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[] = {
104 #ifdef ENABLE_FILEINFO
112 #ifdef ENABLE_FILEINFO
114 const char* NC_RESERVED_SPECIAL_LIST[] = {
124 size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE;
125 size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS;
126 float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION;
131 static hid_t h5_native_type_constant_g[NUM_TYPES];
132 static const char nc_type_name_g[NUM_TYPES][
NC_MAX_NAME + 1] = {
"char",
"byte",
"short",
133 "int",
"float",
"double",
"ubyte",
134 "ushort",
"uint",
"int64",
140 static const int nc_type_size_g[NUM_TYPES] = {
sizeof(char),
sizeof(
char),
sizeof(short),
141 sizeof(
int),
sizeof(float),
sizeof(
double),
sizeof(
unsigned char),
142 sizeof(
unsigned short),
sizeof(
unsigned int),
sizeof(
long long),
143 sizeof(
unsigned long long),
sizeof(
char *)};
148 nc_set_chunk_cache(
size_t size,
size_t nelems,
float preemption)
150 if (preemption < 0 || preemption > 1)
152 nc4_chunk_cache_size = size;
153 nc4_chunk_cache_nelems = nelems;
154 nc4_chunk_cache_preemption = preemption;
161 nc_get_chunk_cache(
size_t *sizep,
size_t *nelemsp,
float *preemptionp)
164 *sizep = nc4_chunk_cache_size;
167 *nelemsp = nc4_chunk_cache_nelems;
170 *preemptionp = nc4_chunk_cache_preemption;
176 nc_set_chunk_cache_ints(
int size,
int nelems,
int preemption)
178 if (size <= 0 || nelems <= 0 || preemption < 0 || preemption > 100)
180 nc4_chunk_cache_size = size;
181 nc4_chunk_cache_nelems = nelems;
182 nc4_chunk_cache_preemption = (float)preemption / 100;
187 nc_get_chunk_cache_ints(
int *sizep,
int *nelemsp,
int *preemptionp)
190 *sizep = (int)nc4_chunk_cache_size;
192 *nelemsp = (int)nc4_chunk_cache_nelems;
194 *preemptionp = (int)(nc4_chunk_cache_preemption * 100);
224 #define MAGIC_NUMBER_LEN 4
225 #define NC_HDF5_FILE 1
226 #define NC_HDF4_FILE 2
228 nc_check_for_hdf(
const char *path,
int flags,
void* parameters,
int *hdf_file)
230 char blob[MAGIC_NUMBER_LEN];
233 NC_MPI_INFO* mpiinfo = (NC_MPI_INFO*)parameters;
234 MPI_Comm comm = MPI_COMM_WORLD;
235 MPI_Info info = MPI_INFO_NULL;
239 NC_MEM_INFO* meminfo = (NC_MEM_INFO*)parameters;
244 comm = mpiinfo->comm;
245 info = mpiinfo->info;
250 LOG((3,
"%s: path %s", __func__, path));
253 if(!inmemory && H5Fis_hdf5(path))
255 *hdf_file = NC_HDF5_FILE;
261 if (!inmemory && use_parallel)
266 if ((retval = MPI_File_open(comm, (
char *)path, MPI_MODE_RDONLY,
267 info, &fh)) != MPI_SUCCESS)
269 if ((retval = MPI_File_read(fh, blob, MAGIC_NUMBER_LEN, MPI_CHAR,
270 &status)) != MPI_SUCCESS)
272 if ((retval = MPI_File_close(&fh)) != MPI_SUCCESS)
279 if (!(fp = fopen(path,
"r")) ||
280 fread(blob, MAGIC_NUMBER_LEN, 1, fp) != 1) {
287 if(meminfo->size < MAGIC_NUMBER_LEN)
289 memcpy(blob,meminfo->memory,MAGIC_NUMBER_LEN);
293 if (memcmp(blob,
"\016\003\023\001", 4)==0)
294 *hdf_file = NC_HDF4_FILE;
295 else if (memcmp(blob,
"HDF", 3)==0)
296 *hdf_file = NC_HDF5_FILE;
306 nc4_create_file(
const char *path,
int cmode, MPI_Comm comm, MPI_Info info,
309 hid_t fcpl_id, fapl_id = -1;
313 NC_HDF5_FILE_INFO_T* nc4_info = NULL;
324 flags = H5F_ACC_TRUNC;
326 flags = H5F_ACC_EXCL;
328 flags = H5F_ACC_TRUNC;
330 LOG((3,
"%s: path %s mode 0x%x", __func__, path, cmode));
335 if (cmode & NC_DISKLESS) {
336 #ifndef USE_PARALLEL4
340 }
else if ((cmode & NC_NOCLOBBER) && (fp = fopen(path,
"r"))) {
346 if ((retval = nc4_nc4f_list_add(nc, path, (
NC_WRITE | cmode))))
348 nc4_info = NC4_DATA(nc);
349 assert(nc4_info && nc4_info->root_grp);
354 if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
360 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
363 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG))
372 nc4_info->parallel = NC_TRUE;
373 if (cmode & NC_MPIIO)
375 LOG((4,
"creating parallel file with MPI/IO"));
376 if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
379 #ifdef USE_PARALLEL_POSIX
382 LOG((4,
"creating parallel file with MPI/posix"));
383 if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
396 if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
399 if (MPI_INFO_NULL != info)
401 if (MPI_SUCCESS != MPI_Info_dup(info, &nc4_info->info))
408 nc4_info->info = info;
412 if(cmode & NC_DISKLESS) {
413 if (H5Pset_fapl_core(fapl_id, 4096, persist))
416 if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
417 nc4_chunk_cache_preemption) < 0)
419 LOG((4,
"%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
420 __func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
423 #ifdef HDF5_HAS_LIBVER_BOUNDS
424 if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST) < 0)
429 if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0)
436 if (H5Pset_obj_track_times(fcpl_id,0)<0)
442 if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
443 H5P_CRT_ORDER_INDEXED)) < 0)
445 if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
446 H5P_CRT_ORDER_INDEXED)) < 0)
450 if ((nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0)
456 if ((nc4_info->root_grp->hdf_grpid = H5Gopen2(nc4_info->hdfid,
"/",
461 if (H5Pclose(fapl_id) < 0 || H5Pclose(fcpl_id) < 0)
469 nc4_info->flags |= NC_INDEF;
471 #ifdef ENABLE_FILEINFO
472 NC4_get_fileinfo(nc4_info,&globalpropinfo);
473 NC4_put_propattr(nc4_info);
480 if (comm_duped) MPI_Comm_free(&nc4_info->comm);
481 if (info_duped) MPI_Info_free(&nc4_info->info);
486 if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
487 if(!nc4_info)
return retval;
488 close_netcdf4_file(nc4_info,1);
508 NC4_create(
const char* path,
int cmode,
size_t initialsz,
int basepe,
509 size_t *chunksizehintp,
int use_parallel,
void *parameters,
510 NC_Dispatch *dispatch, NC* nc_file)
512 MPI_Comm comm = MPI_COMM_WORLD;
513 MPI_Info info = MPI_INFO_NULL;
517 assert(nc_file && path);
519 LOG((1,
"%s: path %s cmode 0x%x comm %d info %d",
520 __func__, path, cmode, comm, info));
525 comm = ((NC_MPI_INFO *)parameters)->comm;
526 info = ((NC_MPI_INFO *)parameters)->info;
531 if (!nc4_hdf5_initialized)
532 nc4_hdf5_initialize();
535 if((cmode & ILLEGAL_CREATE_FLAGS) != 0)
539 if((cmode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
543 if((cmode & (NC_MPIIO | NC_MPIPOSIX)) && (cmode & NC_DISKLESS))
546 #ifndef USE_PARALLEL_POSIX
550 if(cmode & NC_MPIPOSIX)
552 cmode &= ~NC_MPIPOSIX;
567 LOG((2,
"cmode after applying default format: 0x%x", cmode));
569 nc_file->int_ncid = nc_file->ext_ncid;
570 res = nc4_create_file(path, cmode, comm, info, nc_file);
581 read_scale(NC_GRP_INFO_T *grp, hid_t datasetid,
const char *obj_name,
582 const H5G_stat_t *statbuf, hsize_t scale_size, hsize_t max_scale_size,
585 NC_DIM_INFO_T *new_dim;
587 htri_t attr_exists = -1;
589 int dimscale_created = 0;
590 int initial_grp_ndims = grp->ndims;
591 short initial_next_dimid = grp->nc4_info->next_dimid;
595 if ((retval = nc4_dim_list_add(&grp->dim, &new_dim)))
601 if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
605 if ((attid = H5Aopen_name(datasetid, NC_DIMID_ATT_NAME)) < 0)
608 if (H5Aread(attid, H5T_NATIVE_INT, &new_dim->dimid) < 0)
612 if (new_dim->dimid >= grp->nc4_info->next_dimid)
613 grp->nc4_info->next_dimid = new_dim->dimid + 1;
618 new_dim->dimid = grp->nc4_info->next_dimid++;
624 if (!(new_dim->name = strdup(obj_name)))
629 new_dim->too_long = NC_TRUE;
632 new_dim->len = scale_size;
633 new_dim->hdf5_objid.fileno[0] = statbuf->fileno[0];
634 new_dim->hdf5_objid.fileno[1] = statbuf->fileno[1];
635 new_dim->hdf5_objid.objno[0] = statbuf->objno[0];
636 new_dim->hdf5_objid.objno[1] = statbuf->objno[1];
637 new_dim->hash = hash_fast(obj_name, strlen(obj_name));
641 if (max_scale_size == H5S_UNLIMITED)
642 new_dim->unlimited = NC_TRUE;
647 if (H5DSget_scale_name(datasetid, dimscale_name_att,
NC_MAX_NAME) >= 0)
649 if (!strncmp(dimscale_name_att, DIM_WITHOUT_VARIABLE,
650 strlen(DIM_WITHOUT_VARIABLE)))
652 if (new_dim->unlimited)
654 size_t len = 0, *lenp = &len;
656 if ((retval = nc4_find_dim_len(grp, new_dim->dimid, &lenp)))
658 new_dim->len = *lenp;
662 new_dim->hdf_dimscaleid = datasetid;
663 H5Iinc_ref(new_dim->hdf_dimscaleid);
672 if (attid > 0 && H5Aclose(attid) < 0)
676 if (retval < 0 && dimscale_created)
679 if ((retval = nc4_dim_list_del(&grp->dim, new_dim)))
683 grp->ndims = initial_grp_ndims;
684 grp->nc4_info->next_dimid = initial_next_dimid;
693 read_coord_dimids(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
695 hid_t coord_att_typeid = -1, coord_attid = -1, spaceid = -1;
703 if ((coord_attid = H5Aopen_name(var->hdf_datasetid, COORDINATES)) < 0) ret++;
704 if (!ret && (coord_att_typeid = H5Aget_type(coord_attid)) < 0) ret++;
707 if (!ret && (spaceid = H5Aget_space(coord_attid)) < 0) ret++;
711 if (!ret && (npoints = H5Sget_simple_extent_npoints(spaceid)) < 0) ret++;
715 if (!ret && npoints != var->ndims) ret++;
717 if (!ret && H5Aread(coord_attid, coord_att_typeid, var->dimids) < 0) ret++;
718 LOG((4,
"dimscale %s is multidimensional and has coords", var->name));
721 for (d = 0; d < var->ndims; d++) {
723 nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
727 if (spaceid >= 0 && H5Sclose(spaceid) < 0) ret++;
731 if (coord_att_typeid >= 0 && H5Tclose(coord_att_typeid) < 0) ret++;
732 if (coord_attid >= 0 && H5Aclose(coord_attid) < 0) ret++;
739 dimscale_visitor(hid_t did,
unsigned dim, hid_t dsid,
740 void *dimscale_hdf5_objids)
745 if (H5Gget_objinfo(dsid,
".", 1, &statbuf) < 0)
749 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[0] = statbuf.fileno[0];
750 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[1] = statbuf.fileno[1];
751 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[0] = statbuf.objno[0];
752 (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[1] = statbuf.objno[1];
758 get_netcdf_type(NC_HDF5_FILE_INFO_T *h5, hid_t native_typeid,
761 NC_TYPE_INFO_T *type;
763 htri_t is_str, equal = 0;
767 if ((
class = H5Tget_class(native_typeid)) < 0)
772 if (
class == H5T_STRING)
774 if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
782 else if (
class == H5T_INTEGER ||
class == H5T_FLOAT)
786 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SCHAR)) < 0)
793 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SHORT)) < 0)
800 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_INT)) < 0)
807 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_FLOAT)) < 0)
814 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_DOUBLE)) < 0)
821 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UCHAR)) < 0)
828 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_USHORT)) < 0)
835 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UINT)) < 0)
842 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_LLONG)) < 0)
849 if ((equal = H5Tequal(native_typeid, H5T_NATIVE_ULLONG)) < 0)
860 if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
862 *xtype = type->nc_typeid;
874 get_type_info2(NC_HDF5_FILE_INFO_T *h5, hid_t datasetid,
875 NC_TYPE_INFO_T **type_info)
877 htri_t is_str, equal = 0;
879 hid_t native_typeid, hdf_typeid;
883 assert(h5 && type_info);
891 if (!h5_native_type_constant_g[1])
893 h5_native_type_constant_g[1] = H5T_NATIVE_SCHAR;
894 h5_native_type_constant_g[2] = H5T_NATIVE_SHORT;
895 h5_native_type_constant_g[3] = H5T_NATIVE_INT;
896 h5_native_type_constant_g[4] = H5T_NATIVE_FLOAT;
897 h5_native_type_constant_g[5] = H5T_NATIVE_DOUBLE;
898 h5_native_type_constant_g[6] = H5T_NATIVE_UCHAR;
899 h5_native_type_constant_g[7] = H5T_NATIVE_USHORT;
900 h5_native_type_constant_g[8] = H5T_NATIVE_UINT;
901 h5_native_type_constant_g[9] = H5T_NATIVE_LLONG;
902 h5_native_type_constant_g[10] = H5T_NATIVE_ULLONG;
906 if ((hdf_typeid = H5Dget_type(datasetid)) < 0)
911 if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
915 if ((
class = H5Tget_class(native_typeid)) < 0)
919 if (
class == H5T_STRING ||
class == H5T_INTEGER ||
class == H5T_FLOAT)
922 if (!(*type_info = calloc(1,
sizeof(NC_TYPE_INFO_T))))
927 if (
class == H5T_STRING)
929 if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
932 if (is_str || H5Tget_size(hdf_typeid) > 1)
942 (*type_info)->nc_type_class =
NC_CHAR;
945 else if (
class == H5T_INTEGER ||
class == H5T_FLOAT)
947 for (t = 1; t < NUM_TYPES - 1; t++)
949 if ((equal = H5Tequal(native_typeid, h5_native_type_constant_g[t])) < 0)
961 if((order = H5Tget_order(hdf_typeid)) < 0)
964 if(order == H5T_ORDER_LE)
966 else if(order == H5T_ORDER_BE)
971 if(
class == H5T_INTEGER)
972 (*type_info)->nc_type_class =
NC_INT;
974 (*type_info)->nc_type_class =
NC_FLOAT;
976 (*type_info)->nc_typeid = nc_type_constant_g[t];
977 (*type_info)->size = nc_type_size_g[t];
978 if (!((*type_info)->name = strdup(nc_type_name_g[t])))
980 (*type_info)->hdf_typeid = hdf_typeid;
981 (*type_info)->native_hdf_typeid = native_typeid;
986 NC_TYPE_INFO_T *type;
989 if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
995 if (H5Tclose(native_typeid) < 0)
997 if (H5Tclose(hdf_typeid) < 0)
1009 read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
1011 hid_t spaceid = 0, file_typeid = 0;
1012 hsize_t dims[1] = {0};
1016 hssize_t att_npoints;
1017 H5T_class_t att_class;
1018 int fixed_len_string = 0;
1019 size_t fixed_size = 0;
1022 LOG((5,
"%s: att->attnum %d att->name %s att->nc_typeid %d att->len %d",
1023 __func__, att->attnum, att->name, (
int)att->nc_typeid, att->len));
1026 if ((file_typeid = H5Aget_type(attid)) < 0)
1028 if ((att->native_hdf_typeid = H5Tget_native_type(file_typeid, H5T_DIR_DEFAULT)) < 0)
1030 if ((att_class = H5Tget_class(att->native_hdf_typeid)) < 0)
1032 if (att_class == H5T_STRING && !H5Tis_variable_str(att->native_hdf_typeid))
1035 if (!(fixed_size = H5Tget_size(att->native_hdf_typeid)))
1038 if ((retval = get_netcdf_type(grp->nc4_info, att->native_hdf_typeid, &(att->nc_typeid))))
1043 if ((spaceid = H5Aget_space(attid)) < 0)
1048 if ((att_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
1050 if ((att_npoints = H5Sget_simple_extent_npoints(spaceid)) < 0)
1055 if (att_ndims == 0 && att_npoints == 0)
1058 dims[0] = att_npoints;
1059 else if (att->nc_typeid ==
NC_CHAR)
1065 if (!(dims[0] = H5Tget_size(file_typeid)))
1072 dims[0] = att_npoints;
1077 H5S_class_t space_class;
1084 if ((space_class = H5Sget_simple_extent_type(spaceid)) < 0)
1088 if (H5S_NULL == space_class)
1092 if (H5S_SCALAR == space_class)
1097 if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0)
1109 if ((retval = nc4_get_typelen_mem(grp->nc4_info, att->nc_typeid, 0,
1112 if (att_class == H5T_VLEN)
1114 if (!(att->vldata = malloc((
unsigned int)(att->len *
sizeof(hvl_t)))))
1116 if (H5Aread(attid, att->native_hdf_typeid, att->vldata) < 0)
1121 if (!(att->stdata = calloc(att->len,
sizeof(
char *))))
1134 if (fixed_len_string)
1137 char *contig_buf, *cur;
1140 if (!(contig_buf = malloc(att->len * fixed_size *
sizeof(
char))))
1144 if (H5Aread(attid, att->native_hdf_typeid, contig_buf) < 0) {
1153 for (i = 0; i < att->len; i++)
1155 if (!(att->stdata[i] = malloc(fixed_size))) {
1159 strncpy(att->stdata[i], cur, fixed_size);
1169 if (H5Aread(attid, att->native_hdf_typeid, att->stdata) < 0)
1175 if (!(att->data = malloc((
unsigned int)(att->len * type_size))))
1177 if (H5Aread(attid, att->native_hdf_typeid, att->data) < 0)
1182 if (H5Tclose(file_typeid) < 0)
1184 if (H5Sclose(spaceid) < 0)
1193 if (H5Tclose(file_typeid) < 0)
1195 if (spaceid > 0 && H5Sclose(spaceid) < 0)
1206 read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid,
char *type_name)
1208 NC_TYPE_INFO_T *type;
1210 hid_t native_typeid;
1214 assert(grp && type_name);
1216 LOG((4,
"%s: type_name %s grp->name %s", __func__, type_name, grp->name));
1219 if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
1223 if (!(type_size = H5Tget_size(native_typeid)))
1225 LOG((5,
"type_size %d", type_size));
1228 if ((retval = nc4_type_list_add(grp, type_size, type_name, &type)))
1232 type->committed = NC_TRUE;
1233 type->hdf_typeid = hdf_typeid;
1234 H5Iinc_ref(type->hdf_typeid);
1235 type->native_hdf_typeid = native_typeid;
1238 if ((
class = H5Tget_class(hdf_typeid)) < 0)
1250 char* member_name = NULL;
1257 if ((nmembers = H5Tget_nmembers(hdf_typeid)) < 0)
1259 LOG((5,
"compound type has %d members", nmembers));
1260 for (m = 0; m < nmembers; m++)
1262 hid_t member_hdf_typeid;
1263 hid_t member_native_typeid;
1264 size_t member_offset;
1265 H5T_class_t mem_class;
1271 if ((member_hdf_typeid = H5Tget_member_type(type->native_hdf_typeid, m)) < 0)
1274 if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid, H5T_DIR_DEFAULT)) < 0)
1278 member_name = H5Tget_member_name(type->native_hdf_typeid, m);
1279 if (!member_name || strlen(member_name) >
NC_MAX_NAME) {
1285 strncpy(jna,member_name,1000);
1291 member_offset = H5Tget_member_offset(type->native_hdf_typeid, m);
1294 if ((mem_class = H5Tget_class(member_hdf_typeid)) < 0)
1296 if (mem_class == H5T_ARRAY)
1302 if ((ndims = H5Tget_array_ndims(member_hdf_typeid)) < 0) {
1306 if (H5Tget_array_dims(member_hdf_typeid, dims, NULL) != ndims) {
1310 for (d = 0; d < ndims; d++)
1311 dim_size[d] = dims[d];
1314 if ((retval = get_netcdf_type(grp->nc4_info, H5Tget_super(member_hdf_typeid),
1319 if ((retval = nc4_field_list_add(&type->u.c.field, type->u.c.num_fields++, member_name,
1320 member_offset, H5Tget_super(member_hdf_typeid),
1321 H5Tget_super(member_native_typeid),
1322 member_xtype, ndims, dim_size)))
1328 if ((retval = get_netcdf_type(grp->nc4_info, member_native_typeid,
1333 if ((retval = nc4_field_list_add(&type->u.c.field, type->u.c.num_fields++, member_name,
1334 member_offset, member_hdf_typeid, member_native_typeid,
1335 member_xtype, 0, NULL)))
1346 #ifdef HDF5_HAS_H5FREE
1347 if(member_name != NULL) H5free_memory(member_name);
1350 if(member_name != NULL) free(member_name);
1357 if(member_name != NULL)
1373 if ((ret = H5Tis_variable_str(hdf_typeid)) < 0)
1379 hid_t base_hdf_typeid;
1382 type->nc_type_class =
NC_VLEN;
1386 if (!(base_hdf_typeid = H5Tget_super(native_typeid)))
1390 if (!(type_size = H5Tget_size(base_hdf_typeid)))
1394 if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
1397 LOG((5,
"base_hdf_typeid 0x%x type_size %d base_nc_type %d",
1398 base_hdf_typeid, type_size, base_nc_type));
1401 type->u.v.base_nc_typeid = base_nc_type;
1402 type->u.v.base_hdf_typeid = base_hdf_typeid;
1413 hid_t base_hdf_typeid;
1417 char *member_name = NULL;
1422 type->nc_type_class =
NC_ENUM;
1426 if (!(base_hdf_typeid = H5Tget_super(hdf_typeid)))
1429 if (!(type_size = H5Tget_size(base_hdf_typeid)))
1432 if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
1435 LOG((5,
"base_hdf_typeid 0x%x type_size %d base_nc_type %d",
1436 base_hdf_typeid, type_size, base_nc_type));
1439 type->u.e.base_nc_typeid = base_nc_type;
1440 type->u.e.base_hdf_typeid = base_hdf_typeid;
1443 if ((type->u.e.num_members = H5Tget_nmembers(hdf_typeid)) < 0)
1447 if (!(value = calloc(1, type_size)))
1451 for (i = 0; i < type->u.e.num_members; i++)
1455 if (!(member_name = H5Tget_member_name(hdf_typeid, i)))
1461 strncpy(jna,member_name,1000);
1470 if (H5Tget_member_value(hdf_typeid, i, value) < 0)
1477 if ((retval = nc4_enum_member_add(&type->u.e.enum_member, type->size,
1478 member_name, value)))
1485 if(member_name != NULL) free(member_name);
1491 if(member_name != NULL)
1494 if(value) free(value);
1501 LOG((0,
"unknown class"));
1512 read_var(NC_GRP_INFO_T *grp, hid_t datasetid,
const char *obj_name,
1513 size_t ndims, NC_DIM_INFO_T *dim)
1515 NC_VAR_INFO_T *var = NULL;
1516 hid_t access_pid = 0;
1519 const char** reserved;
1523 char att_name[NC_MAX_HDF5_NAME + 1];
1525 #define CD_NELEMS_ZLIB 1
1526 #define CD_NELEMS_SZIP 4
1527 H5Z_filter_t filter;
1529 unsigned int cd_values[CD_NELEMS_SZIP];
1530 size_t cd_nelems = CD_NELEMS_SZIP;
1532 H5D_fill_value_t fill_status;
1533 H5D_layout_t layout;
1539 assert(obj_name && grp);
1540 LOG((4,
"%s: obj_name %s", __func__, obj_name));
1543 if ((retval = nc4_var_list_add(&grp->var, &var)))
1547 var->hdf_datasetid = datasetid;
1548 H5Iinc_ref(var->hdf_datasetid);
1550 var->varid = grp->nvars++;
1551 var->created = NC_TRUE;
1558 if (!(var->dim = calloc(var->ndims,
sizeof(NC_DIM_INFO_T *))))
1560 if (!(var->dimids = calloc(var->ndims,
sizeof(
int))))
1565 if ((access_pid = H5Dget_access_plist(datasetid)) < 0)
1572 if ((H5Pget_chunk_cache(access_pid, &(var->chunk_cache_nelems),
1573 &(var->chunk_cache_size), &rdcc_w0)) < 0)
1575 var->chunk_cache_preemption = rdcc_w0;
1580 if (strlen(obj_name) > strlen(NON_COORD_PREPEND) &&
1581 !strncmp(obj_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)))
1584 if (!(var->name = malloc(((strlen(obj_name) - strlen(NON_COORD_PREPEND))+ 1) *
sizeof(
char))))
1587 strcpy(var->name, &obj_name[strlen(NON_COORD_PREPEND)]);
1590 if (!(var->hdf5_name = malloc((strlen(obj_name) + 1) *
sizeof(
char))))
1593 strcpy(var->hdf5_name, obj_name);
1598 if (!(var->name = malloc((strlen(obj_name) + 1) *
sizeof(
char))))
1601 strcpy(var->name, obj_name);
1604 var->hash = hash_fast(var->name, strlen(var->name));
1608 if ((propid = H5Dget_create_plist(datasetid)) < 0)
1615 if ((layout = H5Pget_layout(propid)) < -1)
1617 if (layout == H5D_CHUNKED)
1621 if (!(var->chunksizes = malloc(var->ndims *
sizeof(
size_t))))
1623 for (d = 0; d < var->ndims; d++)
1624 var->chunksizes[d] = chunksize[d];
1626 else if (layout == H5D_CONTIGUOUS || layout == H5D_COMPACT)
1627 var->contiguous = NC_TRUE;
1631 if ((num_filters = H5Pget_nfilters(propid)) < 0)
1633 for (f = 0; f < num_filters; f++)
1635 if ((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems,
1636 cd_values, 0, NULL, NULL)) < 0)
1640 case H5Z_FILTER_SHUFFLE:
1641 var->shuffle = NC_TRUE;
1644 case H5Z_FILTER_FLETCHER32:
1645 var->fletcher32 = NC_TRUE;
1648 case H5Z_FILTER_DEFLATE:
1649 var->deflate = NC_TRUE;
1650 if (cd_nelems != CD_NELEMS_ZLIB || cd_values[0] > MAX_DEFLATE_LEVEL)
1652 var->deflate_level = cd_values[0];
1655 case H5Z_FILTER_SZIP:
1656 var->szip = NC_TRUE;
1657 if (cd_nelems != CD_NELEMS_SZIP)
1659 var->options_mask = cd_values[0];
1660 var->pixels_per_block = cd_values[1];
1664 LOG((1,
"Yikes! Unknown filter type found on dataset!"));
1670 if ((retval = get_type_info2(grp->nc4_info, datasetid,
1675 var->type_info->rc++;
1678 if (H5Pfill_value_defined(propid, &fill_status) < 0)
1682 if (fill_status == H5D_FILL_VALUE_USER_DEFINED)
1685 if (!var->fill_value)
1687 if (var->type_info->nc_type_class ==
NC_VLEN)
1689 if (!(var->fill_value = malloc(
sizeof(
nc_vlen_t))))
1692 else if (var->type_info->nc_type_class ==
NC_STRING)
1694 if (!(var->fill_value = malloc(
sizeof(
char *))))
1699 assert(var->type_info->size);
1700 if (!(var->fill_value = malloc(var->type_info->size)))
1706 if (H5Pget_fill_value(propid, var->type_info->native_hdf_typeid,
1707 var->fill_value) < 0)
1711 var->no_fill = NC_TRUE;
1717 var->dimscale = NC_TRUE;
1720 if ((retval = read_coord_dimids(grp, var)))
1726 assert(0 == strcmp(var->name, dim->name));
1728 var->dimids[0] = dim->dimid;
1731 dim->coord_var = var;
1743 num_scales = H5DSget_num_scales(datasetid, 0);
1747 if (num_scales && ndims)
1751 if (NULL == (var->dimscale_attached = calloc(ndims,
sizeof(nc_bool_t))))
1756 if (NULL == (var->dimscale_hdf5_objids = malloc(ndims *
sizeof(
struct hdf5_objid))))
1758 for (d = 0; d < var->ndims; d++)
1760 if (H5DSiterate_scales(var->hdf_datasetid, d, NULL, dimscale_visitor,
1761 &(var->dimscale_hdf5_objids[d])) < 0)
1763 var->dimscale_attached[d] = NC_TRUE;
1770 if ((natts = H5Aget_num_attrs(var->hdf_datasetid)) < 0)
1772 for (a = 0; a < natts; a++)
1777 if (attid && H5Aclose(attid) < 0)
1781 if ((attid = H5Aopen_idx(var->hdf_datasetid, (
unsigned int)a)) < 0)
1783 if (H5Aget_name(attid, NC_MAX_HDF5_NAME, att_name) < 0)
1785 LOG((4,
"%s:: a %d att_name %s", __func__, a, att_name));
1788 for(reserved=NC_RESERVED_VARATT_LIST;*reserved;reserved++) {
1789 if (strcmp(att_name, *reserved)==0)
break;
1791 if(*reserved == NULL) {
1793 if ((retval = nc4_att_list_add(&var->att, &att)))
1797 att->attnum = var->natts++;
1798 if (!(att->name = strdup(att_name)))
1803 if ((retval = read_hdf5_att(grp, attid, att)))
1807 if ((retval = nc4_att_list_del(&var->att, att)))
1815 att->created = NC_TRUE;
1821 if ((retval = nc4_adjust_var_cache(grp, var)))
1827 if (incr_id_rc && H5Idec_ref(datasetid) < 0)
1829 if (var && nc4_var_list_del(&grp->var, var))
1832 if (access_pid && H5Pclose(access_pid) < 0)
1837 if (propid > 0 && H5Pclose(propid) < 0)
1842 if (attid > 0 && H5Aclose(attid) < 0)
1850 read_grp_atts(NC_GRP_INFO_T *grp)
1855 NC_TYPE_INFO_T *type;
1856 char obj_name[NC_MAX_HDF5_NAME + 1];
1861 num_obj = H5Aget_num_attrs(grp->hdf_grpid);
1862 for (i = 0; i < num_obj; i++)
1864 if ((attid = H5Aopen_idx(grp->hdf_grpid, (
unsigned int)i)) < 0)
1866 if (H5Aget_name(attid,
NC_MAX_NAME + 1, obj_name) < 0)
1868 LOG((3,
"reading attribute of _netCDF group, named %s", obj_name));
1871 if(grp->nc4_info->root_grp == grp) {
1872 const char** reserved = NC_RESERVED_ATT_LIST;
1874 for(;*reserved;reserved++) {
1875 if(strcmp(*reserved,obj_name)==0) {
1886 if(strcmp(obj_name, NC3_STRICT_ATT_NAME)==0)
1890 if ((retval = nc4_att_list_add(&grp->att, &att)))
1895 if (!(att->name = malloc((max_len + 1) *
sizeof(
char))))
1897 strncpy(att->name, obj_name, max_len);
1898 att->name[max_len] = 0;
1899 att->attnum = grp->natts++;
1900 retval = read_hdf5_att(grp, attid, att);
1902 if((retval = nc4_att_list_del(&grp->att, att)))
1907 att->created = NC_TRUE;
1908 if ((retval = nc4_find_type(grp->nc4_info, att->nc_typeid, &type)))
1919 if(H5Aclose(attid) < 0)
1928 read_dataset(NC_GRP_INFO_T *grp, hid_t datasetid,
const char *obj_name,
1929 const H5G_stat_t *statbuf)
1931 NC_DIM_INFO_T *dim = NULL;
1938 if ((spaceid = H5Dget_space(datasetid)) < 0)
1943 if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
1947 if ((is_scale = H5DSis_scale(datasetid)) < 0)
1951 hsize_t dims[H5S_MAX_RANK];
1952 hsize_t max_dims[H5S_MAX_RANK];
1955 if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0)
1959 if ((retval = read_scale(grp, datasetid, obj_name, statbuf, dims[0],
1960 max_dims[0], &dim)))
1967 if (NULL == dim || (dim && !dim->hdf_dimscaleid))
1968 if ((retval = read_var(grp, datasetid, obj_name, ndims, dim)))
1972 if (spaceid && H5Sclose(spaceid) <0)
1989 if (!(new_oinfo = calloc(1,
sizeof(*new_oinfo))))
1993 memcpy(new_oinfo, oinfo,
sizeof(*oinfo));
1998 (*tail)->next = new_oinfo;
2003 assert(NULL == *head);
2004 *head = *tail = new_oinfo;
2011 nc4_rec_read_metadata_cb(hid_t grpid,
const char *name,
const H5L_info_t *info,
2016 int retval = H5_ITER_CONT;
2019 memset(&oinfo, 0,
sizeof(oinfo));
2022 if ((oinfo.oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0)
2023 BAIL(H5_ITER_ERROR);
2026 if (H5Gget_objinfo(oinfo.oid,
".", 1, &oinfo.statbuf) < 0)
2027 BAIL(H5_ITER_ERROR);
2032 switch(oinfo.statbuf.type)
2035 LOG((3,
"found group %s", oinfo.oname));
2041 if (nc4_rec_read_metadata_cb_list_add(&udata->grps_head, &udata->grps_tail, &oinfo))
2042 BAIL(H5_ITER_ERROR);
2046 LOG((3,
"found dataset %s", oinfo.oname));
2050 if ((retval = read_dataset(udata->grp, oinfo.oid, oinfo.oname, &oinfo.statbuf)))
2058 BAIL(H5_ITER_ERROR);
2060 retval = H5_ITER_CONT;
2064 if (H5Oclose(oinfo.oid) < 0)
2065 BAIL(H5_ITER_ERROR);
2069 LOG((3,
"found datatype %s", oinfo.oname));
2072 if (read_type(udata->grp, oinfo.oid, oinfo.oname))
2073 BAIL(H5_ITER_ERROR);
2076 if (H5Oclose(oinfo.oid) < 0)
2077 BAIL(H5_ITER_ERROR);
2081 LOG((0,
"Unknown object class %d in %s!", oinfo.statbuf.type, __func__));
2082 BAIL(H5_ITER_ERROR);
2088 if (oinfo.oid > 0 && H5Oclose(oinfo.oid) < 0)
2089 BAIL2(H5_ITER_ERROR);
2103 nc4_rec_read_metadata(NC_GRP_INFO_T *grp)
2109 unsigned crt_order_flags = 0;
2110 H5_index_t iter_index;
2113 assert(grp && grp->name);
2114 LOG((3,
"%s: grp->name %s", __func__, grp->name));
2117 memset(&udata, 0,
sizeof(udata));
2121 if (!grp->hdf_grpid)
2125 if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid,
2126 grp->name, H5P_DEFAULT)) < 0)
2131 if ((grp->hdf_grpid = H5Gopen2(grp->nc4_info->hdfid,
2132 "/", H5P_DEFAULT)) < 0)
2136 assert(grp->hdf_grpid > 0);
2139 pid = H5Gget_create_plist(grp->hdf_grpid);
2140 H5Pget_link_creation_order(pid, &crt_order_flags);
2141 if (H5Pclose(pid) < 0)
2145 if (crt_order_flags & H5P_CRT_ORDER_TRACKED)
2146 iter_index = H5_INDEX_CRT_ORDER;
2149 NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
2155 iter_index = H5_INDEX_NAME;
2164 if (H5Literate(grp->hdf_grpid, iter_index, H5_ITER_INC, &idx,
2165 nc4_rec_read_metadata_cb, (
void *)&udata) < 0)
2172 for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
2174 NC_GRP_INFO_T *child_grp;
2175 NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
2178 if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++,
2179 grp, grp->nc4_info->controller, oinfo->oname, &child_grp)))
2183 if ((retval = nc4_rec_read_metadata(child_grp)))
2187 if (H5Oclose(oinfo->oid) < 0)
2191 udata.grps_head = oinfo->next;
2196 if ((retval = read_grp_atts(grp)))
2203 for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
2206 if (H5Oclose(oinfo->oid) < 0)
2210 udata.grps_head = oinfo->next;
2222 nc4_open_file(
const char *path,
int mode,
void* parameters, NC *nc)
2224 hid_t fapl_id = H5P_DEFAULT;
2225 unsigned flags = (mode &
NC_WRITE) ?
2226 H5F_ACC_RDWR : H5F_ACC_RDONLY;
2228 NC_HDF5_FILE_INFO_T* nc4_info = NULL;
2231 NC_MEM_INFO* meminfo = (NC_MEM_INFO*)parameters;
2233 #ifdef USE_PARALLEL4
2234 NC_MPI_INFO* mpiinfo = (NC_MPI_INFO*)parameters;
2239 LOG((3,
"%s: path %s mode %d", __func__, path, mode));
2243 if ((retval = nc4_nc4f_list_add(nc, path, mode)))
2245 nc4_info = NC4_DATA(nc);
2246 assert(nc4_info && nc4_info->root_grp);
2251 if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
2258 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
2261 if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG))
2265 #ifdef USE_PARALLEL4
2268 if (mode & NC_MPIIO || mode & NC_MPIPOSIX)
2270 nc4_info->parallel = NC_TRUE;
2271 if (mode & NC_MPIIO)
2273 LOG((4,
"opening parallel file with MPI/IO"));
2274 if (H5Pset_fapl_mpio(fapl_id, mpiinfo->comm, mpiinfo->info) < 0)
2277 #ifdef USE_PARALLEL_POSIX
2280 LOG((4,
"opening parallel file with MPI/posix"));
2281 if (H5Pset_fapl_mpiposix(fapl_id, mpiinfo->comm, 0) < 0)
2294 if (MPI_SUCCESS != MPI_Comm_dup(mpiinfo->comm, &nc4_info->comm))
2297 if (MPI_INFO_NULL != mpiinfo->info)
2299 if (MPI_SUCCESS != MPI_Info_dup(mpiinfo->info, &nc4_info->info))
2306 nc4_info->info = mpiinfo->info;
2310 if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
2311 nc4_chunk_cache_preemption) < 0)
2313 LOG((4,
"%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
2314 __func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
2321 if((nc4_info->hdfid = H5LTopen_file_image(meminfo->memory,meminfo->size,
2322 H5LT_FILE_IMAGE_DONT_COPY|H5LT_FILE_IMAGE_DONT_RELEASE
2325 nc4_info->no_write = NC_TRUE;
2326 }
else if ((nc4_info->hdfid = H5Fopen(path, flags, fapl_id)) < 0)
2331 nc4_info->no_write = NC_TRUE;
2337 if ((retval = nc4_rec_read_metadata(nc4_info->root_grp)))
2342 if ((retval = nc4_rec_match_dimscales(nc4_info->root_grp)))
2348 log_metadata_nc(nc);
2352 if (H5Pclose(fapl_id) < 0)
2358 #ifdef ENABLE_FILEINFO
2359 NC4_get_fileinfo(nc4_info,NULL);
2365 #ifdef USE_PARALLEL4
2366 if (comm_duped) MPI_Comm_free(&nc4_info->comm);
2367 if (info_duped) MPI_Info_free(&nc4_info->info);
2372 if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
2373 if (!nc4_info)
return retval;
2374 close_netcdf4_file(nc4_info,1);
2393 get_netcdf_type_from_hdf4(NC_HDF5_FILE_INFO_T *h5, int32 hdf4_typeid,
2394 nc_type *xtype, NC_TYPE_INFO_T *type_info)
2406 assert(h5 && xtype);
2494 if (hdf4_typeid == DFNT_FLOAT32)
2495 type_info->nc_type_class =
NC_FLOAT;
2496 else if (hdf4_typeid == DFNT_FLOAT64)
2498 else if (hdf4_typeid == DFNT_CHAR)
2501 type_info->nc_type_class =
NC_INT;
2502 type_info->endianness = endianness;
2503 type_info->nc_typeid = *xtype;
2504 type_info->size = nc_type_size_g[t];
2505 if (!(type_info->name = strdup(nc_type_name_g[t])))
2515 nc4_open_hdf4_file(
const char *path,
int mode, NC *nc)
2517 NC_HDF5_FILE_INFO_T *h5;
2520 int32 num_datasets, num_gatts;
2524 NC_HDF5_FILE_INFO_T* nc4_info = NULL;
2526 LOG((3,
"%s: path %s mode %d", __func__, path, mode));
2530 if (mode & NC_WRITE)
2534 if ((retval = nc4_nc4f_list_add(nc, path, mode)))
2536 nc4_info = NC4_DATA(nc);
2537 assert(nc4_info && nc4_info->root_grp);
2541 h5->no_write = NC_TRUE;
2544 if ((h5->sdid = SDstart(path, DFACC_READ)) == FAIL)
2548 if (SDfileinfo(h5->sdid, &num_datasets, &num_gatts))
2552 for (a = 0; a < num_gatts; a++)
2554 int32 att_data_type, att_count;
2555 size_t att_type_size;
2558 if ((retval = nc4_att_list_add(&h5->root_grp->att, &att)))
2560 att->attnum = grp->natts++;
2561 att->created = NC_TRUE;
2566 if (SDattrinfo(h5->sdid, a, att->name, &att_data_type, &att_count))
2568 if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type,
2569 &att->nc_typeid, NULL)))
2571 att->len = att_count;
2574 if ((retval = nc4_get_typelen_mem(h5, att->nc_typeid, 0, &att_type_size)))
2576 if (!(att->data = malloc(att_type_size * att->len)))
2580 if (SDreadattr(h5->sdid, a, att->data))
2585 for (v = 0; v < num_datasets; v++)
2588 int32 data_type, num_atts;
2597 int32 *dimsize = NULL;
2598 size_t var_type_size;
2602 if ((retval = nc4_var_list_add(&grp->var, &var)))
2605 var->varid = grp->nvars++;
2606 var->created = NC_TRUE;
2607 var->written_to = NC_TRUE;
2610 if ((var->sdsid = SDselect(h5->sdid, v)) == FAIL)
2618 if (SDgetinfo(var->sdsid, var->name, &rank, NULL, &data_type, &num_atts))
2621 var->hash = hash_fast(var->name, strlen(var->name));
2623 if(!(dimsize = (int32*)malloc(
sizeof(int32)*rank)))
2626 if (SDgetinfo(var->sdsid, var->name, &rank, dimsize, &data_type, &num_atts)) {
2627 if(dimsize) free(dimsize);
2632 var->hdf4_data_type = data_type;
2635 if (!(var->type_info = calloc(1,
sizeof(NC_TYPE_INFO_T)))) {
2636 if(dimsize) free(dimsize);
2640 if ((retval = get_netcdf_type_from_hdf4(h5, data_type, &var->type_info->nc_typeid, var->type_info))) {
2641 if(dimsize) free(dimsize);
2646 var->type_info->rc++;
2648 if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0, &var_type_size))) {
2649 if(dimsize) free(dimsize);
2653 var->type_info->size = var_type_size;
2654 LOG((3,
"reading HDF4 dataset %s, rank %d netCDF type %d", var->name,
2655 rank, var->type_info->nc_typeid));
2658 if (!(var->fill_value = malloc(var_type_size))) {
2659 if(dimsize) free(dimsize);
2663 if (SDgetfillvalue(var->sdsid, var->fill_value))
2666 free(var->fill_value);
2667 var->fill_value = NULL;
2673 if (!(var->dim = malloc(
sizeof(NC_DIM_INFO_T *) * var->ndims))) {
2674 if(dimsize) free(dimsize);
2678 if (!(var->dimids = malloc(
sizeof(
int) * var->ndims))) {
2679 if(dimsize) free(dimsize);
2686 for (d = 0; d < var->ndims; d++)
2688 int32 dimid, dim_len, dim_data_type, dim_num_attrs;
2692 if ((dimid = SDgetdimid(var->sdsid, d)) == FAIL) {
2693 if(dimsize) free(dimsize);
2696 if (SDdiminfo(dimid, dim_name, &dim_len, &dim_data_type,
2699 if(dimsize) free(dimsize);
2705 for (dim = grp->dim; dim; dim = dim->l.next)
2706 if (!strcmp(dim->name, dim_name))
2712 LOG((4,
"adding dimension %s for HDF4 dataset %s",
2713 dim_name, var->name));
2714 if ((retval = nc4_dim_list_add(&grp->dim, &dim)))
2717 dim->dimid = grp->nc4_info->next_dimid++;
2720 if (!(dim->name = strdup(dim_name)))
2725 dim->len = *dimsize;
2726 dim->hash = hash_fast(dim_name, strlen(dim_name));
2730 var->dimids[d] = dim->dimid;
2735 for (a = 0; a < num_atts; a++)
2737 int32 att_data_type, att_count;
2738 size_t att_type_size;
2741 if ((retval = nc4_att_list_add(&var->att, &att))) {
2742 if(dimsize) free(dimsize);
2745 att->attnum = var->natts++;
2746 att->created = NC_TRUE;
2750 if(dimsize) free(dimsize);
2753 if (SDattrinfo(var->sdsid, a, att->name, &att_data_type, &att_count)) {
2754 if(dimsize) free(dimsize);
2757 if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type,
2758 &att->nc_typeid, NULL))) {
2759 if(dimsize) free(dimsize);
2763 att->len = att_count;
2766 if ((retval = nc4_get_typelen_mem(h5, att->nc_typeid, 0, &att_type_size))) {
2767 if(dimsize) free(dimsize);
2770 if (!(att->data = malloc(att_type_size * att->len))) {
2771 if(dimsize) free(dimsize);
2776 if (SDreadattr(var->sdsid, a, att->data)) {
2777 if(dimsize) free(dimsize);
2781 if(dimsize) free(dimsize);
2785 HDF_CHUNK_DEF chunkdefs;
2787 if(!SDgetchunkinfo(var->sdsid, &chunkdefs, &flag)) {
2788 if(flag == HDF_NONE)
2789 var->contiguous = NC_TRUE;
2790 else if((flag & HDF_CHUNK) != 0) {
2791 var->contiguous = NC_FALSE;
2792 if (!(var->chunksizes = malloc(var->ndims *
sizeof(
size_t))))
2794 for (d = 0; d < var->ndims; d++) {
2795 var->chunksizes[d] = chunkdefs.chunk_lengths[d];
2806 log_metadata_nc(h5->root_grp->nc4_info->controller);
2814 NC4_open(
const char *path,
int mode,
int basepe,
size_t *chunksizehintp,
2815 int use_parallel,
void *parameters, NC_Dispatch *dispatch, NC *nc_file)
2819 #ifdef USE_PARALLEL4
2820 NC_MPI_INFO mpidfalt = {MPI_COMM_WORLD, MPI_INFO_NULL};
2822 #if defined USE_PARALLEL4 || defined USE_HDF4
2826 assert(nc_file && path);
2828 LOG((1,
"%s: path %s mode %d params %x",
2829 __func__, path, mode, parameters));
2831 #ifdef USE_PARALLEL4
2832 if (!inmemory && use_parallel && parameters == NULL)
2833 parameters = &mpidfalt;
2837 if (!nc4_hdf5_initialized)
2838 nc4_hdf5_initialize();
2841 if((mode & ILLEGAL_OPEN_FLAGS) != 0)
2845 if((mode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
2848 #ifndef USE_PARALLEL_POSIX
2852 if(mode & NC_MPIPOSIX)
2854 mode &= ~NC_MPIPOSIX;
2860 if ((res = nc_check_for_hdf(path, use_parallel, parameters, &hdf_file)))
2864 nc_file->int_ncid = nc_file->ext_ncid;
2865 if (hdf_file == NC_HDF5_FILE)
2866 res = nc4_open_file(path, mode, parameters, nc_file);
2868 else if (hdf_file == NC_HDF4_FILE && inmemory)
2870 else if (hdf_file == NC_HDF4_FILE)
2871 res = nc4_open_hdf4_file(path, mode, nc_file);
2885 NC4_set_fill(
int ncid,
int fillmode,
int *old_modep)
2888 NC_HDF5_FILE_INFO_T* nc4_info;
2890 LOG((2,
"%s: ncid 0x%x fillmode %d", __func__, ncid, fillmode));
2892 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
2897 if (nc4_info->no_write)
2906 *old_modep = nc4_info->fill_mode;
2908 nc4_info->fill_mode = fillmode;
2919 NC_HDF5_FILE_INFO_T* nc4_info;
2921 LOG((1,
"%s: ncid 0x%x", __func__, ncid));
2924 if (!(nc4_find_nc_file(ncid,&nc4_info)))
2929 if (nc4_info->flags & NC_INDEF)
2933 if (nc4_info->no_write)
2937 nc4_info->flags |= NC_INDEF;
2941 nc4_info->redef = NC_TRUE;
2949 NC4__enddef(
int ncid,
size_t h_minfree,
size_t v_align,
2950 size_t v_minfree,
size_t r_align)
2952 if (nc4_find_nc_file(ncid,NULL) == NULL)
2955 return NC4_enddef(ncid);
2960 static int NC4_enddef(
int ncid)
2963 NC_HDF5_FILE_INFO_T* nc4_info;
2965 LOG((1,
"%s: ncid 0x%x", __func__, ncid));
2967 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
2971 return nc4_enddef_netcdf4_file(nc4_info);
2977 sync_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
2982 LOG((3,
"%s", __func__));
2986 if (h5->flags & NC_INDEF)
2992 h5->flags ^= NC_INDEF;
2995 h5->redef = NC_FALSE;
3001 log_metadata_nc(h5->root_grp->nc4_info->controller);
3007 nc_bool_t bad_coord_order = NC_FALSE;
3009 if ((retval = nc4_rec_write_groups_types(h5->root_grp)))
3011 if ((retval = nc4_rec_detect_need_to_preserve_dimids(h5->root_grp, &bad_coord_order)))
3013 if ((retval = nc4_rec_write_metadata(h5->root_grp, bad_coord_order)))
3017 if (H5Fflush(h5->hdfid, H5F_SCOPE_GLOBAL) < 0)
3030 NC_HDF5_FILE_INFO_T* nc4_info;
3032 LOG((2,
"%s: ncid 0x%x", __func__, ncid));
3034 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
3039 if (nc4_info && nc4_info->flags & NC_INDEF)
3043 if ((retval = NC4_enddef(ncid)))
3047 return sync_netcdf4_file(nc4_info);
3054 close_netcdf4_file(NC_HDF5_FILE_INFO_T *h5,
int abort)
3058 assert(h5 && h5->root_grp);
3059 LOG((3,
"%s: h5->path %s abort %d", __func__, h5->controller->path, abort));
3062 if (h5->flags & NC_INDEF)
3063 h5->flags ^= NC_INDEF;
3067 if (!h5->no_write && !abort)
3068 if ((retval = sync_netcdf4_file(h5)))
3073 if ((retval = nc4_rec_grp_del(&h5->root_grp, h5->root_grp)))
3080 if (SDend(h5->sdid))
3086 #ifdef USE_PARALLEL4
3090 if(MPI_COMM_NULL != h5->comm)
3091 MPI_Comm_free(&h5->comm);
3092 if(MPI_INFO_NULL != h5->info)
3093 MPI_Info_free(&h5->info);
3097 #ifdef ENABLE_FILEINFO
3098 if(h5->fileinfo) free(h5->fileinfo);
3101 if (H5Fclose(h5->hdfid) < 0)
3105 nobjs = H5Fget_obj_count(h5->hdfid, H5F_OBJ_ALL);
3109 }
else if(nobjs > 0) {
3117 snprintf(msg,
sizeof(msg),
"There are %d HDF5 objects open!", nobjs);
3121 fprintf(stdout,msg);
3124 reportopenobjects(logit,h5->hdfid);
3147 int delete_file = 0;
3150 NC_HDF5_FILE_INFO_T* nc4_info;
3152 LOG((2,
"%s: ncid 0x%x", __func__, ncid));
3155 if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
3161 if (nc4_info->flags & NC_INDEF && !nc4_info->redef)
3169 if ((retval = close_netcdf4_file(nc4_info, 1)))
3174 if (
remove(path) < 0)
3186 NC_HDF5_FILE_INFO_T *h5;
3189 LOG((1,
"%s: ncid 0x%x", __func__, ncid));
3192 if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
3195 assert(nc && h5 && grp);
3202 if ((retval = close_netcdf4_file(grp->nc4_info, 0)))
3211 NC4_inq(
int ncid,
int *ndimsp,
int *nvarsp,
int *nattsp,
int *unlimdimidp)
3214 NC_HDF5_FILE_INFO_T *h5;
3221 LOG((2,
"%s: ncid 0x%x", __func__, ncid));
3224 if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
3227 assert(h5 && grp && nc);
3233 for (dim = grp->dim; dim; dim = dim->l.next)
3239 for (var = grp->var; var; var= var->l.next)
3245 for (att = grp->att; att; att = att->l.next)
3258 for (dim = grp->dim; dim; dim = dim->l.next)
3261 *unlimdimidp = dim->dimid;
3271 nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
3274 LOG((3,
"%s", __func__));
3277 if (!(h5->flags & NC_INDEF))
3281 h5->flags ^= NC_INDEF;
3284 h5->redef = NC_FALSE;
3286 return sync_netcdf4_file(h5);
3293 if (num_plists || num_spaces)
3300 #ifdef USE_PARALLEL4
3302 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.