.
#define NC_SHORT
signed 2 byte integer
#define NC_CDF5
Alias NC_CDF5 to NC_64BIT_DATA.
#define NC_WRITE
Set read-write access for nc_open().
#define NC_EMAXNAME
NC_MAX_NAME exceeded.
#define NC_EPERM
Write to read only.
#define NC_MAX_HDF4_NAME
This is the max size of an SD dataset name in HDF4 (from HDF4 documentation).
#define NC_NOERR
No Error.
#define NC_ENUM
enum types
#define NC_DISKLESS
Use diskless file.
struct NC4_rec_read_metadata_obj_info NC4_rec_read_metadata_obj_info_t
Struct to track information about objects in a group, for nc4_rec_read_metadata() ...
#define NC_COMPOUND
compound types
#define NC_FORMAT_64BIT_OFFSET
Format specifier for nc_set_default_format() and returned by nc_inq_format.
#define NC_MMAP
Use diskless file with mmap.
#define NC_FILL
Argument to nc_set_fill() to clear NC_NOFILL.
#define NC_FLOAT
single precision floating point number
#define NC_UINT64
unsigned 8-byte int
#define NC_MPIPOSIX
Turn on MPI POSIX I/O.