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netcdf-c/libsrc4/nc4file.c

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/**
* @file
* @internal The netCDF-4 file functions.
*
* This file is part of netcdf-4, a netCDF-like interface for HDF5, or
* a HDF5 backend for netCDF, depending on your point of view.
*
* Copyright 2003, University Corporation for Atmospheric Research. See
* COPYRIGHT file for copying and redistribution conditions.
* @author Ed Hartnett
*/
#include "config.h"
#include <errno.h> /* netcdf functions sometimes return system errors */
#include "nc.h"
#include "nc4internal.h"
#include "nc4dispatch.h"
#include <H5DSpublic.h> /* must be after nc4internal.h */
#include <H5Fpublic.h>
#ifdef USE_HDF4
#include <mfhdf.h>
#endif
#include <hdf5_hl.h>
extern int nc4_vararray_add(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
/** @internal When we have open objects at file close, should
we log them or print to stdout. Default is to log. */
#define LOGOPEN 1
#define CD_NELEMS_ZLIB 1 /**< Number of parameters needed for ZLIB filter. */
/**
* @internal Wrap HDF5 allocated memory free operations
*
* @param memory Pointer to memory to be freed.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static void
hdf5free(void* memory)
{
#ifndef JNA
/* On Windows using the microsoft runtime, it is an error
for one library to free memory allocated by a different library.*/
#ifdef HDF5_HAS_H5FREE
if(memory != NULL) H5free_memory(memory);
#else
#ifndef _MSC_VER
if(memory != NULL) free(memory);
#endif
#endif
#endif
}
/* Custom iteration callback data */
typedef struct {
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var;
} att_iter_info;
/**
* @internal Given an HDF5 type, set a pointer to netcdf type.
*
* @param h5 Pointer to HDF5 file info struct.
* @param native_typeid HDF5 type ID.
* @param xtype Pointer that gets netCDF type.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EBADTYPID Type not found.
* @author Ed Hartnett
*/
static int
get_netcdf_type(NC_HDF5_FILE_INFO_T *h5, hid_t native_typeid,
nc_type *xtype)
{
NC_TYPE_INFO_T *type;
H5T_class_t class;
htri_t is_str, equal = 0;
assert(h5 && xtype);
if ((class = H5Tget_class(native_typeid)) < 0)
return NC_EHDFERR;
/* H5Tequal doesn't work with H5T_C_S1 for some reason. But
* H5Tget_class will return H5T_STRING if this is a string. */
if (class == H5T_STRING)
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
if (is_str)
*xtype = NC_STRING;
else
*xtype = NC_CHAR;
return NC_NOERR;
}
else if (class == H5T_INTEGER || class == H5T_FLOAT)
{
/* For integers and floats, we don't have to worry about
* endianness if we compare native types. */
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SCHAR)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_BYTE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SHORT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_SHORT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_INT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_INT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_FLOAT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_FLOAT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_DOUBLE)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_DOUBLE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UCHAR)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UBYTE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_USHORT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_USHORT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UINT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UINT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_LLONG)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_INT64;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_ULLONG)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UINT64;
return NC_NOERR;
}
}
/* Maybe we already know about this type. */
if (!equal)
if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
{
*xtype = type->nc_typeid;
return NC_NOERR;
}
*xtype = NC_NAT;
return NC_EBADTYPID;
}
/**
* @internal Read an attribute. This is called by att_read_var_callbk().
*
* @param grp Pointer to group info struct.
* @param attid Attribute ID.
* @param att Pointer that gets att info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
{
hid_t spaceid = 0, file_typeid = 0;
hsize_t dims[1] = {0}; /* netcdf attributes always 1-D. */
int retval = NC_NOERR;
size_t type_size;
int att_ndims;
hssize_t att_npoints;
H5T_class_t att_class;
int fixed_len_string = 0;
size_t fixed_size = 0;
assert(att->name);
LOG((5, "%s: att->attnum %d att->name %s att->nc_typeid %d att->len %d",
__func__, att->attnum, att->name, (int)att->nc_typeid, att->len));
/* Get type of attribute in file. */
if ((file_typeid = H5Aget_type(attid)) < 0)
return NC_EATTMETA;
if ((att->native_hdf_typeid = H5Tget_native_type(file_typeid, H5T_DIR_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if ((att_class = H5Tget_class(att->native_hdf_typeid)) < 0)
BAIL(NC_EATTMETA);
if (att_class == H5T_STRING && !H5Tis_variable_str(att->native_hdf_typeid))
{
fixed_len_string++;
if (!(fixed_size = H5Tget_size(att->native_hdf_typeid)))
BAIL(NC_EATTMETA);
}
if ((retval = get_netcdf_type(grp->nc4_info, att->native_hdf_typeid, &(att->nc_typeid))))
BAIL(retval);
/* Get len. */
if ((spaceid = H5Aget_space(attid)) < 0)
BAIL(NC_EATTMETA);
if ((att_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EATTMETA);
if ((att_npoints = H5Sget_simple_extent_npoints(spaceid)) < 0)
BAIL(NC_EATTMETA);
/* If both att_ndims and att_npoints are zero, then this is a
* zero length att. */
if (att_ndims == 0 && att_npoints == 0)
dims[0] = 0;
else if (att->nc_typeid == NC_STRING)
dims[0] = att_npoints;
else if (att->nc_typeid == NC_CHAR)
{
/* NC_CHAR attributes are written as a scalar in HDF5, of type
* H5T_C_S1, of variable length. */
if (att_ndims == 0)
{
if (!(dims[0] = H5Tget_size(file_typeid)))
BAIL(NC_EATTMETA);
}
else
{
/* This is really a string type! */
att->nc_typeid = NC_STRING;
dims[0] = att_npoints;
}
}
else
{
H5S_class_t space_class;
/* All netcdf attributes are scalar or 1-D only. */
if (att_ndims > 1)
BAIL(NC_EATTMETA);
/* Check class of HDF5 dataspace */
if ((space_class = H5Sget_simple_extent_type(spaceid)) < 0)
BAIL(NC_EATTMETA);
/* Check for NULL HDF5 dataspace class (should be weeded out earlier) */
if (H5S_NULL == space_class)
BAIL(NC_EATTMETA);
/* check for SCALAR HDF5 dataspace class */
if (H5S_SCALAR == space_class)
dims[0] = 1;
else /* Must be "simple" dataspace */
{
/* Read the size of this attribute. */
if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0)
BAIL(NC_EATTMETA);
}
}
/* Tell the user what the length if this attribute is. */
att->len = dims[0];
/* Allocate some memory if the len is not zero, and read the
attribute. */
if (dims[0])
{
if ((retval = nc4_get_typelen_mem(grp->nc4_info, att->nc_typeid, 0,
&type_size)))
return retval;
if (att_class == H5T_VLEN)
{
if (!(att->vldata = malloc((unsigned int)(att->len * sizeof(hvl_t)))))
BAIL(NC_ENOMEM);
if (H5Aread(attid, att->native_hdf_typeid, att->vldata) < 0)
BAIL(NC_EATTMETA);
}
else if (att->nc_typeid == NC_STRING)
{
if (!(att->stdata = calloc(att->len, sizeof(char *))))
BAIL(NC_ENOMEM);
/* For a fixed length HDF5 string, the read requires
* contiguous memory. Meanwhile, the netCDF API requires that
* nc_free_string be called on string arrays, which would not
* work if one contiguous memory block were used. So here I
* convert the contiguous block of strings into an array of
* malloced strings (each string with its own malloc). Then I
* copy the data and free the contiguous memory. This
* involves copying the data, which is bad, but this only
* occurs for fixed length string attributes, and presumably
* these are small. (And netCDF-4 does not create them - it
* always uses variable length strings. */
if (fixed_len_string)
{
int i;
char *contig_buf, *cur;
/* Alloc space for the contiguous memory read. */
if (!(contig_buf = malloc(att->len * fixed_size * sizeof(char))))
BAIL(NC_ENOMEM);
/* Read the fixed-len strings as one big block. */
if (H5Aread(attid, att->native_hdf_typeid, contig_buf) < 0) {
free(contig_buf);
BAIL(NC_EATTMETA);
}
/* Copy strings, one at a time, into their new home. Alloc
space for each string. The user will later free this
space with nc_free_string. */
cur = contig_buf;
for (i = 0; i < att->len; i++)
{
if (!(att->stdata[i] = malloc(fixed_size))) {
free(contig_buf);
BAIL(NC_ENOMEM);
}
strncpy(att->stdata[i], cur, fixed_size);
cur += fixed_size;
}
/* Free contiguous memory buffer. */
free(contig_buf);
}
else
{
/* Read variable-length string atts. */
if (H5Aread(attid, att->native_hdf_typeid, att->stdata) < 0)
BAIL(NC_EATTMETA);
}
}
else
{
if (!(att->data = malloc((unsigned int)(att->len * type_size))))
BAIL(NC_ENOMEM);
if (H5Aread(attid, att->native_hdf_typeid, att->data) < 0)
BAIL(NC_EATTMETA);
}
}
if (H5Tclose(file_typeid) < 0)
BAIL(NC_EHDFERR);
if (H5Sclose(spaceid) < 0)
return NC_EHDFERR;
return NC_NOERR;
exit:
if (H5Tclose(file_typeid) < 0)
BAIL2(NC_EHDFERR);
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal Callback function for reading attributes. This is used by read_var().
*
* @param loc_id HDF5 attribute ID.
* @param att_name Name of the attrigute.
* @param ainfo HDF5 info struct for attribute.
* @param att_data The attribute data.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EATTMETA HDF5 can't open attribute.
* @return ::NC_EBADTYPID Can't read attribute type.
*/
static herr_t
att_read_var_callbk(hid_t loc_id, const char *att_name, const H5A_info_t *ainfo, void *att_data)
{
hid_t attid = 0;
int retval = NC_NOERR;
NC_ATT_INFO_T *att;
att_iter_info *att_info = (att_iter_info *)att_data;
const char** reserved;
/* Should we ignore this attribute? */
for(reserved=NC_RESERVED_VARATT_LIST;*reserved;reserved++) {
if (strcmp(att_name, *reserved)==0) break;
}
if(*reserved == NULL) {
/* Open the att by name. */
if ((attid = H5Aopen(loc_id, att_name, H5P_DEFAULT)) < 0)
BAIL(NC_EATTMETA);
LOG((4, "%s:: att_name %s", __func__, att_name));
/* Add to the end of the list of atts for this var. */
if ((retval = nc4_att_list_add(&att_info->var->att, &att)))
BAIL(retval);
/* Fill in the information we know. */
att->attnum = att_info->var->natts++;
if (!(att->name = strdup(att_name)))
BAIL(NC_ENOMEM);
/* Read the rest of the info about the att,
* including its values. */
if ((retval = read_hdf5_att(att_info->grp, attid, att)))
{
if (NC_EBADTYPID == retval)
{
if ((retval = nc4_att_list_del(&att_info->var->att, att)))
BAIL(retval);
att = NULL;
}
else
BAIL(retval);
}
if (att)
att->created = NC_TRUE;
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
} /* endif not HDF5 att */
return NC_NOERR;
exit:
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/** @internal These flags may not be set for open mode. */
static const int ILLEGAL_OPEN_FLAGS = (NC_MMAP|NC_64BIT_OFFSET);
/** @internal These flags may not be set for create. */
static const int ILLEGAL_CREATE_FLAGS = (NC_NOWRITE|NC_MMAP|NC_INMEMORY|NC_64BIT_OFFSET|NC_CDF5);
extern void reportopenobjects(int log, hid_t);
/**
* @internal Struct to track information about objects in a group, for
* nc4_rec_read_metadata()
*/
typedef struct NC4_rec_read_metadata_obj_info
{
hid_t oid; /* HDF5 object ID */
char oname[NC_MAX_NAME + 1]; /* Name of object */
H5G_stat_t statbuf; /* Information about the object */
struct NC4_rec_read_metadata_obj_info *next; /* Pointer to next node in list */
} NC4_rec_read_metadata_obj_info_t;
/**
* @internal User data struct for call to H5Literate() in
* nc4_rec_read_metadata(). Tracks the groups, named datatypes and
* datasets in the group, for later use.
*/
typedef struct NC4_rec_read_metadata_ud
{
NC4_rec_read_metadata_obj_info_t *grps_head, *grps_tail; /* Pointers to head & tail of list of groups */
NC_GRP_INFO_T *grp; /* Pointer to parent group */
} NC4_rec_read_metadata_ud_t;
/* Forward */
static int NC4_enddef(int ncid);
static int nc4_rec_read_metadata(NC_GRP_INFO_T *grp);
/**
* @internal This function will write all changed metadata, and
* (someday) reread all metadata from the file.
*
* @param h5 Pointer to HDF5 file info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
sync_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
{
int retval;
assert(h5);
LOG((3, "%s", __func__));
/* If we're in define mode, that's an error, for strict nc3 rules,
* otherwise, end define mode. */
if (h5->flags & NC_INDEF)
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_EINDEFINE;
/* Turn define mode off. */
h5->flags ^= NC_INDEF;
/* Redef mode needs to be tracked separately for nc_abort. */
h5->redef = NC_FALSE;
}
#ifdef LOGGING
/* This will print out the names, types, lens, etc of the vars and
atts in the file, if the logging level is 2 or greater. */
log_metadata_nc(h5->root_grp->nc4_info->controller);
#endif
/* Write any metadata that has changed. */
if (!(h5->cmode & NC_NOWRITE))
{
nc_bool_t bad_coord_order = NC_FALSE; /* if detected, propagate to all groups to consistently store dimids */
if ((retval = nc4_rec_write_groups_types(h5->root_grp)))
return retval;
if ((retval = nc4_rec_detect_need_to_preserve_dimids(h5->root_grp, &bad_coord_order)))
return retval;
if ((retval = nc4_rec_write_metadata(h5->root_grp, bad_coord_order)))
return retval;
}
if (H5Fflush(h5->hdfid, H5F_SCOPE_GLOBAL) < 0)
return NC_EHDFERR;
return retval;
}
/**
* @internal This function will free all allocated metadata memory,
* and close the HDF5 file. The group that is passed in must be the
* root group of the file.
*
* @param h5 Pointer to HDF5 file info struct.
* @param abort True if this is an abort.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
close_netcdf4_file(NC_HDF5_FILE_INFO_T *h5, int abort)
{
int retval = NC_NOERR;
assert(h5 && h5->root_grp);
LOG((3, "%s: h5->path %s abort %d", __func__, h5->controller->path, abort));
/* According to the docs, always end define mode on close. */
if (h5->flags & NC_INDEF)
h5->flags ^= NC_INDEF;
/* Sync the file, unless we're aborting, or this is a read-only
* file. */
if (!h5->no_write && !abort)
if ((retval = sync_netcdf4_file(h5)))
goto exit;
/* Delete all the list contents for vars, dims, and atts, in each
* group. */
if ((retval = nc4_rec_grp_del(&h5->root_grp, h5->root_grp)))
goto exit;
/* Close hdf file. */
#ifdef USE_HDF4
if (h5->hdf4)
{
if (SDend(h5->sdid))
BAIL_QUIET(NC_EHDFERR);
}
else
#endif /* USE_HDF4 */
{
#ifdef USE_PARALLEL4
/* Free the MPI Comm & Info objects, if we opened the file in parallel */
if(h5->parallel)
{
if(MPI_COMM_NULL != h5->comm)
MPI_Comm_free(&h5->comm);
if(MPI_INFO_NULL != h5->info)
MPI_Info_free(&h5->info);
}
#endif
if(h5->fileinfo) free(h5->fileinfo);
if (H5Fclose(h5->hdfid) < 0)
{
int nobjs;
nobjs = H5Fget_obj_count(h5->hdfid, H5F_OBJ_ALL);
/* Apparently we can get an error even when nobjs == 0 */
if(nobjs < 0) {
BAIL_QUIET(NC_EHDFERR);
} else if(nobjs > 0) {
#ifdef LOGGING
char msg[1024];
int logit = 1;
/* If the close doesn't work, probably there are still some HDF5
* objects open, which means there's a bug in the library. So
* print out some info on to help the poor programmer figure it
* out. */
snprintf(msg,sizeof(msg),"There are %d HDF5 objects open!", nobjs);
#ifdef LOGOPEN
LOG((0, msg));
#else
fprintf(stdout,msg);
logit = 0;
#endif
reportopenobjects(logit,h5->hdfid);
#endif
}
}
}
exit:
/* Free the nc4_info struct; above code should have reclaimed
everything else */
if(!retval && h5 != NULL)
free(h5);
return retval;
}
/**
* @internal Define the names of attributes to ignore added by the
* HDF5 dimension scale; these attached to variables. They cannot be
* modified thru the netcdf-4 API.
*/
const char* NC_RESERVED_VARATT_LIST[] = {
NC_ATT_REFERENCE_LIST,
NC_ATT_CLASS,
NC_ATT_DIMENSION_LIST,
NC_ATT_NAME,
NC_ATT_COORDINATES,
NC_DIMID_ATT_NAME,
NULL
};
/**
* @internal Define the names of attributes to ignore because they are
* "hidden" global attributes. They can be read, but not modified thru
* the netcdf-4 API.
*/
const char* NC_RESERVED_ATT_LIST[] = {
NC_ATT_FORMAT,
NC3_STRICT_ATT_NAME,
NCPROPS,
ISNETCDF4ATT,
SUPERBLOCKATT,
NULL
};
/**
* @internal Define the subset of the reserved list that is readable
* by name only
*/
const char* NC_RESERVED_SPECIAL_LIST[] = {
ISNETCDF4ATT,
SUPERBLOCKATT,
NCPROPS,
NULL
};
size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE; /**< Default chunk cache size. */
size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /**< Default chunk cache number of elements. */
float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION; /**< Default chunk cache preemption. */
#define NUM_TYPES 12 /**< Number of netCDF atomic types. */
/** @internal Native HDF5 constants for atomic types. For performance,
* fill this array only the first time, and keep it in global memory
* for each further use. */
static hid_t h5_native_type_constant_g[NUM_TYPES];
/** @internal NetCDF atomic type names. */
static const char nc_type_name_g[NUM_TYPES][NC_MAX_NAME + 1] = {"char", "byte", "short",
"int", "float", "double", "ubyte",
"ushort", "uint", "int64",
"uint64", "string"};
/** @internal NetCDF atomic types. */
static const nc_type nc_type_constant_g[NUM_TYPES] = {NC_CHAR, NC_BYTE, NC_SHORT,
NC_INT, NC_FLOAT, NC_DOUBLE, NC_UBYTE,
NC_USHORT, NC_UINT, NC_INT64,
NC_UINT64, NC_STRING};
/** @internal NetCDF atomic type sizes. */
static const int nc_type_size_g[NUM_TYPES] = {sizeof(char), sizeof(char), sizeof(short),
sizeof(int), sizeof(float), sizeof(double), sizeof(unsigned char),
sizeof(unsigned short), sizeof(unsigned int), sizeof(long long),
sizeof(unsigned long long), sizeof(char *)};
/**
* Set chunk cache size. Only affects files opened/created *after* it
* is called.
*
* @param size Size in bytes to set cache.
* @param nelems Number of elements to hold in cache.
* @param preemption Premption stragety (between 0 and 1).
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Bad preemption.
* @author Ed Hartnett
*/
int
nc_set_chunk_cache(size_t size, size_t nelems, float preemption)
{
if (preemption < 0 || preemption > 1)
return NC_EINVAL;
nc4_chunk_cache_size = size;
nc4_chunk_cache_nelems = nelems;
nc4_chunk_cache_preemption = preemption;
return NC_NOERR;
}
/**
* Get chunk cache size. Only affects files opened/created *after* it
* is called.
*
* @param sizep Pointer that gets size in bytes to set cache.
* @param nelemsp Pointer that gets number of elements to hold in cache.
* @param preemptionp Pointer that gets premption stragety (between 0 and 1).
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc_get_chunk_cache(size_t *sizep, size_t *nelemsp, float *preemptionp)
{
if (sizep)
*sizep = nc4_chunk_cache_size;
if (nelemsp)
*nelemsp = nc4_chunk_cache_nelems;
if (preemptionp)
*preemptionp = nc4_chunk_cache_preemption;
return NC_NOERR;
}
/**
* @internal Set the chunk cache. Required for fortran to avoid size_t
* issues.
*
* @param size Cache size.
* @param nelems Number of elements.
* @param preemption Preemption * 100.
*
* @return NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc_set_chunk_cache_ints(int size, int nelems, int preemption)
{
if (size <= 0 || nelems <= 0 || preemption < 0 || preemption > 100)
return NC_EINVAL;
nc4_chunk_cache_size = size;
nc4_chunk_cache_nelems = nelems;
nc4_chunk_cache_preemption = (float)preemption / 100;
return NC_NOERR;
}
/**
* @internal Get the chunk cache settings. Required for fortran to
* avoid size_t issues.
*
* @param sizep Pointer that gets cache size.
* @param nelemsp Pointer that gets number of elements.
* @param preemptionp Pointer that gets preemption * 100.
*
* @return NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc_get_chunk_cache_ints(int *sizep, int *nelemsp, int *preemptionp)
{
if (sizep)
*sizep = (int)nc4_chunk_cache_size;
if (nelemsp)
*nelemsp = (int)nc4_chunk_cache_nelems;
if (preemptionp)
*preemptionp = (int)(nc4_chunk_cache_preemption * 100);
return NC_NOERR;
}
/**
* @internal This will return the length of a netcdf data type in bytes.
*
* @param type A netcdf atomic type.
*
* @return Type size in bytes, or -1 if type not found.
* @author Ed Hartnett
*/
int
nc4typelen(nc_type type)
{
switch(type){
case NC_BYTE:
case NC_CHAR:
case NC_UBYTE:
return 1;
case NC_USHORT:
case NC_SHORT:
return 2;
case NC_FLOAT:
case NC_INT:
case NC_UINT:
return 4;
case NC_DOUBLE:
case NC_INT64:
case NC_UINT64:
return 8;
}
return -1;
}
/**
* @internal Create a netCDF-4/HDF5 file.
*
* @param path The file name of the new file.
* @param cmode The creation mode flag.
* @param comm MPI communicator (parallel IO only).
* @param info MPI info (parallel IO only).
* @param nc Pointer to an instance of NC.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid input (check cmode).
* @return ::NC_EEXIST File exists and NC_NOCLOBBER used.
* @return ::NC_EHDFERR HDF5 returned error.
* @ingroup netcdf4
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
NC *nc)
{
hid_t fcpl_id, fapl_id = -1;
unsigned flags;
FILE *fp;
int retval = NC_NOERR;
NC_HDF5_FILE_INFO_T* nc4_info = NULL;
#ifdef USE_PARALLEL4
int comm_duped = 0; /* Whether the MPI Communicator was duplicated */
int info_duped = 0; /* Whether the MPI Info object was duplicated */
#else /* !USE_PARALLEL4 */
int persist = 0; /* Should diskless try to persist its data into file?*/
#endif
assert(nc && path);
LOG((3, "%s: path %s mode 0x%x", __func__, path, cmode));
if(cmode & NC_DISKLESS)
flags = H5F_ACC_TRUNC;
else if(cmode & NC_NOCLOBBER)
flags = H5F_ACC_EXCL;
else
flags = H5F_ACC_TRUNC;
/* If this file already exists, and NC_NOCLOBBER is specified,
return an error. */
if (cmode & NC_DISKLESS) {
#ifndef USE_PARALLEL4
if(cmode & NC_WRITE)
persist = 1;
#endif
} else if ((cmode & NC_NOCLOBBER) && (fp = fopen(path, "r"))) {
fclose(fp);
return NC_EEXIST;
}
/* Add necessary structs to hold netcdf-4 file data. */
if ((retval = nc4_nc4f_list_add(nc, path, (NC_WRITE | cmode))))
BAIL(retval);
nc4_info = NC4_DATA(nc);
assert(nc4_info && nc4_info->root_grp);
/* Need this access plist to control how HDF5 handles open objects
* on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to
* fail if there are any open objects in the file. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
BAIL(NC_EHDFERR);
#ifdef USE_PARALLEL4
/* If this is a parallel file create, set up the file creation
property list. */
if ((cmode & NC_MPIIO) || (cmode & NC_MPIPOSIX))
{
nc4_info->parallel = NC_TRUE;
if (cmode & NC_MPIIO) /* MPI/IO */
{
LOG((4, "creating parallel file with MPI/IO"));
if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
BAIL(NC_EPARINIT);
}
#ifdef USE_PARALLEL_POSIX
else /* MPI/POSIX */
{
LOG((4, "creating parallel file with MPI/posix"));
if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
BAIL(NC_EPARINIT);
}
#else /* USE_PARALLEL_POSIX */
/* Should not happen! Code in NC4_create/NC4_open should alias the
* NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
* available in HDF5. -QAK
*/
else /* MPI/POSIX */
BAIL(NC_EPARINIT);
#endif /* USE_PARALLEL_POSIX */
/* Keep copies of the MPI Comm & Info objects */
if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
BAIL(NC_EMPI);
comm_duped++;
if (MPI_INFO_NULL != info)
{
if (MPI_SUCCESS != MPI_Info_dup(info, &nc4_info->info))
BAIL(NC_EMPI);
info_duped++;
}
else
{
/* No dup, just copy it. */
nc4_info->info = info;
}
}
#else /* only set cache for non-parallel... */
if(cmode & NC_DISKLESS) {
if (H5Pset_fapl_core(fapl_id, 4096, persist))
BAIL(NC_EDISKLESS);
}
if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
nc4_chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
LOG((4, "%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
__func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
#endif /* USE_PARALLEL4 */
#ifdef HDF5_HAS_LIBVER_BOUNDS
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST) < 0)
BAIL(NC_EHDFERR);
#endif
/* Create the property list. */
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0)
BAIL(NC_EHDFERR);
/* RJ: this suppose to be FALSE that is defined in H5 private.h as 0 */
if (H5Pset_obj_track_times(fcpl_id,0)<0)
BAIL(NC_EHDFERR);
/* Set latest_format in access propertly list and
* H5P_CRT_ORDER_TRACKED in the creation property list. This turns
* on HDF5 creation ordering. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0)
BAIL(NC_EHDFERR);
/* Create the file. */
#ifdef HDF5_HAS_COLL_METADATA_OPS
H5Pset_all_coll_metadata_ops(fapl_id, 1 );
H5Pset_coll_metadata_write(fapl_id, 1);
#endif
if ((nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0)
/*Change the return error from NC_EFILEMETADATA to
System error EACCES because that is the more likely problem */
BAIL(EACCES);
/* Open the root group. */
if ((nc4_info->root_grp->hdf_grpid = H5Gopen2(nc4_info->hdfid, "/",
H5P_DEFAULT)) < 0)
BAIL(NC_EFILEMETA);
/* Release the property lists. */
if (H5Pclose(fapl_id) < 0 || H5Pclose(fcpl_id) < 0)
BAIL(NC_EHDFERR);
/* Define mode gets turned on automatically on create. */
nc4_info->flags |= NC_INDEF;
NC4_get_fileinfo(nc4_info,&globalpropinfo);
NC4_put_propattr(nc4_info);
return NC_NOERR;
exit: /*failure exit*/
#ifdef USE_PARALLEL4
if (comm_duped) MPI_Comm_free(&nc4_info->comm);
if (info_duped) MPI_Info_free(&nc4_info->info);
#endif
if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
if(!nc4_info) return retval;
close_netcdf4_file(nc4_info,1); /* treat like abort */
return retval;
}
/**
* @internal Create a netCDF-4/HDF5 file.
*
* @param path The file name of the new file.
* @param cmode The creation mode flag.
* @param initialsz Ignored by this function.
* @param basepe Ignored by this function.
* @param chunksizehintp Ignored by this function.
* @param use_parallel 0 for sequential, non-zero for parallel I/O.
* @param parameters pointer to struct holding extra data (e.g. for parallel I/O)
* layer. Ignored if NULL.
* @param dispatch Pointer to the dispatch table for this file.
* @param nc_file Pointer to an instance of NC.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid input (check cmode).
* @ingroup netcdf4
* @author Ed Hartnett
*/
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)
{
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
int res;
assert(nc_file && path);
LOG((1, "%s: path %s cmode 0x%x comm %d info %d",
__func__, path, cmode, comm, info));
#ifdef USE_PARALLEL4
if (parameters)
{
comm = ((NC_MPI_INFO *)parameters)->comm;
info = ((NC_MPI_INFO *)parameters)->info;
}
#endif /* USE_PARALLEL4 */
/* If this is our first file, turn off HDF5 error messages. */
if (!nc4_hdf5_initialized)
nc4_hdf5_initialize();
/* Check the cmode for validity. */
if((cmode & ILLEGAL_CREATE_FLAGS) != 0)
{res = NC_EINVAL; goto done;}
/* Cannot have both */
if((cmode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
{res = NC_EINVAL; goto done;}
/* Currently no parallel diskless io */
if((cmode & (NC_MPIIO | NC_MPIPOSIX)) && (cmode & NC_DISKLESS))
{res = NC_EINVAL; goto done;}
#ifndef USE_PARALLEL_POSIX
/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
* the NC_MPIPOSIX flag to NC_MPIIO. -QAK
*/
if(cmode & NC_MPIPOSIX)
{
cmode &= ~NC_MPIPOSIX;
cmode |= NC_MPIIO;
}
#endif /* USE_PARALLEL_POSIX */
cmode |= NC_NETCDF4;
/* Apply default create format. */
if (nc_get_default_format() == NC_FORMAT_CDF5)
cmode |= NC_CDF5;
else if (nc_get_default_format() == NC_FORMAT_64BIT_OFFSET)
cmode |= NC_64BIT_OFFSET;
else if (nc_get_default_format() == NC_FORMAT_NETCDF4_CLASSIC)
cmode |= NC_CLASSIC_MODEL;
LOG((2, "cmode after applying default format: 0x%x", cmode));
nc_file->int_ncid = nc_file->ext_ncid;
res = nc4_create_file(path, cmode, comm, info, nc_file);
done:
return res;
}
/**
* @internal This function is called by read_dataset when a dimension
* scale dataset is encountered. It reads in the dimension data
* (creating a new NC_DIM_INFO_T object), and also checks to see if
* this is a dimension without a variable - that is, a coordinate
* dimension which does not have any coordinate data.
*
* @param grp Pointer to group info struct.
* @param datasetid The HDF5 dataset ID.
* @param obj_name
* @param statbuf
* @param scale_size Size of dimension scale.
* @param max_scale_size Maximum size of dim scale.
* @param dim Pointer to pointer that gets new dim info struct.
*
* @returns ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
const H5G_stat_t *statbuf, hsize_t scale_size, hsize_t max_scale_size,
NC_DIM_INFO_T **dim)
{
NC_DIM_INFO_T *new_dim; /* Dimension added to group */
char dimscale_name_att[NC_MAX_NAME + 1] = ""; /* Dimscale name, for checking if dim without var */
htri_t attr_exists = -1; /* Flag indicating hidden attribute exists */
hid_t attid = -1; /* ID of hidden attribute (to store dim ID) */
int dimscale_created = 0; /* Remember if a dimension was created (for error recovery) */
short initial_next_dimid = grp->nc4_info->next_dimid;/* Retain for error recovery */
int retval;
/* Add a dimension for this scale. */
if ((retval = nc4_dim_list_add(&grp->dim, &new_dim)))
BAIL(retval);
dimscale_created++;
/* Does this dataset have a hidden attribute that tells us its
* dimid? If so, read it. */
if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
if ((attid = H5Aopen_name(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (H5Aread(attid, H5T_NATIVE_INT, &new_dim->dimid) < 0)
BAIL(NC_EHDFERR);
/* Check if scale's dimid should impact the group's next dimid */
if (new_dim->dimid >= grp->nc4_info->next_dimid)
grp->nc4_info->next_dimid = new_dim->dimid + 1;
}
else
{
/* Assign dimid */
new_dim->dimid = grp->nc4_info->next_dimid++;
}
if (!(new_dim->name = strdup(obj_name)))
BAIL(NC_ENOMEM);
if (SIZEOF_SIZE_T < 8 && scale_size > NC_MAX_UINT)
{
new_dim->len = NC_MAX_UINT;
new_dim->too_long = NC_TRUE;
}
else
new_dim->len = scale_size;
new_dim->hdf5_objid.fileno[0] = statbuf->fileno[0];
new_dim->hdf5_objid.fileno[1] = statbuf->fileno[1];
new_dim->hdf5_objid.objno[0] = statbuf->objno[0];
new_dim->hdf5_objid.objno[1] = statbuf->objno[1];
new_dim->hash = hash_fast(obj_name, strlen(obj_name));
/* If the dimscale has an unlimited dimension, then this dimension
* is unlimited. */
if (max_scale_size == H5S_UNLIMITED)
new_dim->unlimited = NC_TRUE;
/* If the scale name is set to DIM_WITHOUT_VARIABLE, then this is a
* dimension, but not a variable. (If get_scale_name returns an
* error, just move on, there's no NAME.) */
if (H5DSget_scale_name(datasetid, dimscale_name_att, NC_MAX_NAME) >= 0)
{
if (!strncmp(dimscale_name_att, DIM_WITHOUT_VARIABLE,
strlen(DIM_WITHOUT_VARIABLE)))
{
if (new_dim->unlimited)
{
size_t len = 0, *lenp = &len;
if ((retval = nc4_find_dim_len(grp, new_dim->dimid, &lenp)))
BAIL(retval);
new_dim->len = *lenp;
}
/* Hold open the dataset, since the dimension doesn't have a coordinate variable */
new_dim->hdf_dimscaleid = datasetid;
H5Iinc_ref(new_dim->hdf_dimscaleid); /* Increment number of objects using ID */
}
}
/* Set the dimension created */
*dim = new_dim;
exit:
/* Close the hidden attribute, if it was opened (error, or no error) */
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
/* On error, undo any dimscale creation */
if (retval < 0 && dimscale_created)
{
/* Delete the dimension */
if ((retval = nc4_dim_list_del(&grp->dim, new_dim)))
BAIL2(retval);
/* Reset the group's information */
grp->nc4_info->next_dimid = initial_next_dimid;
}
return retval;
}
/**
* @internal This function reads the hacked in coordinates attribute I
* use for multi-dimensional coordinates.
*
* @param grp Group info pointer.
* @param var Var info pointer.
*
* @return NC_NOERR No error.
* @author Ed Hartnett
*/
static int
read_coord_dimids(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
hid_t coord_att_typeid = -1, coord_attid = -1, spaceid = -1;
hssize_t npoints;
int ret = 0;
int d;
/* There is a hidden attribute telling us the ids of the
* dimensions that apply to this multi-dimensional coordinate
* variable. Read it. */
if ((coord_attid = H5Aopen_name(var->hdf_datasetid, COORDINATES)) < 0) ret++;
if (!ret && (coord_att_typeid = H5Aget_type(coord_attid)) < 0) ret++;
/* How many dimensions are there? */
if (!ret && (spaceid = H5Aget_space(coord_attid)) < 0) ret++;
if (!ret && (npoints = H5Sget_simple_extent_npoints(spaceid)) < 0) ret++;
/* Check that the number of points is the same as the number of dimensions
* for the variable */
if (!ret && npoints != var->ndims) ret++;
if (!ret && H5Aread(coord_attid, coord_att_typeid, var->dimids) < 0) ret++;
LOG((4, "dimscale %s is multidimensional and has coords", var->name));
/* Update var->dim field based on the var->dimids */
for (d = 0; d < var->ndims; d++) {
/* Ok if does not find a dim at this time, but if found set it */
nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
}
/* Set my HDF5 IDs free! */
if (spaceid >= 0 && H5Sclose(spaceid) < 0) ret++;
if (coord_att_typeid >= 0 && H5Tclose(coord_att_typeid) < 0) ret++;
if (coord_attid >= 0 && H5Aclose(coord_attid) < 0) ret++;
return ret ? NC_EATTMETA : NC_NOERR;
}
/**
* @internal This function is called when reading a file's metadata
* for each dimension scale attached to a variable.
*
* @param did HDF5 ID for dimscale.
* @param dim
* @param dsid
* @param dimscale_hdf5_objids
*
* @return 0 for success, -1 for error.
* @author Ed Hartnett
*/
static herr_t
dimscale_visitor(hid_t did, unsigned dim, hid_t dsid,
void *dimscale_hdf5_objids)
{
H5G_stat_t statbuf;
/* Get more info on the dimscale object.*/
if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0)
return -1;
/* Pass this information back to caller. */
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[0] = statbuf.fileno[0];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[1] = statbuf.fileno[1];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[0] = statbuf.objno[0];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[1] = statbuf.objno[1];
return 0;
}
/**
* @internal Given an HDF5 type, set a pointer to netcdf type_info struct,
* either an existing one (for user-defined types) or a newly created
* one.
*
* @param h5 Pointer to HDF5 file info struct.
* @param datasetid HDF5 dataset ID.
* @param type_info Pointer to pointer that gets type info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EBADTYPID Type not found.
* @author Ed Hartnett
*/
static int
get_type_info2(NC_HDF5_FILE_INFO_T *h5, hid_t datasetid,
NC_TYPE_INFO_T **type_info)
{
htri_t is_str, equal = 0;
H5T_class_t class;
hid_t native_typeid, hdf_typeid;
H5T_order_t order;
int t;
assert(h5 && type_info);
/* Because these N5T_NATIVE_* constants are actually function calls
* (!) in H5Tpublic.h, I can't initialize this array in the usual
* way, because at least some C compilers (like Irix) complain
* about calling functions when defining constants. So I have to do
* it like this. Note that there's no native types for char or
* string. Those are handled later. */
if (!h5_native_type_constant_g[1])
{
h5_native_type_constant_g[1] = H5T_NATIVE_SCHAR;
h5_native_type_constant_g[2] = H5T_NATIVE_SHORT;
h5_native_type_constant_g[3] = H5T_NATIVE_INT;
h5_native_type_constant_g[4] = H5T_NATIVE_FLOAT;
h5_native_type_constant_g[5] = H5T_NATIVE_DOUBLE;
h5_native_type_constant_g[6] = H5T_NATIVE_UCHAR;
h5_native_type_constant_g[7] = H5T_NATIVE_USHORT;
h5_native_type_constant_g[8] = H5T_NATIVE_UINT;
h5_native_type_constant_g[9] = H5T_NATIVE_LLONG;
h5_native_type_constant_g[10] = H5T_NATIVE_ULLONG;
}
/* Get the HDF5 typeid - we'll need it later. */
if ((hdf_typeid = H5Dget_type(datasetid)) < 0)
return NC_EHDFERR;
/* Get the native typeid. Will be equivalent to hdf_typeid when
* creating but not necessarily when reading, a variable. */
if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* Is this type an integer, string, compound, or what? */
if ((class = H5Tget_class(native_typeid)) < 0)
return NC_EHDFERR;
/* Is this an atomic type? */
if (class == H5T_STRING || class == H5T_INTEGER || class == H5T_FLOAT)
{
/* Allocate a phony NC_TYPE_INFO_T struct to hold type info. */
if (!(*type_info = calloc(1, sizeof(NC_TYPE_INFO_T))))
return NC_ENOMEM;
/* H5Tequal doesn't work with H5T_C_S1 for some reason. But
* H5Tget_class will return H5T_STRING if this is a string. */
if (class == H5T_STRING)
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
/* Make sure fixed-len strings will work like variable-len strings */
if (is_str || H5Tget_size(hdf_typeid) > 1)
{
/* Set a class for the type */
t = NUM_TYPES - 1;
(*type_info)->nc_type_class = NC_STRING;
}
else
{
/* Set a class for the type */
t = 0;
(*type_info)->nc_type_class = NC_CHAR;
}
}
else if (class == H5T_INTEGER || class == H5T_FLOAT)
{
for (t = 1; t < NUM_TYPES - 1; t++)
{
if ((equal = H5Tequal(native_typeid, h5_native_type_constant_g[t])) < 0)
return NC_EHDFERR;
if (equal)
break;
}
/* Find out about endianness.
* As of HDF 1.8.6, this works with all data types
* Not just H5T_INTEGER.
*
* See https://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetOrder
*/
if((order = H5Tget_order(hdf_typeid)) < 0)
return NC_EHDFERR;
if(order == H5T_ORDER_LE)
(*type_info)->endianness = NC_ENDIAN_LITTLE;
else if(order == H5T_ORDER_BE)
(*type_info)->endianness = NC_ENDIAN_BIG;
else
return NC_EBADTYPE;
if(class == H5T_INTEGER)
(*type_info)->nc_type_class = NC_INT;
else
(*type_info)->nc_type_class = NC_FLOAT;
}
(*type_info)->nc_typeid = nc_type_constant_g[t];
(*type_info)->size = nc_type_size_g[t];
if (!((*type_info)->name = strdup(nc_type_name_g[t])))
return NC_ENOMEM;
(*type_info)->hdf_typeid = hdf_typeid;
(*type_info)->native_hdf_typeid = native_typeid;
return NC_NOERR;
}
else
{
NC_TYPE_INFO_T *type;
/* This is a user-defined type. */
if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
*type_info = type;
/* The type entry in the array of user-defined types already has
* an open data typeid (and native typeid), so close the ones we
* opened above. */
if (H5Tclose(native_typeid) < 0)
return NC_EHDFERR;
if (H5Tclose(hdf_typeid) < 0)
return NC_EHDFERR;
if (type)
return NC_NOERR;
}
return NC_EBADTYPID;
}
/**
* @internal Read information about a user defined type from the HDF5
* file, and stash it in the group's list of types.
*
* @param grp Pointer to group info struct.
* @param hdf_typeid HDF5 type ID.
* @param type_name Pointer that gets the type name.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @return ::NC_EBADTYPID Type not found.
* @author Ed Hartnett
*/
static int
read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
{
NC_TYPE_INFO_T *type;
H5T_class_t class;
hid_t native_typeid;
size_t type_size;
int retval = NC_NOERR;
assert(grp && type_name);
LOG((4, "%s: type_name %s grp->name %s", __func__, type_name, grp->name));
/* What is the native type for this platform? */
if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* What is the size of this type on this platform. */
if (!(type_size = H5Tget_size(native_typeid)))
return NC_EHDFERR;
LOG((5, "type_size %d", type_size));
/* Add to the list for this new type, and get a local pointer to it. */
if ((retval = nc4_type_list_add(grp, type_size, type_name, &type)))
return retval;
/* Remember common info about this type. */
type->committed = NC_TRUE;
type->hdf_typeid = hdf_typeid;
H5Iinc_ref(type->hdf_typeid); /* Increment number of objects using ID */
type->native_hdf_typeid = native_typeid;
/* What is the class of this type, compound, vlen, etc. */
if ((class = H5Tget_class(hdf_typeid)) < 0)
return NC_EHDFERR;
switch (class)
{
case H5T_STRING:
type->nc_type_class = NC_STRING;
break;
case H5T_COMPOUND:
{
int nmembers;
unsigned int m;
char* member_name = NULL;
#ifdef JNA
char jna[1001];
#endif
type->nc_type_class = NC_COMPOUND;
if ((nmembers = H5Tget_nmembers(hdf_typeid)) < 0)
return NC_EHDFERR;
LOG((5, "compound type has %d members", nmembers));
for (m = 0; m < nmembers; m++)
{
hid_t member_hdf_typeid;
hid_t member_native_typeid;
size_t member_offset;
H5T_class_t mem_class;
nc_type member_xtype;
/* Get the typeid and native typeid of this member of the
* compound type. */
if ((member_hdf_typeid = H5Tget_member_type(type->native_hdf_typeid, m)) < 0)
return NC_EHDFERR;
if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid, H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* Get the name of the member.*/
member_name = H5Tget_member_name(type->native_hdf_typeid, m);
if (!member_name || strlen(member_name) > NC_MAX_NAME) {
retval = NC_EBADNAME;
break;
}
#ifdef JNA
else {
strncpy(jna,member_name,1000);
member_name = jna;
}
#endif
/* Offset in bytes on *this* platform. */
member_offset = H5Tget_member_offset(type->native_hdf_typeid, m);
/* Get dimensional data if this member is an array of something. */
if ((mem_class = H5Tget_class(member_hdf_typeid)) < 0)
return NC_EHDFERR;
if (mem_class == H5T_ARRAY)
{
int ndims, dim_size[NC_MAX_VAR_DIMS];
hsize_t dims[NC_MAX_VAR_DIMS];
int d;
if ((ndims = H5Tget_array_ndims(member_hdf_typeid)) < 0) {
retval = NC_EHDFERR;
break;
}
if (H5Tget_array_dims(member_hdf_typeid, dims, NULL) != ndims) {
retval = NC_EHDFERR;
break;
}
for (d = 0; d < ndims; d++)
dim_size[d] = dims[d];
/* What is the netCDF typeid of this member? */
if ((retval = get_netcdf_type(grp->nc4_info, H5Tget_super(member_hdf_typeid),
&member_xtype)))
break;
/* Add this member to our list of fields in this compound type. */
if ((retval = nc4_field_list_add(&type->u.c.field, type->u.c.num_fields++, member_name,
member_offset, H5Tget_super(member_hdf_typeid),
H5Tget_super(member_native_typeid),
member_xtype, ndims, dim_size)))
break;
}
else
{
/* What is the netCDF typeid of this member? */
if ((retval = get_netcdf_type(grp->nc4_info, member_native_typeid,
&member_xtype)))
break;
/* Add this member to our list of fields in this compound type. */
if ((retval = nc4_field_list_add(&type->u.c.field, type->u.c.num_fields++, member_name,
member_offset, member_hdf_typeid, member_native_typeid,
member_xtype, 0, NULL)))
break;
}
hdf5free(member_name);
member_name = NULL;
}
hdf5free(member_name);
member_name = NULL;
if(retval) /* error exit from loop */
return retval;
}
break;
case H5T_VLEN:
{
htri_t ret;
/* For conveninence we allow user to pass vlens of strings
* with null terminated strings. This means strings are
* treated slightly differently by the API, although they are
* really just VLENs of characters. */
if ((ret = H5Tis_variable_str(hdf_typeid)) < 0)
return NC_EHDFERR;
if (ret)
type->nc_type_class = NC_STRING;
else
{
hid_t base_hdf_typeid;
nc_type base_nc_type = NC_NAT;
type->nc_type_class = NC_VLEN;
/* Find the base type of this vlen (i.e. what is this a
* vlen of?) */
if (!(base_hdf_typeid = H5Tget_super(native_typeid)))
return NC_EHDFERR;
/* What size is this type? */
if (!(type_size = H5Tget_size(base_hdf_typeid)))
return NC_EHDFERR;
/* What is the netcdf corresponding type. */
if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
&base_nc_type)))
return retval;
LOG((5, "base_hdf_typeid 0x%x type_size %d base_nc_type %d",
base_hdf_typeid, type_size, base_nc_type));
/* Remember the base types for this vlen */
type->u.v.base_nc_typeid = base_nc_type;
type->u.v.base_hdf_typeid = base_hdf_typeid;
}
}
break;
case H5T_OPAQUE:
type->nc_type_class = NC_OPAQUE;
break;
case H5T_ENUM:
{
hid_t base_hdf_typeid;
nc_type base_nc_type = NC_NAT;
void *value;
int i;
char *member_name = NULL;
#ifdef JNA
char jna[1001];
#endif
type->nc_type_class = NC_ENUM;
/* Find the base type of this enum (i.e. what is this a
* enum of?) */
if (!(base_hdf_typeid = H5Tget_super(hdf_typeid)))
return NC_EHDFERR;
/* What size is this type? */
if (!(type_size = H5Tget_size(base_hdf_typeid)))
return NC_EHDFERR;
/* What is the netcdf corresponding type. */
if ((retval = get_netcdf_type(grp->nc4_info, base_hdf_typeid,
&base_nc_type)))
return retval;
LOG((5, "base_hdf_typeid 0x%x type_size %d base_nc_type %d",
base_hdf_typeid, type_size, base_nc_type));
/* Remember the base types for this enum */
type->u.e.base_nc_typeid = base_nc_type;
type->u.e.base_hdf_typeid = base_hdf_typeid;
/* Find out how many member are in the enum. */
if ((type->u.e.num_members = H5Tget_nmembers(hdf_typeid)) < 0)
return NC_EHDFERR;
/* Allocate space for one value. */
if (!(value = calloc(1, type_size)))
return NC_ENOMEM;
/* Read each name and value defined in the enum. */
for (i = 0; i < type->u.e.num_members; i++)
{
/* Get the name and value from HDF5. */
if (!(member_name = H5Tget_member_name(hdf_typeid, i)))
{
retval = NC_EHDFERR;
break;
}
#ifdef JNA
strncpy(jna,member_name,1000);
member_name = jna;
#endif
if (strlen(member_name) > NC_MAX_NAME)
{
retval = NC_EBADNAME;
break;
}
if (H5Tget_member_value(hdf_typeid, i, value) < 0)
{
retval = NC_EHDFERR;
break;
}
/* Insert new field into this type's list of fields. */
if ((retval = nc4_enum_member_add(&type->u.e.enum_member, type->size,
member_name, value)))
{
break;
}
hdf5free(member_name);
member_name = NULL;
}
hdf5free(member_name);
member_name = NULL;
if(value) free(value);
if(retval) /* error exit from loop */
return retval;
}
break;
default:
LOG((0, "unknown class"));
return NC_EBADCLASS;
}
return retval;
}
/**
* @internal This function is called by read_dataset(), (which is called
* by nc4_rec_read_metadata()) when a netCDF variable is found in the
* file. This function reads in all the metadata about the var,
* including the attributes.
*
* @param grp Pointer to group info struct.
* @param datasetid HDF5 dataset ID.
* @param obj_name Name of the HDF5 object to read.
* @param ndims Number of dimensions.
* @param dim
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
size_t ndims, NC_DIM_INFO_T *dim)
{
NC_VAR_INFO_T *var = NULL;
hid_t access_pid = 0;
int incr_id_rc = 0; /* Whether the dataset ID's ref count has been incremented */
int d;
att_iter_info att_info; /* Custom iteration information */
H5Z_filter_t filter;
int num_filters;
unsigned int cd_values_zip[CD_NELEMS_ZLIB];
size_t cd_nelems = CD_NELEMS_ZLIB;
hid_t propid = 0;
H5D_fill_value_t fill_status;
H5D_layout_t layout;
hsize_t chunksize[NC_MAX_VAR_DIMS] = {0};
int retval = NC_NOERR;
double rdcc_w0;
int f;
assert(obj_name && grp);
LOG((4, "%s: obj_name %s", __func__, obj_name));
/* Add a variable to the end of the group's var list. */
if ((retval = nc4_var_add(&var)))
BAIL(retval);
/* Fill in what we already know. */
var->hdf_datasetid = datasetid;
H5Iinc_ref(var->hdf_datasetid); /* Increment number of objects using ID */
incr_id_rc++; /* Indicate that we've incremented the ref. count (for errors) */
var->varid = grp->nvars++;
var->created = NC_TRUE;
var->ndims = ndims;
/* We need some room to store information about dimensions for this
* var. */
if (var->ndims)
{
if (!(var->dim = calloc(var->ndims, sizeof(NC_DIM_INFO_T *))))
BAIL(NC_ENOMEM);
if (!(var->dimids = calloc(var->ndims, sizeof(int))))
BAIL(NC_ENOMEM);
}
/* Get the current chunk cache settings. */
if ((access_pid = H5Dget_access_plist(datasetid)) < 0)
BAIL(NC_EVARMETA);
/* Learn about current chunk cache settings. */
if ((H5Pget_chunk_cache(access_pid, &(var->chunk_cache_nelems),
&(var->chunk_cache_size), &rdcc_w0)) < 0)
BAIL(NC_EHDFERR);
var->chunk_cache_preemption = rdcc_w0;
/* Check for a weird case: a non-coordinate variable that has the
* same name as a dimension. It's legal in netcdf, and requires
* that the HDF5 dataset name be changed. */
if (strlen(obj_name) > strlen(NON_COORD_PREPEND) &&
!strncmp(obj_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)))
{
/* Allocate space for the name. */
if (!(var->name = malloc(((strlen(obj_name) - strlen(NON_COORD_PREPEND))+ 1) * sizeof(char))))
BAIL(NC_ENOMEM);
strcpy(var->name, &obj_name[strlen(NON_COORD_PREPEND)]);
/* Allocate space for the HDF5 name. */
if (!(var->hdf5_name = malloc((strlen(obj_name) + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
strcpy(var->hdf5_name, obj_name);
}
else
{
/* Allocate space for the name. */
if (!(var->name = malloc((strlen(obj_name) + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
strcpy(var->name, obj_name);
}
var->hash = hash_fast(var->name, strlen(var->name));
/* Find out what filters are applied to this HDF5 dataset,
* fletcher32, deflate, and/or shuffle. All other filters are
* just dumped */
if ((propid = H5Dget_create_plist(datasetid)) < 0)
BAIL(NC_EHDFERR);
/* Get the chunking info for non-scalar vars. */
if ((layout = H5Pget_layout(propid)) < -1)
BAIL(NC_EHDFERR);
if (layout == H5D_CHUNKED)
{
if (H5Pget_chunk(propid, NC_MAX_VAR_DIMS, chunksize) < 0)
BAIL(NC_EHDFERR);
if (!(var->chunksizes = malloc(var->ndims * sizeof(size_t))))
BAIL(NC_ENOMEM);
for (d = 0; d < var->ndims; d++)
var->chunksizes[d] = chunksize[d];
}
else if (layout == H5D_CONTIGUOUS || layout == H5D_COMPACT)
var->contiguous = NC_TRUE;
/* The possible values of filter (which is just an int) can be
* found in H5Zpublic.h. */
if ((num_filters = H5Pget_nfilters(propid)) < 0)
BAIL(NC_EHDFERR);
for (f = 0; f < num_filters; f++)
{
if ((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems,
cd_values_zip, 0, NULL, NULL)) < 0)
BAIL(NC_EHDFERR);
switch (filter)
{
case H5Z_FILTER_SHUFFLE:
var->shuffle = NC_TRUE;
break;
case H5Z_FILTER_FLETCHER32:
var->fletcher32 = NC_TRUE;
break;
case H5Z_FILTER_DEFLATE:
var->deflate = NC_TRUE;
if (cd_nelems != CD_NELEMS_ZLIB || cd_values_zip[0] > NC_MAX_DEFLATE_LEVEL)
BAIL(NC_EHDFERR);
var->deflate_level = cd_values_zip[0];
break;
default:
var->filterid = filter;
var->nparams = cd_nelems;
if(cd_nelems == 0)
var->params = NULL;
else {
/* We have to re-read the parameters based on actual nparams */
var->params = (unsigned int*)calloc(1,sizeof(unsigned int)*var->nparams);
if(var->params == NULL)
BAIL(NC_ENOMEM);
if((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems,
var->params, 0, NULL, NULL)) < 0)
BAIL(NC_EHDFERR);
}
break;
}
}
/* Learn all about the type of this variable. */
if ((retval = get_type_info2(grp->nc4_info, datasetid,
&var->type_info)))
BAIL(retval);
/* Indicate that the variable has a pointer to the type */
var->type_info->rc++;
/* Is there a fill value associated with this dataset? */
if (H5Pfill_value_defined(propid, &fill_status) < 0)
BAIL(NC_EHDFERR);
/* Get the fill value, if there is one defined. */
if (fill_status == H5D_FILL_VALUE_USER_DEFINED)
{
/* Allocate space to hold the fill value. */
if (!var->fill_value)
{
if (var->type_info->nc_type_class == NC_VLEN)
{
if (!(var->fill_value = malloc(sizeof(nc_vlen_t))))
BAIL(NC_ENOMEM);
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if (!(var->fill_value = malloc(sizeof(char *))))
BAIL(NC_ENOMEM);
}
else
{
assert(var->type_info->size);
if (!(var->fill_value = malloc(var->type_info->size)))
BAIL(NC_ENOMEM);
}
}
/* Get the fill value from the HDF5 property lust. */
if (H5Pget_fill_value(propid, var->type_info->native_hdf_typeid,
var->fill_value) < 0)
BAIL(NC_EHDFERR);
}
else
var->no_fill = NC_TRUE;
/* If it's a scale, mark it as such. */
if (dim)
{
assert(ndims);
var->dimscale = NC_TRUE;
if (var->ndims > 1)
{
if ((retval = read_coord_dimids(grp, var)))
BAIL(retval);
}
else
{
/* sanity check */
assert(0 == strcmp(var->name, dim->name));
var->dimids[0] = dim->dimid;
var->dim[0] = dim;
}
dim->coord_var = var;
}
/* If this is not a scale, but has scales, iterate
* through them. (i.e. this is a variable that is not a
* coordinate variable) */
else
{
int num_scales = 0;
/* Find out how many scales are attached to this
* dataset. H5DSget_num_scales returns an error if there are no
* scales, so convert a negative return value to zero. */
num_scales = H5DSget_num_scales(datasetid, 0);
if (num_scales < 0)
num_scales = 0;
if (num_scales && ndims)
{
/* Allocate space to remember whether the dimscale has been attached
* for each dimension. */
if (NULL == (var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
BAIL(NC_ENOMEM);
/* Store id information allowing us to match hdf5
* dimscales to netcdf dimensions. */
if (NULL == (var->dimscale_hdf5_objids = malloc(ndims * sizeof(struct hdf5_objid))))
BAIL(NC_ENOMEM);
for (d = 0; d < var->ndims; d++)
{
if (H5DSiterate_scales(var->hdf_datasetid, d, NULL, dimscale_visitor,
&(var->dimscale_hdf5_objids[d])) < 0)
BAIL(NC_EHDFERR);
var->dimscale_attached[d] = NC_TRUE;
}
}
}
/* Now read all the attributes of this variable, ignoring the
ones that hold HDF5 dimension scale information. */
att_info.var = var;
att_info.grp = grp;
if ((H5Aiterate2(var->hdf_datasetid, H5_INDEX_CRT_ORDER, H5_ITER_INC, NULL,
att_read_var_callbk, &att_info)) < 0)
BAIL(NC_EATTMETA);
/* Add a var to the variable array, growing it as needed. */
if ((retval = nc4_vararray_add(grp, var)))
BAIL(retval);
/* Is this a deflated variable with a chunksize greater than the
* current cache size? */
if ((retval = nc4_adjust_var_cache(grp, var)))
BAIL(retval);
exit:
if (retval)
{
if (incr_id_rc && H5Idec_ref(datasetid) < 0)
BAIL2(NC_EHDFERR);
if (var && nc4_var_del(var))
BAIL2(NC_EHDFERR);
}
if (access_pid && H5Pclose(access_pid) < 0)
BAIL2(NC_EHDFERR);
if (propid > 0 && H5Pclose(propid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/**
* @internal This function is called by nc4_rec_read_metadata to read
* all the group level attributes (the NC_GLOBAL atts for this
* group).
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
read_grp_atts(NC_GRP_INFO_T *grp)
{
hid_t attid = -1;
hsize_t num_obj, i;
NC_ATT_INFO_T *att;
NC_TYPE_INFO_T *type;
char obj_name[NC_MAX_HDF5_NAME + 1];
int max_len;
int retval = NC_NOERR;
int hidden = 0;
num_obj = H5Aget_num_attrs(grp->hdf_grpid);
for (i = 0; i < num_obj; i++)
{
if ((attid = H5Aopen_idx(grp->hdf_grpid, (unsigned int)i)) < 0)
BAIL(NC_EATTMETA);
if (H5Aget_name(attid, NC_MAX_NAME + 1, obj_name) < 0)
BAIL(NC_EATTMETA);
LOG((3, "reading attribute of _netCDF group, named %s", obj_name));
/* See if this a hidden, global attribute */
if(grp->nc4_info->root_grp == grp) {
const char** reserved = NC_RESERVED_ATT_LIST;
hidden = 0;
for(;*reserved;reserved++) {
if(strcmp(*reserved,obj_name)==0) {
hidden = 1;
break;
}
}
}
/* This may be an attribute telling us that strict netcdf-3
* rules are in effect. If so, we will make note of the fact,
* but not add this attribute to the metadata. It's not a user
* attribute, but an internal netcdf-4 one. */
if(strcmp(obj_name, NC3_STRICT_ATT_NAME)==0)
grp->nc4_info->cmode |= NC_CLASSIC_MODEL;
else if(!hidden) {
/* Add an att struct at the end of the list, and then go to it. */
if ((retval = nc4_att_list_add(&grp->att, &att)))
BAIL(retval);
/* Add the info about this attribute. */
max_len = strlen(obj_name) > NC_MAX_NAME ? NC_MAX_NAME : strlen(obj_name);
if (!(att->name = malloc((max_len + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
strncpy(att->name, obj_name, max_len);
att->name[max_len] = 0;
att->attnum = grp->natts++;
retval = read_hdf5_att(grp, attid, att);
if(retval == NC_EBADTYPID) {
if((retval = nc4_att_list_del(&grp->att, att)))
BAIL(retval);
} else if(retval) {
BAIL(retval);
} else {
att->created = NC_TRUE;
if ((retval = nc4_find_type(grp->nc4_info, att->nc_typeid, &type)))
BAIL(retval);
}
}
/* Unconditionally close the open attribute */
H5Aclose(attid);
attid = -1;
}
exit:
if (attid > 0) {
if(H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
}
return retval;
}
/**
* @internal This function is called when nc4_rec_read_metadata
* encounters an HDF5 dataset when reading a file.
*
* @param grp Pointer to group info struct.
* @param datasetid HDF5 dataset ID.
* @param obj_name Object name.
* @param statbuf HDF5 status buffer.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EHDFERR HDF5 returned error.
* @author Ed Hartnett
*/
static int
read_dataset(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
const H5G_stat_t *statbuf)
{
NC_DIM_INFO_T *dim = NULL; /* Dimension created for scales */
hid_t spaceid = 0;
int ndims;
htri_t is_scale;
int retval = NC_NOERR;
/* Get the dimension information for this dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0)
BAIL(NC_EHDFERR);
if (is_scale)
{
hsize_t dims[H5S_MAX_RANK];
hsize_t max_dims[H5S_MAX_RANK];
/* Query the scale's size & max. size */
if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0)
BAIL(NC_EHDFERR);
/* Read the scale information. */
if ((retval = read_scale(grp, datasetid, obj_name, statbuf, dims[0],
max_dims[0], &dim)))
BAIL(retval);
}
/* Add a var to the linked list, and get its metadata,
* unless this is one of those funny dimscales that are a
* dimension in netCDF but not a variable. (Spooky!) */
if (NULL == dim || (dim && !dim->hdf_dimscaleid))
if ((retval = read_var(grp, datasetid, obj_name, ndims, dim)))
BAIL(retval);
exit:
if (spaceid && H5Sclose(spaceid) <0)
BAIL2(retval);
return retval;
}
/**
* @internal Add callback function to list.
*
* @param head
* @param tail
* @param oinfo The object info.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
static int
nc4_rec_read_metadata_cb_list_add(NC4_rec_read_metadata_obj_info_t **head,
NC4_rec_read_metadata_obj_info_t **tail,
const NC4_rec_read_metadata_obj_info_t *oinfo)
{
NC4_rec_read_metadata_obj_info_t *new_oinfo; /* Pointer to info for object */
/* Allocate memory for the object's info */
if (!(new_oinfo = calloc(1, sizeof(*new_oinfo))))
return NC_ENOMEM;
/* Make a copy of the object's info */
memcpy(new_oinfo, oinfo, sizeof(*oinfo));
if (*tail)
{
assert(*head);
(*tail)->next = new_oinfo;
*tail = new_oinfo;
}
else
{
assert(NULL == *head);
*head = *tail = new_oinfo;
}
return (NC_NOERR);
}
/**
* @internal Callback function called from nc4_rec_read_metadata().
*
* @param grpid HDF5 group ID.
* @param name Name of object.
* @param info Info struct for object.
* @param _op_data Pointer to data.
*
* @return ::NC_NOERR No error.
* @return H5_ITER_ERROR HDF5 error.
* @author Ed Hartnett
*/
static int
nc4_rec_read_metadata_cb(hid_t grpid, const char *name, const H5L_info_t *info,
void *_op_data)
{
NC4_rec_read_metadata_ud_t *udata = (NC4_rec_read_metadata_ud_t *)_op_data; /* Pointer to user data for callback */
NC4_rec_read_metadata_obj_info_t oinfo; /* Pointer to info for object */
int retval = H5_ITER_CONT;
/* Reset the memory for the object's info */
memset(&oinfo, 0, sizeof(oinfo));
/* Open this critter. */
if ((oinfo.oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0)
BAIL(H5_ITER_ERROR);
/* Get info about the object.*/
if (H5Gget_objinfo(oinfo.oid, ".", 1, &oinfo.statbuf) < 0)
BAIL(H5_ITER_ERROR);
strncpy(oinfo.oname, name, NC_MAX_NAME);
/* Add object to list, for later */
switch(oinfo.statbuf.type)
{
case H5G_GROUP:
LOG((3, "found group %s", oinfo.oname));
/* Defer descending into child group immediately, so that the types
* in the current group can be processed and be ready for use by
* vars in the child group(s).
*/
if (nc4_rec_read_metadata_cb_list_add(&udata->grps_head, &udata->grps_tail, &oinfo))
BAIL(H5_ITER_ERROR);
break;
case H5G_DATASET:
LOG((3, "found dataset %s", oinfo.oname));
/* Learn all about this dataset, which may be a dimscale
* (i.e. dimension metadata), or real data. */
if ((retval = read_dataset(udata->grp, oinfo.oid, oinfo.oname, &oinfo.statbuf)))
{
/* Allow NC_EBADTYPID to transparently skip over datasets
* which have a datatype that netCDF-4 doesn't undertand
* (currently), but break out of iteration for other
* errors.
*/
if(NC_EBADTYPID != retval)
BAIL(H5_ITER_ERROR);
else
retval = H5_ITER_CONT;
}
/* Close the object */
if (H5Oclose(oinfo.oid) < 0)
BAIL(H5_ITER_ERROR);
break;
case H5G_TYPE:
LOG((3, "found datatype %s", oinfo.oname));
/* Process the named datatype */
if (read_type(udata->grp, oinfo.oid, oinfo.oname))
BAIL(H5_ITER_ERROR);
/* Close the object */
if (H5Oclose(oinfo.oid) < 0)
BAIL(H5_ITER_ERROR);
break;
default:
LOG((0, "Unknown object class %d in %s!", oinfo.statbuf.type, __func__));
BAIL(H5_ITER_ERROR);
}
exit:
if (retval)
{
if (oinfo.oid > 0 && H5Oclose(oinfo.oid) < 0)
BAIL2(H5_ITER_ERROR);
}
return (retval);
}
/**
* @internal This is the main function to recursively read all the
* metadata for the file. The links in the 'grp' are iterated over
* and added to the file's metadata information. Note that child
* groups are not immediately processed, but are deferred until all
* the other links in the group are handled (so that vars in the child
* groups are guaranteed to have types that they use in a parent group
* in place).
*
* @param grp Pointer to a group.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
nc4_rec_read_metadata(NC_GRP_INFO_T *grp)
{
NC4_rec_read_metadata_ud_t udata; /* User data for iteration */
NC4_rec_read_metadata_obj_info_t *oinfo; /* Pointer to info for object */
hsize_t idx=0;
hid_t pid = 0;
unsigned crt_order_flags = 0;
H5_index_t iter_index;
int i, retval = NC_NOERR; /* everything worked! */
assert(grp && grp->name);
LOG((3, "%s: grp->name %s", __func__, grp->name));
/* Portably initialize user data for later */
memset(&udata, 0, sizeof(udata));
/* Open this HDF5 group and retain its grpid. It will remain open
* with HDF5 until this file is nc_closed. */
if (!grp->hdf_grpid)
{
if (grp->parent)
{
if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid,
grp->name, H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
}
else
{
if ((grp->hdf_grpid = H5Gopen2(grp->nc4_info->hdfid,
"/", H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
}
}
assert(grp->hdf_grpid > 0);
/* Get the group creation flags, to check for creation ordering */
pid = H5Gget_create_plist(grp->hdf_grpid);
H5Pget_link_creation_order(pid, &crt_order_flags);
if (H5Pclose(pid) < 0)
BAIL(NC_EHDFERR);
/* Set the iteration index to use */
if (crt_order_flags & H5P_CRT_ORDER_TRACKED)
iter_index = H5_INDEX_CRT_ORDER;
else
{
NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
/* Without creation ordering, file must be read-only. */
if (!h5->no_write)
BAIL(NC_ECANTWRITE);
iter_index = H5_INDEX_NAME;
}
/* Set user data for iteration */
udata.grp = grp;
/* Iterate over links in this group, building lists for the types,
* datasets and groups encountered
*/
if (H5Literate(grp->hdf_grpid, iter_index, H5_ITER_INC, &idx,
nc4_rec_read_metadata_cb, (void *)&udata) < 0)
BAIL(NC_EHDFERR);
/* Process the child groups found */
/* (Deferred until now, so that the types in the current group get
* processed and are available for vars in the child group(s).)
*/
for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
{
NC_GRP_INFO_T *child_grp;
NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
/* Add group to file's hierarchy */
if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++,
grp, grp->nc4_info->controller, oinfo->oname, &child_grp)))
BAIL(retval);
/* Recursively read the child group's metadata */
if ((retval = nc4_rec_read_metadata(child_grp)))
BAIL(retval);
/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL(NC_EHDFERR);
/* Advance to next node, free current node */
udata.grps_head = oinfo->next;
free(oinfo);
}
/* Scan the group for global (i.e. group-level) attributes. */
if ((retval = read_grp_atts(grp)))
BAIL(retval);
/* when exiting define mode, mark all variable written */
for (i=0; i<grp->vars.nelems; i++)
grp->vars.value[i]->written_to = NC_TRUE;
exit:
/* Clean up local information on error, if anything remains */
if (retval)
{
for (oinfo = udata.grps_head; oinfo; oinfo = udata.grps_head)
{
/* Close the object */
if (H5Oclose(oinfo->oid) < 0)
BAIL2(NC_EHDFERR);
/* Advance to next node, free current node */
udata.grps_head = oinfo->next;
free(oinfo);
}
}
return retval;
}
/**
* @internal Open a netcdf-4 file. Things have already been kicked off
* in ncfunc.c in nc_open, but here the netCDF-4 part of opening a
* file is handled.
*
* @param path The file name of the new file.
* @param mode The open mode flag.
* @param parameters File parameters.
* @param nc Pointer to NC file info.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
nc4_open_file(const char *path, int mode, void* parameters, NC *nc)
{
hid_t fapl_id = H5P_DEFAULT;
unsigned flags = (mode & NC_WRITE) ?
H5F_ACC_RDWR : H5F_ACC_RDONLY;
int retval;
NC_HDF5_FILE_INFO_T* nc4_info = NULL;
int inmemory = ((mode & NC_INMEMORY) == NC_INMEMORY);
NC_MEM_INFO* meminfo = (NC_MEM_INFO*)parameters;
#ifdef USE_PARALLEL4
NC_MPI_INFO* mpiinfo = (NC_MPI_INFO*)parameters;
int comm_duped = 0; /* Whether the MPI Communicator was duplicated */
int info_duped = 0; /* Whether the MPI Info object was duplicated */
#endif /* !USE_PARALLEL4 */
LOG((3, "%s: path %s mode %d", __func__, path, mode));
assert(path && nc);
/* Add necessary structs to hold netcdf-4 file data. */
if ((retval = nc4_nc4f_list_add(nc, path, mode)))
BAIL(retval);
nc4_info = NC4_DATA(nc);
assert(nc4_info && nc4_info->root_grp);
/* Need this access plist to control how HDF5 handles open objects
* on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to
* fail if there are any open objects in the file. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
BAIL(NC_EHDFERR);
#ifdef USE_PARALLEL4
/* If this is a parallel file create, set up the file creation
property list. */
if (mode & NC_MPIIO || mode & NC_MPIPOSIX)
{
nc4_info->parallel = NC_TRUE;
if (mode & NC_MPIIO) /* MPI/IO */
{
LOG((4, "opening parallel file with MPI/IO"));
if (H5Pset_fapl_mpio(fapl_id, mpiinfo->comm, mpiinfo->info) < 0)
BAIL(NC_EPARINIT);
}
#ifdef USE_PARALLEL_POSIX
else /* MPI/POSIX */
{
LOG((4, "opening parallel file with MPI/posix"));
if (H5Pset_fapl_mpiposix(fapl_id, mpiinfo->comm, 0) < 0)
BAIL(NC_EPARINIT);
}
#else /* USE_PARALLEL_POSIX */
/* Should not happen! Code in NC4_create/NC4_open should alias the
* NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
* available in HDF5. -QAK
*/
else /* MPI/POSIX */
BAIL(NC_EPARINIT);
#endif /* USE_PARALLEL_POSIX */
/* Keep copies of the MPI Comm & Info objects */
if (MPI_SUCCESS != MPI_Comm_dup(mpiinfo->comm, &nc4_info->comm))
BAIL(NC_EMPI);
comm_duped++;
if (MPI_INFO_NULL != mpiinfo->info)
{
if (MPI_SUCCESS != MPI_Info_dup(mpiinfo->info, &nc4_info->info))
BAIL(NC_EMPI);
info_duped++;
}
else
{
/* No dup, just copy it. */
nc4_info->info = mpiinfo->info;
}
}
#else /* only set cache for non-parallel. */
if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
nc4_chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
LOG((4, "%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
__func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
#endif /* USE_PARALLEL4 */
/* 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. */
#ifdef HDF5_HAS_COLL_METADATA_OPS
H5Pset_all_coll_metadata_ops(fapl_id, 1 );
#endif
if(inmemory) {
if((nc4_info->hdfid = H5LTopen_file_image(meminfo->memory,meminfo->size,
H5LT_FILE_IMAGE_DONT_COPY|H5LT_FILE_IMAGE_DONT_RELEASE
)) < 0)
BAIL(NC_EHDFERR);
nc4_info->no_write = NC_TRUE;
} else if ((nc4_info->hdfid = H5Fopen(path, flags, fapl_id)) < 0)
BAIL(NC_EHDFERR);
/* Does the mode specify that this file is read-only? */
if ((mode & NC_WRITE) == 0)
nc4_info->no_write = NC_TRUE;
/* Now read in all the metadata. Some types and dimscale
* information may be difficult to resolve here, if, for example, a
* dataset of user-defined type is encountered before the
* definition of that type. */
if ((retval = nc4_rec_read_metadata(nc4_info->root_grp)))
BAIL(retval);
/* Now figure out which netCDF dims are indicated by the dimscale
* information. */
if ((retval = nc4_rec_match_dimscales(nc4_info->root_grp)))
BAIL(retval);
#ifdef LOGGING
/* This will print out the names, types, lens, etc of the vars and
atts in the file, if the logging level is 2 or greater. */
log_metadata_nc(nc);
#endif
/* Close the property list. */
if (H5Pclose(fapl_id) < 0)
BAIL(NC_EHDFERR);
NC4_get_fileinfo(nc4_info,NULL);
return NC_NOERR;
exit:
#ifdef USE_PARALLEL4
if (comm_duped) MPI_Comm_free(&nc4_info->comm);
if (info_duped) MPI_Info_free(&nc4_info->info);
#endif
if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
if (!nc4_info) return retval;
close_netcdf4_file(nc4_info,1); /* treat like abort*/
return retval;
}
#ifdef USE_HDF4
/**
* @internal Given an HDF4 type, set a pointer to netcdf type.
*
* See http://www.hdfgroup.org/training/HDFtraining/UsersGuide/Fundmtls.fm3.html
* for more information re: HDF4 types.
*
* @param h5 Pointer to HDF5 file info struct.
* @param hdf4_typeid Type ID for hdf4 datatype.
* @param xtype Pointer to netcdf type, where result will be stored.
* @param type_info Pointer to type info for the variable.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
get_netcdf_type_from_hdf4(NC_HDF5_FILE_INFO_T *h5, int32 hdf4_typeid,
nc_type *xtype, NC_TYPE_INFO_T *type_info)
{
int t = 0;
/* Added this variable in the course of fixing NCF-332.
* Prior to the fix, all data types were assigned
* NC_ENDIAN_BIG, so I am preserving that here for now.
* Not sure why it wouldn't be NC_ENDIAN_NATIVE, although
* I can hazard a guess or two.
*/
int endianness = NC_ENDIAN_BIG;
assert(h5 && xtype);
switch(hdf4_typeid)
{
case DFNT_CHAR:
*xtype = NC_CHAR;
t = 0;
break;
case DFNT_UCHAR:
case DFNT_UINT8:
*xtype = NC_UBYTE;
t = 6;
break;
case DFNT_LUINT8:
*xtype = NC_UBYTE;
t = 6;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_INT8:
*xtype = NC_BYTE;
t = 1;
break;
case DFNT_LINT8:
*xtype = NC_BYTE;
t = 1;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_INT16:
*xtype = NC_SHORT;
t = 2;
break;
case DFNT_LINT16:
*xtype = NC_SHORT;
t = 2;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_UINT16:
*xtype = NC_USHORT;
t = 7;
break;
case DFNT_LUINT16:
*xtype = NC_USHORT;
t = 7;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_INT32:
*xtype = NC_INT;
t = 3;
break;
case DFNT_LINT32:
*xtype = NC_INT;
t = 3;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_UINT32:
*xtype = NC_UINT;
t = 8;
break;
case DFNT_LUINT32:
*xtype = NC_UINT;
t = 8;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_FLOAT32:
*xtype = NC_FLOAT;
t = 4;
break;
case DFNT_LFLOAT32:
*xtype = NC_FLOAT;
t = 4;
endianness = NC_ENDIAN_LITTLE;
break;
case DFNT_FLOAT64:
*xtype = NC_DOUBLE;
t = 5;
break;
case DFNT_LFLOAT64:
*xtype = NC_DOUBLE;
t = 5;
endianness = NC_ENDIAN_LITTLE;
break;
default:
*xtype = NC_NAT;
return NC_EBADTYPID;
}
if (type_info)
{
if (hdf4_typeid == DFNT_FLOAT32)
type_info->nc_type_class = NC_FLOAT;
else if (hdf4_typeid == DFNT_FLOAT64)
type_info->nc_type_class = NC_DOUBLE;
else if (hdf4_typeid == DFNT_CHAR)
type_info->nc_type_class = NC_STRING;
else
type_info->nc_type_class = NC_INT;
type_info->endianness = endianness;
type_info->nc_typeid = *xtype;
type_info->size = nc_type_size_g[t];
if (!(type_info->name = strdup(nc_type_name_g[t])))
return NC_ENOMEM;
}
return NC_NOERR;
}
/**
* @internal Open a HDF4 file. Things have already been kicked off in
* nc_open, but here the netCDF-4 part of opening a file is
* handled.
*
* @param path The file name of the new file.
* @param mode The open mode flag.
* @param nc Pointer that gets the NC file info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
nc4_open_hdf4_file(const char *path, int mode, NC *nc)
{
NC_HDF5_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_ATT_INFO_T *att;
int32 num_datasets, num_gatts;
int32 rank;
int v, d, a;
int retval;
NC_HDF5_FILE_INFO_T* nc4_info = NULL;
LOG((3, "%s: path %s mode %d", __func__, path, mode));
assert(path && nc);
/* Must be read-only access to hdf4 files. */
if (mode & NC_WRITE)
return NC_EINVAL;
/* Add necessary structs to hold netcdf-4 file data. */
if ((retval = nc4_nc4f_list_add(nc, path, mode)))
return retval;
nc4_info = NC4_DATA(nc);
assert(nc4_info && nc4_info->root_grp);
h5 = nc4_info;
h5->hdf4 = NC_TRUE;
grp = h5->root_grp;
h5->no_write = NC_TRUE;
/* Open the file and initialize SD interface. */
if ((h5->sdid = SDstart(path, DFACC_READ)) == FAIL)
return NC_EHDFERR;
/* Learn how many datasets and global atts we have. */
if (SDfileinfo(h5->sdid, &num_datasets, &num_gatts))
return NC_EHDFERR;
/* Read the atts. */
for (a = 0; a < num_gatts; a++)
{
int32 att_data_type, att_count;
size_t att_type_size;
/* Add to the end of the list of atts for this var. */
if ((retval = nc4_att_list_add(&h5->root_grp->att, &att)))
return retval;
att->attnum = grp->natts++;
att->created = NC_TRUE;
/* Learn about this attribute. */
if (!(att->name = malloc(NC_MAX_HDF4_NAME * sizeof(char))))
return NC_ENOMEM;
if (SDattrinfo(h5->sdid, a, att->name, &att_data_type, &att_count))
return NC_EATTMETA;
if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type,
&att->nc_typeid, NULL)))
return retval;
att->len = att_count;
/* Allocate memory to hold the data. */
if ((retval = nc4_get_typelen_mem(h5, att->nc_typeid, 0, &att_type_size)))
return retval;
if (!(att->data = malloc(att_type_size * att->len)))
return NC_ENOMEM;
/* Read the data. */
if (SDreadattr(h5->sdid, a, att->data))
return NC_EHDFERR;
}
/* Read each dataset. */
for (v = 0; v < num_datasets; v++)
{
NC_VAR_INFO_T *var;
int32 data_type, num_atts;
/* Problem: Number of dims is returned by the call that requires
a pre-allocated array, 'dimsize'.
From SDS_SD website:
http://www.hdfgroup.org/training/HDFtraining/UsersGuide/SDS_SD.fm3.html
The maximum rank is 32, or MAX_VAR_DIMS (as defined in netcdf.h).
int32 dimsize[MAX_VAR_DIMS];
*/
int32 *dimsize = NULL;
size_t var_type_size;
int a;
/* Add a variable. */
if ((retval = nc4_var_add(&var)))
return retval;
var->varid = grp->nvars++;
var->created = NC_TRUE;
var->written_to = NC_TRUE;
/* Add a var to the variable array, growing it as needed. */
if ((retval = nc4_vararray_add(grp, var)))
return retval;
/* Open this dataset in HDF4 file. */
if ((var->sdsid = SDselect(h5->sdid, v)) == FAIL)
return NC_EVARMETA;
/* Get shape, name, type, and attribute info about this dataset. */
if (!(var->name = malloc(NC_MAX_HDF4_NAME + 1)))
return NC_ENOMEM;
/* Invoke SDgetInfo with null dimsize to get rank. */
if (SDgetinfo(var->sdsid, var->name, &rank, NULL, &data_type, &num_atts))
return NC_EVARMETA;
var->hash = hash_fast(var->name, strlen(var->name));
if(!(dimsize = (int32*)malloc(sizeof(int32)*rank)))
return NC_ENOMEM;
if (SDgetinfo(var->sdsid, var->name, &rank, dimsize, &data_type, &num_atts)) {
if(dimsize) free(dimsize);
return NC_EVARMETA;
}
var->ndims = rank;
var->hdf4_data_type = data_type;
/* Fill special type_info struct for variable type information. */
if (!(var->type_info = calloc(1, sizeof(NC_TYPE_INFO_T)))) {
if(dimsize) free(dimsize);
return NC_ENOMEM;
}
if ((retval = get_netcdf_type_from_hdf4(h5, data_type, &var->type_info->nc_typeid, var->type_info))) {
if(dimsize) free(dimsize);
return retval;
}
/* Indicate that the variable has a pointer to the type */
var->type_info->rc++;
if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0, &var_type_size))) {
if(dimsize) free(dimsize);
return retval;
}
var->type_info->size = var_type_size;
LOG((3, "reading HDF4 dataset %s, rank %d netCDF type %d", var->name,
rank, var->type_info->nc_typeid));
/* Get the fill value. */
if (!(var->fill_value = malloc(var_type_size))) {
if(dimsize) free(dimsize);
return NC_ENOMEM;
}
if (SDgetfillvalue(var->sdsid, var->fill_value))
{
/* Whoops! No fill value! */
free(var->fill_value);
var->fill_value = NULL;
}
/* Allocate storage for dimension info in this variable. */
if (var->ndims)
{
if (!(var->dim = malloc(sizeof(NC_DIM_INFO_T *) * var->ndims))) {
if(dimsize) free(dimsize);
return NC_ENOMEM;
}
if (!(var->dimids = malloc(sizeof(int) * var->ndims))) {
if(dimsize) free(dimsize);
return NC_ENOMEM;
}
}
/* Find its dimensions. */
for (d = 0; d < var->ndims; d++)
{
int32 dimid, dim_len, dim_data_type, dim_num_attrs;
char dim_name[NC_MAX_NAME + 1];
NC_DIM_INFO_T *dim;
if ((dimid = SDgetdimid(var->sdsid, d)) == FAIL) {
if(dimsize) free(dimsize);
return NC_EDIMMETA;
}
if (SDdiminfo(dimid, dim_name, &dim_len, &dim_data_type,
&dim_num_attrs))
{
if(dimsize) free(dimsize);
return NC_EDIMMETA;
}
/* Do we already have this dimension? HDF4 explicitly uses
* the name to tell. */
for (dim = grp->dim; dim; dim = dim->l.next)
if (!strcmp(dim->name, dim_name))
break;
/* If we didn't find this dimension, add one. */
if (!dim)
{
LOG((4, "adding dimension %s for HDF4 dataset %s",
dim_name, var->name));
if ((retval = nc4_dim_list_add(&grp->dim, &dim)))
return retval;
dim->dimid = grp->nc4_info->next_dimid++;
if (strlen(dim_name) > NC_MAX_HDF4_NAME)
return NC_EMAXNAME;
if (!(dim->name = strdup(dim_name)))
return NC_ENOMEM;
if (dim_len)
dim->len = dim_len;
else
dim->len = *dimsize;
dim->hash = hash_fast(dim_name, strlen(dim_name));
}
/* Tell the variable the id of this dimension. */
var->dimids[d] = dim->dimid;
var->dim[d] = dim;
}
/* Read the atts. */
for (a = 0; a < num_atts; a++)
{
int32 att_data_type, att_count;
size_t att_type_size;
/* Add to the end of the list of atts for this var. */
if ((retval = nc4_att_list_add(&var->att, &att))) {
if(dimsize) free(dimsize);
return retval;
}
att->attnum = var->natts++;
att->created = NC_TRUE;
/* Learn about this attribute. */
if (!(att->name = malloc(NC_MAX_HDF4_NAME * sizeof(char)))) {
if(dimsize) free(dimsize);
return NC_ENOMEM;
}
if (SDattrinfo(var->sdsid, a, att->name, &att_data_type, &att_count)) {
if(dimsize) free(dimsize);
return NC_EATTMETA;
}
if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type,
&att->nc_typeid, NULL))) {
if(dimsize) free(dimsize);
return retval;
}
att->len = att_count;
/* Allocate memory to hold the data. */
if ((retval = nc4_get_typelen_mem(h5, att->nc_typeid, 0, &att_type_size))) {
if(dimsize) free(dimsize);
return retval;
}
if (!(att->data = malloc(att_type_size * att->len))) {
if(dimsize) free(dimsize);
return NC_ENOMEM;
}
/* Read the data. */
if (SDreadattr(var->sdsid, a, att->data)) {
if(dimsize) free(dimsize);
return NC_EHDFERR;
}
}
if(dimsize) free(dimsize);
{
/* HDF4 files can be chunked */
HDF_CHUNK_DEF chunkdefs;
int flag;
if(!SDgetchunkinfo(var->sdsid, &chunkdefs, &flag)) {
if(flag == HDF_NONE)
var->contiguous = NC_TRUE;
else if((flag & HDF_CHUNK) != 0) {
var->contiguous = NC_FALSE;
if (!(var->chunksizes = malloc(var->ndims * sizeof(size_t))))
return NC_ENOMEM;
for (d = 0; d < var->ndims; d++) {
var->chunksizes[d] = chunkdefs.chunk_lengths[d];
}
}
}
}
} /* next var */
#ifdef LOGGING
/* This will print out the names, types, lens, etc of the vars and
atts in the file, if the logging level is 2 or greater. */
log_metadata_nc(h5->root_grp->nc4_info->controller);
#endif
return NC_NOERR;
}
#endif /* USE_HDF4 */
/**
* @internal Open a netCDF-4 file.
*
* @param path The file name of the new file.
* @param mode The open mode flag.
* @param basepe Ignored by this function.
* @param chunksizehintp Ignored by this function.
* @param use_parallel 0 for sequential, non-zero for parallel I/O.
* @param parameters pointer to struct holding extra data (e.g. for parallel I/O)
* layer. Ignored if NULL.
* @param dispatch Pointer to the dispatch table for this file.
* @param nc_file Pointer to an instance of NC.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
int use_parallel, void *parameters, NC_Dispatch *dispatch, NC *nc_file)
{
int res;
int is_hdf5_file = 0;
#ifdef USE_HDF4
int is_hdf4_file = 0;
#endif /* USE_HDF4 */
#ifdef USE_PARALLEL4
NC_MPI_INFO mpidfalt = {MPI_COMM_WORLD, MPI_INFO_NULL};
#endif
#if defined USE_PARALLEL4 || defined USE_HDF4
int inmemory = ((mode & NC_INMEMORY) == NC_INMEMORY);
#endif
assert(nc_file && path);
LOG((1, "%s: path %s mode %d params %x",
__func__, path, mode, parameters));
#ifdef USE_PARALLEL4
if (!inmemory && use_parallel && parameters == NULL)
parameters = &mpidfalt;
#endif /* USE_PARALLEL4 */
/* If this is our first file, initialize HDF5. */
if (!nc4_hdf5_initialized)
nc4_hdf5_initialize();
/* Check the mode for validity */
if((mode & ILLEGAL_OPEN_FLAGS) != 0)
{res = NC_EINVAL; goto done;}
/* Cannot have both */
if((mode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
{res = NC_EINVAL; goto done;}
#ifndef USE_PARALLEL_POSIX
/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
* the NC_MPIPOSIX flag to NC_MPIIO. -QAK
*/
if(mode & NC_MPIPOSIX)
{
mode &= ~NC_MPIPOSIX;
mode |= NC_MPIIO;
}
#endif /* USE_PARALLEL_POSIX */
/* Figure out if this is a hdf4 or hdf5 file. */
if(nc_file->model == NC_FORMATX_NC4)
is_hdf5_file = 1;
#ifdef USE_HDF4
else if(nc_file->model == NC_FORMATX_NC_HDF4)
is_hdf4_file = 1;
#endif /* USE_HDF4 */
/* Depending on the type of file, open it. */
nc_file->int_ncid = nc_file->ext_ncid;
if (is_hdf5_file)
res = nc4_open_file(path, mode, parameters, nc_file);
#ifdef USE_HDF4
else if (is_hdf4_file && inmemory)
{res = NC_EDISKLESS; goto done;}
else if (is_hdf4_file)
res = nc4_open_hdf4_file(path, mode, nc_file);
#endif /* USE_HDF4 */
else
res = NC_ENOTNC;
done:
return res;
}
/**
* @internal Unfortunately HDF only allows specification of fill value
* only when a dataset is created. Whereas in netcdf, you first create
* the variable and then (optionally) specify the fill value. To
* accomplish this in HDF5 I have to delete the dataset, and recreate
* it, with the fill value specified.
*
* @param ncid File and group ID.
* @param fillmode File mode.
* @param old_modep Pointer that gets old mode. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_set_fill(int ncid, int fillmode, int *old_modep)
{
NC *nc;
NC_HDF5_FILE_INFO_T* nc4_info;
LOG((2, "%s: ncid 0x%x fillmode %d", __func__, ncid, fillmode));
if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
return NC_EBADID;
assert(nc4_info);
/* Trying to set fill on a read-only file? You sicken me! */
if (nc4_info->no_write)
return NC_EPERM;
/* Did you pass me some weird fillmode? */
if (fillmode != NC_FILL && fillmode != NC_NOFILL)
return NC_EINVAL;
/* If the user wants to know, tell him what the old mode was. */
if (old_modep)
*old_modep = nc4_info->fill_mode;
nc4_info->fill_mode = fillmode;
return NC_NOERR;
}
/**
* @internal Put the file back in redef mode. This is done
* automatically for netcdf-4 files, if the user forgets.
*
* @param ncid File and group ID.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_redef(int ncid)
{
NC_HDF5_FILE_INFO_T* nc4_info;
LOG((1, "%s: ncid 0x%x", __func__, ncid));
/* Find this file's metadata. */
if (!(nc4_find_nc_file(ncid,&nc4_info)))
return NC_EBADID;
assert(nc4_info);
/* If we're already in define mode, return an error. */
if (nc4_info->flags & NC_INDEF)
return NC_EINDEFINE;
/* If the file is read-only, return an error. */
if (nc4_info->no_write)
return NC_EPERM;
/* Set define mode. */
nc4_info->flags |= NC_INDEF;
/* For nc_abort, we need to remember if we're in define mode as a
redef. */
nc4_info->redef = NC_TRUE;
return NC_NOERR;
}
/**
* @internal For netcdf-4 files, this just calls nc_enddef, ignoring
* the extra parameters.
*
* @param ncid File and group ID.
* @param h_minfree Ignored for netCDF-4 files.
* @param v_align Ignored for netCDF-4 files.
* @param v_minfree Ignored for netCDF-4 files.
* @param r_align Ignored for netCDF-4 files.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4__enddef(int ncid, size_t h_minfree, size_t v_align,
size_t v_minfree, size_t r_align)
{
if (nc4_find_nc_file(ncid,NULL) == NULL)
return NC_EBADID;
return NC4_enddef(ncid);
}
/**
* @internal Take the file out of define mode. This is called
* automatically for netcdf-4 files, if the user forgets.
*
* @param ncid File and group ID.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int NC4_enddef(int ncid)
{
NC *nc;
NC_HDF5_FILE_INFO_T* nc4_info;
NC_GRP_INFO_T *grp;
int i;
LOG((1, "%s: ncid 0x%x", __func__, ncid));
if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
return NC_EBADID;
assert(nc4_info);
/* Find info for this file and group */
if (!(grp = nc4_rec_find_grp(nc4_info->root_grp, (ncid & GRP_ID_MASK))))
return NC_EBADGRPID;
/* when exiting define mode, mark all variable written */
for (i=0; i<grp->vars.nelems; i++)
grp->vars.value[i]->written_to = NC_TRUE;
return nc4_enddef_netcdf4_file(nc4_info);
}
/**
* @internal Flushes all buffers associated with the file, after
* writing all changed metadata. This may only be called in data mode.
*
* @param ncid File and group ID.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_sync(int ncid)
{
NC *nc;
int retval;
NC_HDF5_FILE_INFO_T* nc4_info;
LOG((2, "%s: ncid 0x%x", __func__, ncid));
if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
return NC_EBADID;
assert(nc4_info);
/* If we're in define mode, we can't sync. */
if (nc4_info && nc4_info->flags & NC_INDEF)
{
if (nc4_info->cmode & NC_CLASSIC_MODEL)
return NC_EINDEFINE;
if ((retval = NC4_enddef(ncid)))
return retval;
}
return sync_netcdf4_file(nc4_info);
}
/**
* @internal From the netcdf-3 docs: The function nc_abort just closes
* the netCDF dataset, if not in define mode. If the dataset is being
* created and is still in define mode, the dataset is deleted. If
* define mode was entered by a call to nc_redef, the netCDF dataset
* is restored to its state before definition mode was entered and the
* dataset is closed.
*
* @param ncid File and group ID.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_abort(int ncid)
{
NC *nc;
int delete_file = 0;
char path[NC_MAX_NAME + 1];
int retval = NC_NOERR;
NC_HDF5_FILE_INFO_T* nc4_info;
LOG((2, "%s: ncid 0x%x", __func__, ncid));
/* Find metadata for this file. */
if (!(nc = nc4_find_nc_file(ncid,&nc4_info)))
return NC_EBADID;
assert(nc4_info);
/* If we're in define mode, but not redefing the file, delete it. */
if (nc4_info->flags & NC_INDEF && !nc4_info->redef)
{
delete_file++;
strncpy(path, nc->path,NC_MAX_NAME);
}
/* Free any resources the netcdf-4 library has for this file's
* metadata. */
if ((retval = close_netcdf4_file(nc4_info, 1)))
return retval;
/* Delete the file, if we should. */
if (delete_file)
if (remove(path) < 0)
return NC_ECANTREMOVE;
return retval;
}
/**
* @internal Close the netcdf file, writing any changes first.
*
* @param ncid File and group ID.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_close(int ncid)
{
NC_GRP_INFO_T *grp;
NC *nc;
NC_HDF5_FILE_INFO_T *h5;
int retval;
LOG((1, "%s: ncid 0x%x", __func__, ncid));
/* Find our metadata for this file. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(nc && h5 && grp);
/* This must be the root group. */
if (grp->parent)
return NC_EBADGRPID;
/* Call the nc4 close. */
if ((retval = close_netcdf4_file(grp->nc4_info, 0)))
return retval;
return NC_NOERR;
}
/**
* @internal Learn number of dimensions, variables, global attributes,
* and the ID of the first unlimited dimension (if any).
*
* @note It's possible for any of these pointers to be NULL, in which
* case don't try to figure out that value.
*
* @param ncid File and group ID.
* @param ndimsp Pointer that gets number of dimensions.
* @param nvarsp Pointer that gets number of variables.
* @param nattsp Pointer that gets number of global attributes.
* @param unlimdimidp Pointer that gets first unlimited dimension ID,
* or -1 if there are no unlimied dimensions.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
{
NC *nc;
NC_HDF5_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_DIM_INFO_T *dim;
NC_ATT_INFO_T *att;
int retval;
LOG((2, "%s: ncid 0x%x", __func__, ncid));
/* Find file metadata. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(h5 && grp && nc);
/* Count the number of dims, vars, and global atts. */
if (ndimsp)
{
*ndimsp = 0;
for (dim = grp->dim; dim; dim = dim->l.next)
(*ndimsp)++;
}
if (nvarsp)
{
int i;
*nvarsp = 0;
for (i=0; i < grp->vars.nelems; i++)
{
if (grp->vars.value[i])
(*nvarsp)++;
}
}
if (nattsp)
{
*nattsp = 0;
for (att = grp->att; att; att = att->l.next)
(*nattsp)++;
}
if (unlimdimidp)
{
/* Default, no unlimited dimension */
*unlimdimidp = -1;
/* If there's more than one unlimited dim, which was not possible
with netcdf-3, then only the last unlimited one will be reported
back in xtendimp. */
/* Note that this code is inconsistent with nc_inq_unlimid() */
for (dim = grp->dim; dim; dim = dim->l.next)
if (dim->unlimited)
{
*unlimdimidp = dim->dimid;
break;
}
}
return NC_NOERR;
}
/**
* @internal This function will do the enddef stuff for a netcdf-4 file.
*
* @param h5 Pointer to HDF5 file info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
{
assert(h5);
LOG((3, "%s", __func__));
/* If we're not in define mode, return an error. */
if (!(h5->flags & NC_INDEF))
return NC_ENOTINDEFINE;
/* Turn define mode off. */
h5->flags ^= NC_INDEF;
/* Redef mode needs to be tracked separately for nc_abort. */
h5->redef = NC_FALSE;
return sync_netcdf4_file(h5);
}
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