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Merged latest trunk changes into my branch.

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This commit is contained in:
Russ Rew 2010-10-04 16:53:34 +00:00
commit 4b3ea48bbd
12 changed files with 453 additions and 194 deletions
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3
RELEASE_NOTES
View File

@ -5,6 +5,9 @@ VERSION COMMENTS
------- --------
4.1.2-beta2 2010-08-08
Refactor of HDF5 file metadata scan for large speedup
in opening files, especially large files.
Complete rewrite of the handling of character datalist
constants. The heuristics are documented in ncgen.1.

2
configure.ac
View File

@ -17,7 +17,7 @@ AC_REVISION([$Id: configure.ac,v 1.450 2010/05/28 19:42:47 dmh Exp $])
AC_PREREQ([2.59])
# Initialize with name, version, and support email address.
AC_INIT([netCDF], [4.1.2-beta1], [support-netcdf@unidata.ucar.edu])
AC_INIT([netCDF], [4.1.2-beta2], [support-netcdf@unidata.ucar.edu])
# Create the VERSION file, which contains the package version from
# AC_INIT.

22
libsrc4/Makefile.am
View File

@ -40,17 +40,17 @@ if BUILD_V2
LDADD += ${top_builddir}/libdispatch/libnetcdf2.la
endif
NC4_TESTS = tst_h_files tst_h_files2 tst_h_atts tst_h_atts3 tst_h_vars \
tst_h_vars2 tst_h_vars3 tst_h_grps tst_h_compounds tst_h_compounds2 \
tst_h_wrt_cmp tst_h_rd_cmp tst_h_vl tst_h_opaques tst_h_strings \
tst_h_strings1 tst_h_dimscales tst_h_dimscales1 tst_h_dimscales2 \
tst_h_dimscales3 tst_h_enums tst_dims tst_dims2 tst_dims3 tst_files \
tst_files4 tst_vars tst_varms tst_unlim_vars tst_converts \
tst_converts2 tst_grps tst_compounds tst_compounds2 tst_compounds3 \
tst_opaques tst_strings tst_interops tst_interops4 tst_interops5 \
tst_interops6 tst_enums tst_coords tst_coords2 tst_coords3 tst_vars3 \
tst_chunks tst_utf8 tst_fills tst_fillbug tst_xplatform tst_xplatform2 \
tst_h_atts2 tst_endian_fill
NC4_TESTS = tst_h_files tst_h_files2 tst_h_files4 tst_h_atts \
tst_h_atts3 tst_h_vars tst_h_vars2 tst_h_vars3 tst_h_grps \
tst_h_compounds tst_h_compounds2 tst_h_wrt_cmp tst_h_rd_cmp tst_h_vl \
tst_h_opaques tst_h_strings tst_h_strings1 tst_h_dimscales \
tst_h_dimscales1 tst_h_dimscales2 tst_h_dimscales3 tst_h_enums \
tst_dims tst_dims2 tst_dims3 tst_files tst_files4 tst_vars tst_varms \
tst_unlim_vars tst_converts tst_converts2 tst_grps tst_compounds \
tst_compounds2 tst_compounds3 tst_opaques tst_strings tst_interops \
tst_interops4 tst_interops5 tst_interops6 tst_enums tst_coords \
tst_coords2 tst_coords3 tst_vars3 tst_chunks tst_utf8 tst_fills \
tst_fillbug tst_xplatform tst_xplatform2 tst_h_atts2 tst_endian_fill
check_PROGRAMS = $(NC4_TESTS)
if LARGE_FILE_TESTS

246
libsrc4/nc4file.c
View File

@ -1680,53 +1680,145 @@ read_dataset(NC_GRP_INFO_T *grp, char *obj_name)
return retval;
}
/* Given index, get the HDF5 name of an object. This function will try
* to use creation ordering, but if that fails (which causes a HDF5
* error message to be printed) then it will use default
/* Given index, get the HDF5 name of an object and the class of the
* object (group, type, dataset, etc.). This function will try to use
* creation ordering, but if that fails it will use default
* (i.e. alphabetical) ordering. (This is necessary to read existing
* HDF5 archives without creation ordering). */
static int
get_name_by_idx(NC_HDF5_FILE_INFO_T *h5, hid_t hdf_grpid, int i,
int *obj_class, char *obj_name)
{
H5O_info_t obj_info;
H5_index_t idx_field = H5_INDEX_CRT_ORDER;
ssize_t size;
herr_t res;
/* static int */
/* get_name_by_idx(NC_HDF5_FILE_INFO_T *h5, hid_t hdf_grpid, int i, */
/* int *obj_class, char *obj_name) */
/* { */
/* H5O_info_t obj_info; */
/* H5_index_t idx_field = H5_INDEX_CRT_ORDER; */
/* ssize_t size; */
/* herr_t res; */
/* These HDF5 macros prevent an HDF5 error message when a
* non-creation-ordered HDF5 file is opened. */
H5E_BEGIN_TRY {
res = H5Oget_info_by_idx(hdf_grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT);
} H5E_END_TRY;
/* /\* These HDF5 macros prevent an HDF5 error message when a */
/* * non-creation-ordered HDF5 file is opened. *\/ */
/* H5E_BEGIN_TRY { */
/* res = H5Oget_info_by_idx(hdf_grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, */
/* i, &obj_info, H5P_DEFAULT); */
/* } H5E_END_TRY; */
/* Creation ordering not available, so make sure this file is
* opened for read-only access. This is a plain old HDF5 file being
* read by netCDF-4. */
if (res < 0)
/* /\* Creation ordering not available, so make sure this file is */
/* * opened for read-only access. This is a plain old HDF5 file being */
/* * read by netCDF-4. *\/ */
/* if (res < 0) */
/* { */
/* if (H5Oget_info_by_idx(hdf_grpid, ".", H5_INDEX_NAME, H5_ITER_INC, */
/* i, &obj_info, H5P_DEFAULT) < 0) */
/* return NC_EHDFERR; */
/* if (!h5->no_write) */
/* return NC_ECANTWRITE; */
/* h5->ignore_creationorder = 1; */
/* idx_field = H5_INDEX_NAME; */
/* } */
/* *obj_class = obj_info.type; */
/* if ((size = H5Lget_name_by_idx(hdf_grpid, ".", idx_field, H5_ITER_INC, i, */
/* NULL, 0, H5P_DEFAULT)) < 0) */
/* return NC_EHDFERR; */
/* if (size > NC_MAX_NAME) */
/* return NC_EMAXNAME; */
/* if (H5Lget_name_by_idx(hdf_grpid, ".", idx_field, H5_ITER_INC, i, */
/* obj_name, size+1, H5P_DEFAULT) < 0) */
/* return NC_EHDFERR; */
/* LOG((4, "get_name_by_idx: encountered HDF5 object obj_name %s", obj_name)); */
/* return NC_NOERR; */
/* } */
/* This struct is used to pass information back from the callback
* function used with H5Literate. */
struct nc_hdf5_link_info
{
char name[NC_MAX_NAME + 1];
H5I_type_t obj_type;
};
/* This is a callback function for H5Literate().
The parameters of this callback function have the following values or
meanings:
g_id Group that serves as root of the iteration; same value as the
H5Lvisit group_id parameter
name Name of link, relative to g_id, being examined at current step of
the iteration
info H5L_info_t struct containing information regarding that link
op_data User-defined pointer to data required by the application in
processing the link; a pass-through of the op_data pointer provided
with the H5Lvisit function call
*/
static herr_t
visit_link(hid_t g_id, const char *name, const H5L_info_t *info,
void *op_data)
{
/* A positive return value causes the visit iterator to immediately
* return that positive value, indicating short-circuit
* success. The iterator can be restarted at the next group
* member. */
int ret = 1;
hid_t id;
/* Get the name, truncating at NC_MAX_NAME. */
strncpy(((struct nc_hdf5_link_info *)op_data)->name, name,
NC_MAX_NAME);
/* Open this critter. */
if ((id = H5Oopen_by_addr(g_id, info->u.address)) < 0)
return NC_EHDFERR;
/* Is this critter a group, type, data, attribute, or what? */
if ((((struct nc_hdf5_link_info *)op_data)->obj_type = H5Iget_type(id)) < 0)
ret = NC_EHDFERR;
/* Close the critter to release resouces. */
if (H5Oclose(id) < 0)
return NC_EHDFERR;
return ret;
}
/* Iterate over one link in the group at a time, returning
* link_info. The creation_ordering and idx pointers keep track of
* whether creation ordering works and the most recently examined
* link. */
static int
nc4_iterate_link(int *ordering_checked, int *creation_ordering,
hid_t grpid, hsize_t *idx, struct nc_hdf5_link_info *link_info)
{
int res = 0;
if (*creation_ordering)
{
if (H5Oget_info_by_idx(hdf_grpid, ".", H5_INDEX_NAME, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT) < 0)
return NC_EHDFERR;
if (!h5->no_write)
return NC_ECANTWRITE;
h5->ignore_creationorder = 1;
idx_field = H5_INDEX_NAME;
/* These HDF5 macros prevent an HDF5 error message when a
* non-creation-ordered HDF5 file is opened. */
H5E_BEGIN_TRY {
res = H5Literate(grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC,
idx, visit_link, (void *)link_info);
if (res < 0 && *ordering_checked)
return NC_EHDFERR;
} H5E_END_TRY;
}
*obj_class = obj_info.type;
if ((size = H5Lget_name_by_idx(hdf_grpid, ".", idx_field, H5_ITER_INC, i,
NULL, 0, H5P_DEFAULT)) < 0)
return NC_EHDFERR;
if (size > NC_MAX_NAME)
return NC_EMAXNAME;
if (H5Lget_name_by_idx(hdf_grpid, ".", idx_field, H5_ITER_INC, i,
obj_name, size+1, H5P_DEFAULT) < 0)
return NC_EHDFERR;
LOG((4, "get_name_by_idx: encountered HDF5 object obj_name %s", obj_name));
if (!*creation_ordering || res < 0)
{
if (H5Literate(grpid, H5_INDEX_NAME, H5_ITER_INC, idx,
visit_link, link_info) != 1)
return NC_EHDFERR;
/* If it didn't work with creation ordering, but did without,
* then we don't have creation ordering. */
*creation_ordering = 0;
}
*ordering_checked = 1;
return NC_NOERR;
}
@ -1735,10 +1827,12 @@ int
nc4_rec_read_types(NC_GRP_INFO_T *grp)
{
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_HDF5_NAME + 1];
NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info;
NC_GRP_INFO_T *child_grp;
hsize_t idx = 0;
struct nc_hdf5_link_info link_info;
int ordering_checked = 0;
int creation_ordering = 1; /* Assume we have it. */
int retval = NC_NOERR;
assert(grp && grp->name);
@ -1770,23 +1864,28 @@ nc4_rec_read_types(NC_GRP_INFO_T *grp)
/* For each object in the group... */
for (i = 0; i < num_obj; i++)
{
if ((retval = get_name_by_idx(h5, grp->hdf_grpid, i, &obj_class, obj_name)))
if ((retval = nc4_iterate_link(&ordering_checked, &creation_ordering,
grp->hdf_grpid, &idx, &link_info)))
return retval;
/* Without creation ordering, file must be read-only. */
if (!i && !creation_ordering && !h5->no_write)
return NC_ECANTWRITE;
/* Deal with groups and types; ignore the rest. */
if (obj_class == H5O_TYPE_GROUP)
if (link_info.obj_type == H5I_GROUP)
{
LOG((3, "found group %s", obj_name));
LOG((3, "found group %s", link_info.name));
if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++,
grp, grp->file, obj_name, &child_grp)))
grp, grp->file, link_info.name, &child_grp)))
return retval;
if ((retval = nc4_rec_read_types(child_grp)))
return retval;
}
else if (obj_class == H5O_TYPE_NAMED_DATATYPE)
else if (link_info.obj_type == H5I_DATATYPE)
{
LOG((3, "found datatype %s", obj_name));
if ((retval = read_type(grp, obj_name)))
LOG((3, "found datatype %s", link_info.name));
if ((retval = read_type(grp, link_info.name)))
return retval;
}
}
@ -1801,10 +1900,11 @@ int
nc4_rec_read_vars(NC_GRP_INFO_T *grp)
{
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_HDF5_NAME + 1];
NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info;
NC_GRP_INFO_T *child_grp;
struct nc_hdf5_link_info link_info;
hsize_t idx = 0;
int ordering_checked = 0;
int creation_ordering = 1; /* Assume we have it. */
int retval = NC_NOERR;
assert(grp && grp->name && grp->hdf_grpid > 0);
@ -1817,18 +1917,19 @@ nc4_rec_read_vars(NC_GRP_INFO_T *grp)
/* For each object in the group... */
for (i = 0; i < num_obj; i++)
{
if ((retval = get_name_by_idx(h5, grp->hdf_grpid, i, &obj_class, obj_name)))
if ((retval = nc4_iterate_link(&ordering_checked, &creation_ordering,
grp->hdf_grpid, &idx, &link_info)))
return retval;
/* Deal with datasets. */
switch(obj_class)
switch(link_info.obj_type)
{
case H5O_TYPE_GROUP:
LOG((3, "re-encountering group %s", obj_name));
case H5I_GROUP:
LOG((3, "re-encountering group %s", link_info.name));
/* The NC_GROUP_INFO_T for this group already exists. Find it. */
for (child_grp = grp->children; child_grp; child_grp = child_grp->next)
if (!strcmp(child_grp->name, obj_name))
if (!strcmp(child_grp->name, link_info.name))
break;
if (!child_grp)
return NC_EHDFERR;
@ -1837,25 +1938,20 @@ nc4_rec_read_vars(NC_GRP_INFO_T *grp)
if ((retval = nc4_rec_read_vars(child_grp)))
return retval;
break;
case H5O_TYPE_DATASET:
LOG((3, "found dataset %s", obj_name));
case H5I_DATASET:
LOG((3, "found dataset %s", link_info.name));
/* Learn all about this dataset, which may be a dimscale
* (i.e. dimension metadata), or real data. */
if ((retval = read_dataset(grp, obj_name)))
if ((retval = read_dataset(grp, link_info.name)))
return retval;
break;
case H5O_TYPE_NAMED_DATATYPE:
LOG((3, "already handled type %s", obj_name));
break;
case H5G_LINK:
/* Since I don't know what to do with linkes, I'll just
* ignore them. */
LOG((3, "This is a link object. Have a nice day."));
case H5I_DATATYPE:
LOG((3, "already handled type %s", link_info.name));
break;
default:
LOG((0, "Unknown object class %d in nc4_rec_read_vars!",
obj_class));
link_info.obj_type));
}
}
@ -1929,9 +2025,6 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm,
nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
#endif /* USE_PARALLEL */
/*if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
BAIL(NC_EHDFERR);*/
/* The NetCDF-3.x prototype contains an mode option NC_SHARE for
multiple processes accessing the dataset concurrently. As there
is no HDF5 equivalent, NC_SHARE is treated as NC_NOWRITE. */
@ -2698,16 +2791,9 @@ NC4_close(int ncid)
nc4_file_list_del(nc);
}
/* Reset the ncid numbers if there are no more files open. */
if(count_NCList() == 0)
{
/* If all files have been closed, close he HDF5 library. This will
* clean up some stuff that HDF5 is leaving open. */
/* if ((retval = H5close()) < 0)
return NC_EHDFERR;*/
/* Reset the ncid numbers. */
nc4_file_list_free();
}
return NC_NOERR;
}

6
libsrc4/nc4internal.c
View File

@ -227,7 +227,7 @@ nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp)
/* If we can't find it, the grp id part of ncid is bad. */
if (!(*grp = nc4_rec_find_grp(f->nc4_info->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADGRPID;
return NC_EBADID;
return NC_NOERR;
}
@ -243,7 +243,7 @@ nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_HDF5_FILE_INFO_T **h5)
assert(f->nc4_info->root_grp);
/* If we can't find it, the grp id part of ncid is bad. */
if (!(*grp = nc4_rec_find_grp(f->nc4_info->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADGRPID;
return NC_EBADID;
*h5 = (*grp)->file->nc4_info;
assert(*h5);
} else {
@ -264,7 +264,7 @@ nc4_find_nc_grp_h5(int ncid, NC_FILE_INFO_T **nc, NC_GRP_INFO_T **grp,
assert(f->nc4_info->root_grp);
/* If we can't find it, the grp id part of ncid is bad. */
if (!(*grp = nc4_rec_find_grp(f->nc4_info->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADGRPID;
return NC_EBADID;
*h5 = (*grp)->file->nc4_info;
assert(*h5);

13
libsrc4/nc4var.c
View File

@ -924,12 +924,13 @@ nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int *chunksizesp
NULL, NULL, NULL, NULL);
/* Copy to size_t array. */
for (i = 0; i < var->ndims; i++)
{
chunksizesp[i] = cs[i];
if (cs[i] > NC_MAX_INT)
retval = NC_ERANGE;
}
if (*contiguousp == NC_CHUNKED)
for (i = 0; i < var->ndims; i++)
{
chunksizesp[i] = cs[i];
if (cs[i] > NC_MAX_INT)
retval = NC_ERANGE;
}
if (var->ndims)
free(cs);

55
libsrc4/tst_h_files.c
View File

@ -223,61 +223,6 @@ main()
ERR;
}
SUMMARIZE_ERR;
printf("*** Creating HDF5 file in the canonical netCDF-4 way...");
{
hid_t fapl_id, fcpl_id, fileid, grpid, fileid2;
hsize_t num_obj;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Set close degree. */
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
/* Create the file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Close up. */
if (H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
/* Reopen the file and check it. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, fapl_id)) < 0) ERR;
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
if (num_obj) ERR;
/* Open another copy of the same file. Must use the same file
* access degree or HDF5 will not open the file. */
if ((fileid2 = H5Fopen(FILE_NAME, H5F_ACC_RDWR, fapl_id)) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Fclose(fileid2) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
#ifdef LARGE_FILE_TESTS
#define NDIMS2 2

204
libsrc4/tst_h_files4.c Normal file
View File

@ -0,0 +1,204 @@
/* This is part of the netCDF package.
Copyright 2005 University Corporation for Atmospheric Research/Unidata
See COPYRIGHT file for conditions of use.
Test HDF5 file code. These are not intended to be exhaustive tests,
but they use HDF5 the same way that netCDF-4 does, so if these
tests don't work, than netCDF-4 won't work either.
$Id$
*/
#include <config.h>
#include <nc_tests.h>
#include "netcdf.h"
#include <nc4internal.h>
#include <H5DSpublic.h>
#define FILE_NAME "tst_h_files4.h5"
/* Heavy duty test file...*/
/*#define FILE_NAME "/machine/downloads/T159_1978110112.nc4"*/
herr_t
obj_iter(hid_t o_id, const char *name, const H5O_info_t *object_info,
void *op_data)
{
*(int *)op_data = object_info->type;
return 1;
}
/* This is a callback function for H5Literate().
The parameters of this callback function have the following values or
meanings:
g_id Group that serves as root of the iteration; same value as the
H5Lvisit group_id parameter
name Name of link, relative to g_id, being examined at current step of
the iteration
info H5L_info_t struct containing information regarding that link
op_data User-defined pointer to data required by the application in
processing the link; a pass-through of the op_data pointer provided
with the H5Lvisit function call
*/
herr_t
op_func (hid_t g_id, const char *name, const H5L_info_t *info,
void *op_data)
{
hid_t id;
H5I_type_t obj_type;
strcpy((char *)op_data, name);
if ((id = H5Oopen_by_addr(g_id, info->u.address)) < 0) ERR;
/* Using H5Ovisit is really slow. Use H5Iget_type for a fast
* answer. */
/* if (H5Ovisit(id, H5_INDEX_CRT_ORDER, H5_ITER_INC, obj_iter, */
/* (void *)&obj_class) != 1) ERR; */
if ((obj_type = H5Iget_type(id)) < 0) ERR;
if (H5Oclose(id) < 0) ERR;
/* Turn this on to learn what type of object you've opened. */
/* switch (obj_type) */
/* { */
/* case H5I_GROUP: */
/* printf("group %s\n", name); */
/* break; */
/* case H5I_DATATYPE: */
/* printf("type %s\n", name); */
/* break; */
/* case H5I_DATASET: */
/* printf("data %s\n", name); */
/* break; */
/* default: */
/* printf("unknown class\n"); */
/* } */
return 1;
}
int
main()
{
printf("\n*** Checking HDF5 file functions.\n");
printf("*** Creating HDF5 file in the canonical netCDF-4 way...");
{
hid_t fapl_id, fcpl_id, fileid, grpid, fileid2;
hsize_t num_obj;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
/* if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST,
H5F_LIBVER_LATEST) < 0) ERR;*/
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Set close degree. */
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
/* Create the file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Close up. */
if (H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
/* Reopen the file and check it. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, fapl_id)) < 0) ERR;
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
if (num_obj) ERR;
/* Open another copy of the same file. Must use the same file
* access degree or HDF5 will not open the file. */
if ((fileid2 = H5Fopen(FILE_NAME, H5F_ACC_RDWR, fapl_id)) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Fclose(fileid2) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Opening a HDF5 file with H5Literate...");
{
hid_t fapl_id, fileid, grpid;
hsize_t idx = 0;
char obj_name[NC_MAX_NAME + 1];
hsize_t num_obj;
int i;
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, CHUNK_CACHE_NELEMS, CHUNK_CACHE_SIZE,
CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
if (H5Literate(grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, &idx, op_func,
(void *)obj_name) != 1) ERR;
printf("encountered object %s\n", obj_name);
}
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Opening a HDF5 file in the canonical netCDF-4 way...");
{
hid_t fapl_id, fileid, grpid;
H5_index_t idx_field = H5_INDEX_CRT_ORDER;
H5O_info_t obj_info;
hsize_t num_obj;
ssize_t size;
char obj_name[NC_MAX_NAME + 1];
int i;
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, CHUNK_CACHE_NELEMS, CHUNK_CACHE_SIZE,
CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* How many objects in this group? */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
if (H5Oget_info_by_idx(grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT)) ERR;
if ((size = H5Lget_name_by_idx(grpid, ".", idx_field, H5_ITER_INC, i,
NULL, 0, H5P_DEFAULT)) < 0) ERR;
if (H5Lget_name_by_idx(grpid, ".", idx_field, H5_ITER_INC, i,
obj_name, size+1, H5P_DEFAULT) < 0) ERR;
}
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}

2
libsrc4/tst_h_vars.c
View File

@ -200,6 +200,7 @@ main()
dims[0] = DIM1_LEN;
if ((propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_layout(propid, H5D_CHUNKED)) ERR;
if (H5Pset_chunk(propid, 1, dims)) ERR;
if (H5Pset_deflate(propid, DEFLATE_LEVEL)) ERR;
if ((spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
if ((datasetid = H5Dcreate(grpid, VAR_BOOL_NAME, H5T_NATIVE_HBOOL,
@ -258,6 +259,7 @@ main()
dims[0] = DIM1_LEN;
if ((propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_layout(propid, H5D_CHUNKED)) ERR;
if (H5Pset_chunk(propid, 1, dims)) ERR;
if (H5Pset_shuffle(propid)) ERR;
if (H5Pset_deflate(propid, DEFLATE_LEVEL)) ERR;
if (H5Pset_fletcher32(propid)) ERR;

40
nf_test/f90tst_vars_vlen.f90
View File

@ -80,21 +80,21 @@ program f90tst_vars_vlen
! if (retval .ne. nf_noerr) call handle_err(retval)
! if (num_types .ne. max_types) stop 2
! ! Use nf_inq_user_type to confirm this is an vlen type, with base
! ! size 4, base type NF_INT.
! ! Use nf_inq_user_type to confirm this is an vlen type, with vlen
! ! size 16, base type NF_INT.
! retval = nf_inq_user_type(ncid, typeids(1), type_name, type_size, &
! base_type, nfields, class)
! if (retval .ne. nf_noerr) call handle_err(retval)
! if (type_name(1:len(vlen_type_name)) .ne. vlen_type_name .or. &
! type_size .ne. 4 .or. base_type .ne. nf_int .or. &
! nfields .ne. 0 .or. class .ne. nf_vlen) stop 2
! type_size .ne. 16 .or. base_type .ne. nf_int .or. &
! nfields .ne. 0 .or. class .ne. nf_vlen) stop 3
! ! Use nf_inq_vlen and make sure we get the same answers as we did
! ! with nf_inq_user_type.
! retval = nf_inq_vlen(ncid, typeids(1), type_name, base_size, base_type)
! if (retval .ne. nf_noerr) call handle_err(retval)
! if (type_name(1:len(vlen_type_name)) .ne. vlen_type_name .or. &
! base_type .ne. nf_int .or. base_size .ne. 4) stop 2
! base_type .ne. nf_int .or. base_size .ne. 16) stop 4
! ! Read the vlen attribute.
! retval = nf_get_att(ncid, NF_GLOBAL, 'att1', vlen_in)
@ -104,29 +104,29 @@ program f90tst_vars_vlen
! retval = nf_get_vlen_element(ncid, vlen_typeid, vlen_in, &
! vlen_len_in, data1_in)
! if (retval .ne. nf_noerr) call handle_err(retval)
! if (vlen_len_in .ne. vlen_len) stop 2
! if (vlen_len_in .ne. vlen_len) stop 5
! ! Check the data
! do x = 1, vlen_len
! if (data1(x) .ne. data1_in(x)) stop 2
! if (data1(x) .ne. data1_in(x)) stop 6
! end do
! ! Close the file.
! retval = nf_close(ncid)
! if (retval .ne. nf_noerr) call handle_err(retval)
print *,'*** SUCCESS!'
contains
! This subroutine handles errors by printing an error message and
! exiting with a non-zero status.
subroutine handle_err(errcode)
use netcdf
implicit none
integer, intent(in) :: errcode
! print *,'*** SUCCESS!'
! contains
! ! This subroutine handles errors by printing an error message and
! ! exiting with a non-zero status.
! subroutine handle_err(errcode)
! use netcdf
! implicit none
! integer, intent(in) :: errcode
if(errcode /= nf90_noerr) then
print *, 'Error: ', trim(nf90_strerror(errcode))
stop 2
endif
end subroutine handle_err
! if(errcode /= nf90_noerr) then
! print *, 'Error: ', trim(nf90_strerror(errcode))
! stop 1
! endif
! end subroutine handle_err
end program f90tst_vars_vlen

1
oc/dap.y
View File

@ -115,6 +115,7 @@ array_decls:
array_decl:
'[' SCAN_WORD ']' {$$=dap_arraydecl(parsestate,null,$2);}
| '[' name '=' SCAN_WORD ']' {$$=dap_arraydecl(parsestate,$2,$4);}
| '[' '=' SCAN_WORD ']' {$$=dap_arraydecl(parsestate,null,$3);}
| error
{daperror(parsestate,"Illegal dimension declaration"); YYABORT;}
;

53
oc/ocinternal.c
View File

@ -22,11 +22,12 @@
/* Note: TMPPATH must end in '/' */
#ifdef __CYGWIN__
/*#define TMPPATH "c:/temp/"*/
#define TMPPATH1 "c:/temp/"
#define TMPPATH2 "./"
#else
/*#define TMPPATH "/tmp/"*/
#define TMPPATH1 "/tmp/"
#define TMPPATH2 "./"
#endif
#define TMPPATH "./"
/* Define default rc files */
#define DODSRC ".dodsrc"
@ -36,6 +37,7 @@ static int ocextractdds(OCstate*,OCtree*);
static char* constraintescape(const char* url);
#ifdef OC_DISK_STORAGE
static OCerror createtempfile(OCstate*,OCtree*);
static int createtempfile1(char*,char*);
#endif
static void ocsetcurlproperties(OCstate*);
@ -455,12 +457,36 @@ ocextractdds(OCstate* state, OCtree* tree)
static OCerror
createtempfile(OCstate* state, OCtree* tree)
{
int fd,c,slen = strlen(TMPPATH) + strlen("datadds") + strlen("XXXXXX");
char* name = (char*)ocmalloc(slen+1);
char* p;
int fd,slen;
char* name;
slen = strlen(TMPPATH1);
if(slen < strlen(TMPPATH2)) slen = strlen(TMPPATH2);
slen += strlen("datadds") + strlen("XXXXXX");
name = (char*)ocmalloc(slen+1);
MEMCHECK(name,OC_ENOMEM);
strcpy(name,TMPPATH);
strcpy(name,"datadds");
fd = createtempfile1(name, TMPPATH1);
if(fd < 0)
fd = createtempfile1(name, TMPPATH2);
if(fd < 0) {
oc_log(LOGERR,"oc_open: attempt to open tmp file %s failed",name);
return errno;
}
oc_log(LOGNOTE,"oc_open: using tmp file: %s",name);
tree->data.filename = name; /* remember our tmp file name */
tree->data.file = fdopen(fd,"w+");
if(tree->data.file == NULL) return OC_EOPEN;
/* unlink the temp file so it will automatically be reclaimed */
if(ocdebug == 0) unlink(tree->data.filename);
return OC_NOERR;
}
int
createtempfile1(char* name, char* tmppath)
{
char* p;
int c,fd;
strcpy(name,tmppath);
strcat(name,"datadds");
strcat(name,"XXXXXX");
p = name + strlen("datadds");
/* \', and '/' to '_' and '.' to '-'*/
@ -471,16 +497,7 @@ createtempfile(OCstate* state, OCtree* tree)
/* Note Potential problem: old versions of this function
leave the file in mode 0666 instead of 0600 */
fd = mkstemp(name);
if(fd < 0) {
oc_log(LOGERR,"oc_open: attempt to open tmp file %s failed",name);
return errno;
}
tree->data.filename = name; /* remember our tmp file name */
tree->data.file = fdopen(fd,"w+");
if(tree->data.file == NULL) return OC_EOPEN;
/* unlink the temp file so it will automatically be reclaimed */
if(ocdebug == 0) unlink(tree->data.filename);
return OC_NOERR;
return fd;
}
#endif /*OC_DISK_STORAGE*/