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netcdf-c/libhdf5/hdf5var.c
Wei-keng Liao 0ed70756cc Ignore flags NC_MPIIO and NC_MPIPOSIX.
2018-09-22 20:22:34 -05:00

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64 KiB
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/* Copyright 2003-2006, University Corporation for Atmospheric
* Research. See COPYRIGHT file for copying and redistribution
* conditions.*/
/**
* @file
* @internal This file handles the HDF5 variable functions.
*
* @author Ed Hartnett
*/
#include "config.h"
#include <hdf5internal.h>
#include <math.h>
/** @internal Default size for unlimited dim chunksize */
#define DEFAULT_1D_UNLIM_SIZE (4096)
/**
* @internal If the HDF5 dataset for this variable is open, then close
* it and reopen it, with the perhaps new settings for chunk caching.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
int
nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
hid_t access_pid;
if (var->hdf_datasetid)
{
if ((access_pid = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
return NC_EHDFERR;
if (H5Pset_chunk_cache(access_pid, var->chunk_cache_nelems,
var->chunk_cache_size,
var->chunk_cache_preemption) < 0)
return NC_EHDFERR;
if (H5Dclose(var->hdf_datasetid) < 0)
return NC_EHDFERR;
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, var->hdr.name,
access_pid)) < 0)
return NC_EHDFERR;
if (H5Pclose(access_pid) < 0)
return NC_EHDFERR;
}
return NC_NOERR;
}
/**
* @internal Check a set of chunksizes to see if they specify a chunk
* that is too big.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info.
* @param chunksizes Array of chunksizes to check.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_EBADCHUNK Bad chunksize.
*/
static int
check_chunksizes(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, const size_t *chunksizes)
{
double dprod;
size_t type_len;
int d;
int retval;
if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id, &type_len)))
return retval;
if (var->type_info->nc_type_class == NC_VLEN)
dprod = (double)sizeof(hvl_t);
else
dprod = (double)type_len;
for (d = 0; d < var->ndims; d++)
dprod *= (double)chunksizes[d];
if (dprod > (double) NC_MAX_UINT)
return NC_EBADCHUNK;
return NC_NOERR;
}
/**
* @internal Determine some default chunksizes for a variable.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @author Ed Hartnett
*/
static int
nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
int d;
size_t type_size;
float num_values = 1, num_unlim = 0;
int retval;
size_t suggested_size;
#ifdef LOGGING
double total_chunk_size;
#endif
if (var->type_info->nc_type_class == NC_STRING)
type_size = sizeof(char *);
else
type_size = var->type_info->size;
#ifdef LOGGING
/* Later this will become the total number of bytes in the default
* chunk. */
total_chunk_size = (double) type_size;
#endif
/* How many values in the variable (or one record, if there are
* unlimited dimensions). */
for (d = 0; d < var->ndims; d++)
{
assert(var->dim[d]);
if (! var->dim[d]->unlimited)
num_values *= (float)var->dim[d]->len;
else {
num_unlim++;
var->chunksizes[d] = 1; /* overwritten below, if all dims are unlimited */
}
}
/* Special case to avoid 1D vars with unlim dim taking huge amount
of space (DEFAULT_CHUNK_SIZE bytes). Instead we limit to about
4KB */
if (var->ndims == 1 && num_unlim == 1) {
if (DEFAULT_CHUNK_SIZE / type_size <= 0)
suggested_size = 1;
else if (DEFAULT_CHUNK_SIZE / type_size > DEFAULT_1D_UNLIM_SIZE)
suggested_size = DEFAULT_1D_UNLIM_SIZE;
else
suggested_size = DEFAULT_CHUNK_SIZE / type_size;
var->chunksizes[0] = suggested_size / type_size;
LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[0]));
}
if (var->ndims > 1 && var->ndims == num_unlim) { /* all dims unlimited */
suggested_size = pow((double)DEFAULT_CHUNK_SIZE/type_size, 1.0/(double)(var->ndims));
for (d = 0; d < var->ndims; d++)
{
var->chunksizes[d] = suggested_size ? suggested_size : 1;
LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d]));
}
}
/* Pick a chunk length for each dimension, if one has not already
* been picked above. */
for (d = 0; d < var->ndims; d++)
if (!var->chunksizes[d])
{
suggested_size = (pow((double)DEFAULT_CHUNK_SIZE/(num_values * type_size),
1.0/(double)(var->ndims - num_unlim)) * var->dim[d]->len - .5);
if (suggested_size > var->dim[d]->len)
suggested_size = var->dim[d]->len;
var->chunksizes[d] = suggested_size ? suggested_size : 1;
LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d]));
}
#ifdef LOGGING
/* Find total chunk size. */
for (d = 0; d < var->ndims; d++)
total_chunk_size *= (double) var->chunksizes[d];
LOG((4, "total_chunk_size %f", total_chunk_size));
#endif
/* But did this result in a chunk that is too big? */
retval = check_chunksizes(grp, var, var->chunksizes);
if (retval)
{
/* Other error? */
if (retval != NC_EBADCHUNK)
return retval;
/* Chunk is too big! Reduce each dimension by half and try again. */
for ( ; retval == NC_EBADCHUNK; retval = check_chunksizes(grp, var, var->chunksizes))
for (d = 0; d < var->ndims; d++)
var->chunksizes[d] = var->chunksizes[d]/2 ? var->chunksizes[d]/2 : 1;
}
/* Do we have any big data overhangs? They can be dangerous to
* babies, the elderly, or confused campers who have had too much
* beer. */
for (d = 0; d < var->ndims; d++)
{
size_t num_chunks;
size_t overhang;
assert(var->chunksizes[d] > 0);
num_chunks = (var->dim[d]->len + var->chunksizes[d] - 1) / var->chunksizes[d];
if(num_chunks > 0) {
overhang = (num_chunks * var->chunksizes[d]) - var->dim[d]->len;
var->chunksizes[d] -= overhang / num_chunks;
}
}
return NC_NOERR;
}
/**
* @internal This is called when a new netCDF-4 variable is defined
* with nc_def_var().
*
* @param ncid File ID.
* @param name Name.
* @param xtype Type.
* @param ndims Number of dims. HDF5 has maximim of 32.
* @param dimidsp Array of dim IDs.
* @param varidp Gets the var ID.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EMAXDIMS Classic model file exceeds ::NC_MAX_VAR_DIMS.
* @returns ::NC_ESTRICTNC3 Attempting to create netCDF-4 type var in
* classic model file
* @returns ::NC_EBADNAME Bad name.
* @returns ::NC_EBADTYPE Bad type.
* @returns ::NC_ENOMEM Out of memory.
* @returns ::NC_EHDFERR Error returned by HDF5 layer.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var(int ncid, const char *name, nc_type xtype,
int ndims, const int *dimidsp, int *varidp)
{
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
NC_FILE_INFO_T *h5;
NC_TYPE_INFO_T *type_info = NULL;
char norm_name[NC_MAX_NAME + 1];
int d;
int retval;
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
BAIL(retval);
assert(grp && h5);
/* HDF5 allows maximum of 32 dimensions. */
if (ndims > H5S_MAX_RANK)
BAIL(NC_EMAXDIMS);
/* If it's not in define mode, strict nc3 files error out,
* otherwise switch to define mode. This will also check that the
* file is writable. */
if (!(h5->flags & NC_INDEF))
{
if (h5->cmode & NC_CLASSIC_MODEL)
BAIL(NC_ENOTINDEFINE);
if ((retval = NC4_redef(ncid)))
BAIL(retval);
}
assert(!h5->no_write);
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
BAIL(retval);
/* Not a Type is, well, not a type.*/
if (xtype == NC_NAT)
BAIL(NC_EBADTYPE);
/* For classic files, only classic types are allowed. */
if (h5->cmode & NC_CLASSIC_MODEL && xtype > NC_DOUBLE)
BAIL(NC_ESTRICTNC3);
/* For classic files */
if (h5->cmode & NC_CLASSIC_MODEL && ndims > NC_MAX_VAR_DIMS)
BAIL(NC_EMAXDIMS);
/* cast needed for braindead systems with signed size_t */
if((unsigned long) ndims > X_INT_MAX) /* Backward compat */
BAIL(NC_EINVAL);
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
BAIL(retval);
/* For non-scalar vars, dim IDs must be provided. */
if (ndims && !dimidsp)
BAIL(NC_EINVAL);
/* Check all the dimids to make sure they exist. */
for (d = 0; d < ndims; d++)
if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, NULL)))
BAIL(retval);
/* These degrubbing messages sure are handy! */
LOG((2, "%s: name %s type %d ndims %d", __func__, norm_name, xtype, ndims));
#ifdef LOGGING
{
int dd;
for (dd = 0; dd < ndims; dd++)
LOG((4, "dimid[%d] %d", dd, dimidsp[dd]));
}
#endif
/* If this is a user-defined type, there is a type_info struct with
* all the type information. For atomic types, fake up a type_info
* struct. */
if (xtype <= NC_STRING)
{
size_t len;
char name[NC_MAX_NAME+1];
char* atomname = nc4_atomic_name[xtype];
size_t namelen = strlen(atomname);
memcpy(name,atomname,namelen);
name[namelen] = '\0';
nc4_get_typelen_mem(h5,xtype,&len);
if((retval = nc4_type_new(grp,len,name,xtype,&type_info)))
BAIL(retval);
type_info->endianness = NC_ENDIAN_NATIVE;
if ((retval = nc4_get_hdf_typeid(h5, xtype, &type_info->hdf_typeid,
type_info->endianness)))
BAIL(retval);
if ((type_info->native_hdf_typeid = H5Tget_native_type(type_info->hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if ((retval = nc4_get_typelen_mem(h5, type_info->hdr.id, &type_info->size)))
BAIL(retval);
/* Set the "class" of the type */
if (xtype == NC_CHAR)
type_info->nc_type_class = NC_CHAR;
else
{
H5T_class_t class;
if ((class = H5Tget_class(type_info->hdf_typeid)) < 0)
BAIL(NC_EHDFERR);
switch(class)
{
case H5T_STRING:
type_info->nc_type_class = NC_STRING;
break;
case H5T_INTEGER:
type_info->nc_type_class = NC_INT;
break;
case H5T_FLOAT:
type_info->nc_type_class = NC_FLOAT;
break;
default:
BAIL(NC_EBADTYPID);
}
}
}
/* If this is a user defined type, find it. */
else
{
if (nc4_find_type(grp->nc4_info, xtype, &type_info))
BAIL(NC_EBADTYPE);
}
/* Create a new var and fill in some HDF5 cache setting values. */
if ((retval = nc4_var_list_add(grp, norm_name, ndims, &var)))
BAIL(retval);
var->is_new_var = NC_TRUE;
/* Point to the type, and increment its ref. count */
var->type_info = type_info;
var->type_info->rc++;
type_info = NULL;
/* Set variables no_fill to match the database default
* unless the variable type is variable length (NC_STRING or NC_VLEN)
* or is user-defined type.
*/
if (var->type_info->nc_type_class < NC_STRING)
var->no_fill = h5->fill_mode;
/* Assign dimensions to the variable */
/* At the same time, check to see if this is a coordinate
* variable. If so, it will have the same name as one of its
* dimensions. If it is a coordinate var, is it a coordinate var in
* the same group as the dim? */
/* Also, check whether we should use contiguous or chunked storage */
var->contiguous = NC_TRUE;
for (d = 0; d < ndims; d++)
{
NC_GRP_INFO_T *dim_grp;
/* Look up each dimension */
if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, &dim_grp)))
BAIL(retval);
/* Check for dim index 0 having the same name, in the same group */
if (d == 0 && dim_grp == grp && strcmp(dim->hdr.name, norm_name) == 0)
{
var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Use variable's dataset ID for the dimscale ID. So delete
* the HDF5 DIM_WITHOUT_VARIABLE dataset that was created for
* this dim. */
if (dim->hdf_dimscaleid)
{
/* Detach dimscale from any variables using it */
if ((retval = rec_detach_scales(grp, dimidsp[d], dim->hdf_dimscaleid)) < 0)
BAIL(retval);
/* Close the HDF5 DIM_WITHOUT_VARIABLE dataset. */
if (H5Dclose(dim->hdf_dimscaleid) < 0)
BAIL(NC_EHDFERR);
dim->hdf_dimscaleid = 0;
/* Now delete the DIM_WITHOUT_VARIABLE dataset (it will be
* recreated later, if necessary). */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
BAIL(NC_EDIMMETA);
}
}
/* Check for unlimited dimension and turn off contiguous storage. */
if (dim->unlimited)
var->contiguous = NC_FALSE;
/* Track dimensions for variable */
var->dimids[d] = dimidsp[d];
var->dim[d] = dim;
}
/* Determine default chunksizes for this variable. (Even for
* variables which may be contiguous.) */
LOG((4, "allocating array of %d size_t to hold chunksizes for var %s",
var->ndims, var->hdr.name));
if (var->ndims)
if (!(var->chunksizes = calloc(var->ndims, sizeof(size_t))))
BAIL(NC_ENOMEM);
if ((retval = nc4_find_default_chunksizes2(grp, var)))
BAIL(retval);
/* Is this a variable with a chunksize greater than the current
* cache size? */
if ((retval = nc4_adjust_var_cache(grp, var)))
BAIL(retval);
/* If the user names this variable the same as a dimension, but
* doesn't use that dimension first in its list of dimension ids,
* is not a coordinate variable. I need to change its HDF5 name,
* because the dimension will cause a HDF5 dataset to be created,
* and this var has the same name. */
dim = (NC_DIM_INFO_T*)ncindexlookup(grp->dim,norm_name);
if (dim && (!var->ndims || dimidsp[0] != dim->hdr.id))
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
BAIL(NC_EMAXNAME);
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(norm_name) + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name);
}
/* If this is a coordinate var, it is marked as a HDF5 dimension
* scale. (We found dim above.) Otherwise, allocate space to
* remember whether dimension scales have been attached to each
* dimension. */
if (!var->dimscale && ndims)
if (!(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
BAIL(NC_ENOMEM);
/* Return the varid. */
if (varidp)
*varidp = var->hdr.id;
LOG((4, "new varid %d", var->hdr.id));
exit:
if (type_info)
if ((retval = nc4_type_free(type_info)))
BAIL2(retval);
return retval;
}
/**
* @internal This functions sets extra stuff about a netCDF-4 variable which
* must be set before the enddef but after the def_var.
*
* @note All pointer parameters may be NULL, in which case they are ignored.
* @param ncid File ID.
* @param varid Variable ID.
* @param shuffle Pointer to shuffle setting.
* @param deflate Pointer to deflate setting.
* @param deflate_level Pointer to deflate level.
* @param fletcher32 Pointer to fletcher32 setting.
* @param contiguous Pointer to contiguous setting.
* @param chunksizes Array of chunksizes.
* @param no_fill Pointer to no_fill setting.
* @param fill_value Pointer to fill value.
* @param endianness Pointer to endianness setting.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EINVAL Invalid input
* @returns ::NC_EBADCHUNK Bad chunksize.
* @author Ed Hartnett
*/
static int
nc_def_var_extra(int ncid, int varid, int *shuffle, int *deflate,
int *deflate_level, int *fletcher32, int *contiguous,
const size_t *chunksizes, int *no_fill,
const void *fill_value, int *endianness)
{
NC *nc;
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_FILE_INFO_T *nc4_info=NULL;
int d;
int retval;
/* All or none of these will be provided. */
assert((deflate && deflate_level && shuffle) ||
(!deflate && !deflate_level && !shuffle));
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(nc && grp && h5);
/* Trying to write to a read-only file? No way, Jose! */
if (h5->no_write)
return NC_EPERM;
/* Find the var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if(!var)
return NC_ENOTVAR;
assert(var && var->hdr.id == varid);
/* Can't turn on parallel and deflate/fletcher32/szip/shuffle. */
nc4_info = NC4_DATA(nc);
if (nc4_info->parallel == NC_TRUE) {
if (deflate || fletcher32 || shuffle)
return NC_EINVAL;
}
/* If the HDF5 dataset has already been created, then it is too
* late to set all the extra stuff. */
if (var->created)
return NC_ELATEDEF;
/* Check compression options. */
if (deflate && !deflate_level)
return NC_EINVAL;
/* Valid deflate level? */
if (deflate)
{
if (*deflate)
if (*deflate_level < NC_MIN_DEFLATE_LEVEL ||
*deflate_level > NC_MAX_DEFLATE_LEVEL)
return NC_EINVAL;
/* For scalars, just ignore attempt to deflate. */
if (!var->ndims)
return NC_NOERR;
/* Well, if we couldn't find any errors, I guess we have to take
* the users settings. Darn! */
var->contiguous = NC_FALSE;
var->deflate = *deflate;
if (*deflate)
var->deflate_level = *deflate_level;
LOG((3, "%s: *deflate_level %d", __func__, *deflate_level));
}
/* Shuffle filter? */
if (shuffle)
{
var->shuffle = *shuffle;
var->contiguous = NC_FALSE;
}
/* Fletcher32 checksum error protection? */
if (fletcher32)
{
var->fletcher32 = *fletcher32;
var->contiguous = NC_FALSE;
}
/* Does the user want a contiguous dataset? Not so fast! Make sure
* that there are no unlimited dimensions, and no filters in use
* for this data. */
if (contiguous && *contiguous)
{
if (var->deflate || var->fletcher32 || var->shuffle)
return NC_EINVAL;
for (d = 0; d < var->ndims; d++)
if (var->dim[d]->unlimited)
return NC_EINVAL;
var->contiguous = NC_TRUE;
}
/* Chunksizes anyone? */
if (contiguous && *contiguous == NC_CHUNKED)
{
var->contiguous = NC_FALSE;
/* If the user provided chunksizes, check that they are not too
* big, and that their total size of chunk is less than 4 GB. */
if (chunksizes)
{
if ((retval = check_chunksizes(grp, var, chunksizes)))
return retval;
/* Ensure chunksize is smaller than dimension size */
for (d = 0; d < var->ndims; d++)
if(!var->dim[d]->unlimited && var->dim[d]->len > 0 && chunksizes[d] > var->dim[d]->len)
return NC_EBADCHUNK;
/* Set the chunksizes for this variable. */
for (d = 0; d < var->ndims; d++)
var->chunksizes[d] = chunksizes[d];
}
}
/* Is this a variable with a chunksize greater than the current
* cache size? */
if (!var->contiguous && (deflate || contiguous))
{
/* Determine default chunksizes for this variable (do nothing
* for scalar vars). */
if (var->chunksizes && !var->chunksizes[0])
if ((retval = nc4_find_default_chunksizes2(grp, var)))
return retval;
/* Adjust the cache. */
if ((retval = nc4_adjust_var_cache(grp, var)))
return retval;
}
/* Are we setting a fill modes? */
if (no_fill)
{
if (*no_fill)
{
/* NC_STRING types may not turn off fill mode. It's disallowed
* by HDF5 and will cause a HDF5 error later. */
if (*no_fill)
if (var->type_info->hdr.id == NC_STRING)
return NC_EINVAL;
/* Set the no-fill mode. */
var->no_fill = NC_TRUE;
}
else
var->no_fill = NC_FALSE;
}
/* Are we setting a fill value? */
if (fill_value && !var->no_fill)
{
/* Copy the fill_value. */
LOG((4, "Copying fill value into metadata for variable %s",
var->hdr.name));
/* If there's a _FillValue attribute, delete it. */
retval = NC4_del_att(ncid, varid, _FillValue);
if (retval && retval != NC_ENOTATT)
return retval;
/* Create a _FillValue attribute. */
if ((retval = nc_put_att(ncid, varid, _FillValue, var->type_info->hdr.id, 1, fill_value)))
return retval;
}
/* Is the user setting the endianness? */
if (endianness)
var->type_info->endianness = *endianness;
return NC_NOERR;
}
/**
* @internal Set compression settings on a variable. This is called by
* nc_def_var_deflate().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param shuffle True to turn on the shuffle filter.
* @param deflate True to turn on deflation.
* @param deflate_level A number between 0 (no compression) and 9
* (maximum compression).
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
int deflate_level)
{
return nc_def_var_extra(ncid, varid, &shuffle, &deflate,
&deflate_level, NULL, NULL, NULL, NULL, NULL, NULL);
}
/**
* @internal Set checksum on a variable. This is called by
* nc_def_var_fletcher32().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param fletcher32 Pointer to fletcher32 setting.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var_fletcher32(int ncid, int varid, int fletcher32)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, &fletcher32,
NULL, NULL, NULL, NULL, NULL);
}
/**
* @internal Define chunking stuff for a var. This is called by
* nc_def_var_chunking(). Chunking is required in any dataset with one
* or more unlimited dimensions in HDF5, or any dataset using a
* filter.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param contiguous Pointer to contiguous setting.
* @param chunksizesp Array of chunksizes.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @returns ::NC_EBADCHUNK Bad chunksize.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var_chunking(int ncid, int varid, int contiguous, const size_t *chunksizesp)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL,
&contiguous, chunksizesp, NULL, NULL, NULL);
}
/**
* @internal Define chunking stuff for a var. This is called by
* the fortran API.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param contiguous Pointer to contiguous setting.
* @param chunksizesp Array of chunksizes.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @returns ::NC_EBADCHUNK Bad chunksize.
* @author Ed Hartnett
*/
int
nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizesp)
{
NC_VAR_INFO_T *var;
size_t *cs;
int i, retval;
/* Get pointer to the var. */
if ((retval = nc4_find_grp_h5_var(ncid, varid, NULL, NULL, &var)))
return retval;
assert(var);
/* Allocate space for the size_t copy of the chunksizes array. */
if (var->ndims)
if (!(cs = malloc(var->ndims * sizeof(size_t))))
return NC_ENOMEM;
/* Copy to size_t array. */
for (i = 0; i < var->ndims; i++)
cs[i] = chunksizesp[i];
retval = nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL,
&contiguous, cs, NULL, NULL, NULL);
if (var->ndims)
free(cs);
return retval;
}
/**
* @internal This functions sets fill value and no_fill mode for a
* netCDF-4 variable. It is called by nc_def_var_fill().
*
* @note All pointer parameters may be NULL, in which case they are ignored.
* @param ncid File ID.
* @param varid Variable ID.
* @param no_fill No_fill setting.
* @param fill_value Pointer to fill value.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett
*/
int
NC4_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL,
NULL, &no_fill, fill_value, NULL);
}
/**
* @internal This functions sets endianness for a netCDF-4
* variable. Called by nc_def_var_endian().
*
* @note All pointer parameters may be NULL, in which case they are ignored.
* @param ncid File ID.
* @param varid Variable ID.
* @param endianness Endianness setting.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett
*/
int
NC4_def_var_endian(int ncid, int varid, int endianness)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, &endianness);
}
/**
* @internal Define filter settings. Called by nc_def_var_filter().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param id Filter ID
* @param nparams Number of parameters for filter.
* @param parms Filter parameters.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_EFILTER Filter error.
* @returns ::NC_EINVAL Invalid input
* @author Dennis Heimbigner
*/
int
NC4_def_var_filter(int ncid, int varid, unsigned int id, size_t nparams,
const unsigned int* parms)
{
int retval = NC_NOERR;
NC *nc;
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(nc && grp && h5);
/* Find the var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if(!var)
return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* If the HDF5 dataset has already been created, then it is too
* late to set all the extra stuff. */
if (var->created)
return NC_ELATEDEF;
#ifdef HAVE_H5Z_SZIP
if(id == H5Z_FILTER_SZIP) {
if(nparams != 2)
return NC_EFILTER; /* incorrect no. of parameters */
}
#else /*!HAVE_H5Z_SZIP*/
if(id == H5Z_FILTER_SZIP)
return NC_EFILTER; /* Not allowed */
#endif
#if 0
{
unsigned int fcfg = 0;
herr_t herr = H5Zget_filter_info(id,&fcfg);
if(herr < 0)
return NC_EFILTER;
if((H5Z_FILTER_CONFIG_ENCODE_ENABLED & fcfg) == 0
|| (H5Z_FILTER_CONFIG_DECODE_ENABLED & fcfg) == 0)
return NC_EFILTER;
}
#endif /*0*/
var->filterid = id;
var->nparams = nparams;
var->params = NULL;
if(parms != NULL) {
var->params = (unsigned int*)calloc(nparams,sizeof(unsigned int));
if(var->params == NULL) return NC_ENOMEM;
memcpy(var->params,parms,sizeof(unsigned int)*var->nparams);
}
return NC_NOERR;
}
/**
* @internal Rename a var to "bubba," for example. This is called by
* nc_rename_var() for netCDF-4 files.
*
* @param ncid File ID.
* @param varid Variable ID
* @param name New name of the variable.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_EBADNAME Bad name.
* @returns ::NC_EMAXNAME Name is too long.
* @returns ::NC_ENAMEINUSE Name in use.
* @returns ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
int
NC4_rename_var(int ncid, int varid, const char *name)
{
NC *nc;
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var, *tmpvar;
int retval = NC_NOERR;
if (!name)
return NC_EINVAL;
LOG((2, "%s: ncid 0x%x varid %d name %s", __func__, ncid, varid,
name));
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(h5 && grp && h5);
/* Is the new name too long? */
if (strlen(name) > NC_MAX_NAME)
return NC_EMAXNAME;
/* Trying to write to a read-only file? No way, Jose! */
if (h5->no_write)
return NC_EPERM;
/* Check name validity, if strict nc3 rules are in effect for this
* file. */
if ((retval = NC_check_name(name)))
return retval;
/* Get the variable wrt varid */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if (!var)
return NC_ENOTVAR;
/* Check if new name is in use; note that renaming to same name is still an error
according to the nc_test/test_write.c code. Why?*/
tmpvar = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name);
if(tmpvar != NULL)
return NC_ENAMEINUSE;
/* If we're not in define mode, new name must be of equal or
less size, if strict nc3 rules are in effect for this . */
if (!(h5->flags & NC_INDEF) && strlen(name) > strlen(var->hdr.name) &&
(h5->cmode & NC_CLASSIC_MODEL))
return NC_ENOTINDEFINE;
/* Change the HDF5 file, if this var has already been created
there. Should we check here to ensure there is not already a
dimscale dataset of name name??? */
if (var->created)
{
/* Is there an existing dimscale-only dataset of this name? If
* so, it must be deleted. */
if (var->ndims && var->dim[0]->hdf_dimscaleid)
{
if ((retval = delete_existing_dimscale_dataset(grp, var->dim[0]->hdr.id, var->dim[0])))
return retval;
}
LOG((3, "Moving dataset %s to %s", var->hdr.name, name));
if (H5Gmove(grp->hdf_grpid, var->hdr.name, name) < 0)
BAIL(NC_EHDFERR);
}
/* Now change the name in our metadata. */
free(var->hdr.name);
if (!(var->hdr.name = strdup(name)))
return NC_ENOMEM;
LOG((3, "var is now %s", var->hdr.name));
var->hdr.hashkey = NC_hashmapkey(var->hdr.name,strlen(var->hdr.name)); /* Fix hash key */
if(!ncindexrebuild(grp->vars))
return NC_EINTERNAL;
/* Check if this was a coordinate variable previously, but names are different now */
if (var->dimscale && strcmp(var->hdr.name, var->dim[0]->hdr.name))
{
/* Break up the coordinate variable */
if ((retval = nc4_break_coord_var(grp, var, var->dim[0])))
return retval;
}
/* Check if this should become a coordinate variable */
if (!var->dimscale)
{
/* Only variables with >0 dimensions can become coordinate variables */
if (var->ndims)
{
NC_GRP_INFO_T *dim_grp;
NC_DIM_INFO_T *dim;
/* Check to see if this is became a coordinate variable. If so, it
* will have the same name as dimension index 0. If it is a
* coordinate var, is it a coordinate var in the same group as the dim?
*/
if ((retval = nc4_find_dim(grp, var->dimids[0], &dim, &dim_grp)))
return retval;
if (!strcmp(dim->hdr.name, name) && dim_grp == grp)
{
/* Reform the coordinate variable */
if ((retval = nc4_reform_coord_var(grp, var, dim)))
return retval;
var->became_coord_var = NC_TRUE;
}
}
}
exit:
return retval;
}
/**
* @internal Write an array of data to a variable. This is called by
* nc_put_vara() and other nc_put_vara_* functions, for netCDF-4
* files.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices.
* @param countp Array of counts.
* @param op pointer that gets the data.
* @param memtype The type of these data in memory.
*
* @returns ::NC_NOERR for success
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_put_vara(int ncid, int varid, const size_t *startp,
const size_t *countp, const void *op, int memtype)
{
return NC4_put_vars(ncid, varid, startp, countp, NULL, op, memtype);
}
/**
* @internal Read an array of values. This is called by nc_get_vara()
* for netCDF-4 files, as well as all the other nc_get_vara_*
* functions.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices.
* @param countp Array of counts.
* @param ip pointer that gets the data.
* @param memtype The type of these data after it is read into memory.
* @returns ::NC_NOERR for success
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_get_vara(int ncid, int varid, const size_t *startp,
const size_t *countp, void *ip, int memtype)
{
return NC4_get_vars(ncid, varid, startp, countp, NULL, ip, memtype);
}
/**
* @internal Do some common check for NC4_put_vars and
* NC4_get_vars. These checks have to be done when both reading and
* writing data.
*
* @param mem_nc_type Pointer to type of data in memory.
* @param var Pointer to var info struct.
* @param h5 Pointer to HDF5 file info struct.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
check_for_vara(nc_type *mem_nc_type, NC_VAR_INFO_T *var, NC_FILE_INFO_T *h5)
{
int retval;
/* If mem_nc_type is NC_NAT, it means we want to use the file type
* as the mem type as well. */
assert(mem_nc_type);
if (*mem_nc_type == NC_NAT)
*mem_nc_type = var->type_info->hdr.id;
assert(*mem_nc_type);
/* No NC_CHAR conversions, you pervert! */
if (var->type_info->hdr.id != *mem_nc_type &&
(var->type_info->hdr.id == NC_CHAR || *mem_nc_type == NC_CHAR))
return NC_ECHAR;
/* If we're in define mode, we can't read or write data. */
if (h5->flags & NC_INDEF)
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_EINDEFINE;
if ((retval = nc4_enddef_netcdf4_file(h5)))
return retval;
}
return NC_NOERR;
}
#ifdef LOGGING
/**
* @intarnal Print some debug info about dimensions to the log.
*/
static void
log_dim_info(NC_VAR_INFO_T *var, hsize_t *fdims, hsize_t *fmaxdims,
hsize_t *start, hsize_t *count)
{
int d2;
/* Print some debugging info... */
LOG((4, "%s: var name %s ndims %d", __func__, var->hdr.name, var->ndims));
LOG((4, "File space, and requested:"));
for (d2 = 0; d2 < var->ndims; d2++)
{
LOG((4, "fdims[%d]=%Ld fmaxdims[%d]=%Ld", d2, fdims[d2], d2,
fmaxdims[d2]));
LOG((4, "start[%d]=%Ld count[%d]=%Ld", d2, start[d2], d2, count[d2]));
}
}
#endif /* LOGGING */
#ifdef USE_PARALLEL4
/**
* @internal Set the parallel access for a var (collective
* vs. independent).
*
* @param h5 Pointer to HDF5 file info struct.
* @param var Pointer to var info struct.
* @param xfer_plistid H5FD_MPIO_COLLECTIVE or H5FD_MPIO_INDEPENDENT.
*
* @returns NC_NOERR No error.
* @author Ed Hartnett
*/
static int
set_par_access(NC_FILE_INFO_T *h5, NC_VAR_INFO_T *var, hid_t xfer_plistid)
{
/* If netcdf is built with parallel I/O, then parallel access can
* be used, and, if this file was opened or created for parallel
* access, we need to set the transfer mode. */
if (h5->parallel)
{
H5FD_mpio_xfer_t hdf5_xfer_mode;
/* Decide on collective or independent. */
hdf5_xfer_mode = (var->parallel_access != NC_INDEPENDENT) ?
H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT;
/* Set the mode in the transfer property list. */
if (H5Pset_dxpl_mpio(xfer_plistid, hdf5_xfer_mode) < 0)
return NC_EPARINIT;
LOG((4, "%s: %d H5FD_MPIO_COLLECTIVE: %d H5FD_MPIO_INDEPENDENT: %d",
__func__, (int)hdf5_xfer_mode, H5FD_MPIO_COLLECTIVE, H5FD_MPIO_INDEPENDENT));
}
return NC_NOERR;
}
#endif
/**
* @internal Write a strided array of data to a variable. This is
* called by nc_put_vars() and other nc_put_vars_* functions, for
* netCDF-4 files. Also the nc_put_vara() calls end up calling this
* with a NULL stride parameter.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices. Must always be provided by
* caller for non-scalar vars.
* @param countp Array of counts. Will default to counts of full
* dimension size if NULL.
* @param stridep Array of strides. Will default to strides of 1 if
* NULL.
* @param data The data to be written.
* @param mem_nc_type The type of the data in memory.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Var not found.
* @returns ::NC_EHDFERR HDF5 function returned error.
* @returns ::NC_EINVALCOORDS Incorrect start.
* @returns ::NC_EEDGE Incorrect start/count.
* @returns ::NC_ENOMEM Out of memory.
* @returns ::NC_EMPI MPI library error (parallel only)
* @returns ::NC_ECANTEXTEND Can't extend dimension for write.
* @returns ::NC_ERANGE Data conversion error.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
const ptrdiff_t *stridep, const void *data, nc_type mem_nc_type)
{
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
hid_t file_spaceid = 0, mem_spaceid = 0, xfer_plistid = 0;
long long unsigned xtend_size[NC_MAX_VAR_DIMS];
hsize_t fdims[NC_MAX_VAR_DIMS], fmaxdims[NC_MAX_VAR_DIMS];
hsize_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
hsize_t stride[NC_MAX_VAR_DIMS];
int need_to_extend = 0;
#ifdef USE_PARALLEL4
int extend_possible = 0;
#endif
int retval, range_error = 0, i, d2;
void *bufr = NULL;
int need_to_convert = 0;
int zero_count = 0; /* true if a count is zero */
size_t len = 1;
/* Find info for this file, group, and var. */
if ((retval = nc4_find_grp_h5_var(ncid, varid, &h5, &grp, &var)))
return retval;
assert(h5 && grp && var && var->hdr.id == varid);
/* Cannot convert to user-defined types. */
if (mem_nc_type >= NC_FIRSTUSERTYPEID)
mem_nc_type = NC_NAT;
LOG((3, "%s: var->hdr.name %s mem_nc_type %d", __func__,
var->hdr.name, mem_nc_type));
/* Check some stuff about the type and the file. If the file must
* be switched from define mode, it happens here. */
if ((retval = check_for_vara(&mem_nc_type, var, h5)))
return retval;
assert(var->hdf_datasetid && (!var->ndims || (startp && countp)));
/* Convert from size_t and ptrdiff_t to hssize_t, and hsize_t. */
/* Also do sanity checks */
for (i = 0; i < var->ndims; i++)
{
/* Check for non-positive stride. */
if (stridep && stridep[i] <= 0)
return NC_ESTRIDE;
start[i] = startp[i];
count[i] = countp ? countp[i] : var->dim[i]->len;
stride[i] = stridep ? stridep[i] : 1;
/* Check to see if any counts are zero. */
if (!count[i])
zero_count++;
}
/* Get file space of data. */
if ((file_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
/* Get the sizes of all the dims and put them in fdims. */
if (H5Sget_simple_extent_dims(file_spaceid, fdims, fmaxdims) < 0)
BAIL(NC_EHDFERR);
#ifdef LOGGING
log_dim_info(var, fdims, fmaxdims, start, count);
#endif
/* Check dimension bounds. Remember that unlimited dimensions can
* put data beyond their current length. */
for (d2 = 0; d2 < var->ndims; d2++)
{
hsize_t endindex = start[d2] + stride[d2] * (count[d2] - 1); /* last index written */
dim = var->dim[d2];
assert(dim && dim->hdr.id == var->dimids[d2]);
if (count[d2] == 0)
endindex = start[d2]; /* fixup for zero read count */
if (!dim->unlimited)
{
#ifdef RELAX_COORD_BOUND
/* Allow start to equal dim size if count is zero. */
if (start[d2] > (hssize_t)fdims[d2] ||
(start[d2] == (hssize_t)fdims[d2] && count[d2] > 0))
BAIL_QUIET(NC_EINVALCOORDS);
if (!zero_count && endindex >= fdims[d2])
BAIL_QUIET(NC_EEDGE);
#else
if (start[d2] >= (hssize_t)fdims[d2])
BAIL_QUIET(NC_EINVALCOORDS);
if (endindex >= fdims[d2])
BAIL_QUIET(NC_EEDGE);
#endif
}
}
/* Now you would think that no one would be crazy enough to write
a scalar dataspace with one of the array function calls, but you
would be wrong. So let's check to see if the dataset is
scalar. If it is, we won't try to set up a hyperslab. */
if (H5Sget_simple_extent_type(file_spaceid) == H5S_SCALAR)
{
if ((mem_spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
}
else
{
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, stride,
count, NULL) < 0)
BAIL(NC_EHDFERR);
/* Create a space for the memory, just big enough to hold the slab
we want. */
if ((mem_spaceid = H5Screate_simple(var->ndims, count, NULL)) < 0)
BAIL(NC_EHDFERR);
}
/* Are we going to convert any data? (No converting of compound or
* opaque types.) */
if (mem_nc_type != var->type_info->hdr.id &&
mem_nc_type != NC_COMPOUND && mem_nc_type != NC_OPAQUE)
{
size_t file_type_size;
/* We must convert - allocate a buffer. */
need_to_convert++;
if (var->ndims)
for (d2=0; d2<var->ndims; d2++)
len *= countp[d2];
LOG((4, "converting data for var %s type=%d len=%d", var->hdr.name,
var->type_info->hdr.id, len));
/* Later on, we will need to know the size of this type in the
* file. */
assert(var->type_info->size);
file_type_size = var->type_info->size;
/* If we're reading, we need bufr to have enough memory to store
* the data in the file. If we're writing, we need bufr to be
* big enough to hold all the data in the file's type. */
if (len > 0)
if (!(bufr = malloc(len * file_type_size)))
BAIL(NC_ENOMEM);
}
else
bufr = (void *)data;
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
#ifdef USE_PARALLEL4
/* Set up parallel I/O, if needed. */
if ((retval = set_par_access(h5, var, xfer_plistid)))
BAIL(retval);
#endif
/* Read this hyperslab from memory. */
/* Does the dataset have to be extended? If it's already
extended to the required size, it will do no harm to reextend
it to that size. */
if (var->ndims)
{
for (d2 = 0; d2 < var->ndims; d2++)
{
hsize_t endindex = start[d2] + stride[d2] * (count[d2] - 1); /* last index written */
if (count[d2] == 0)
endindex = start[d2];
dim = var->dim[d2];
assert(dim && dim->hdr.id == var->dimids[d2]);
if (dim->unlimited)
{
#ifdef USE_PARALLEL4
extend_possible = 1;
#endif
if (!zero_count && endindex >= fdims[d2])
{
xtend_size[d2] = (long long unsigned)(endindex+1);
need_to_extend++;
}
else
xtend_size[d2] = (long long unsigned)fdims[d2];
if (!zero_count && endindex >= dim->len)
{
dim->len = endindex+1;
dim->extended = NC_TRUE;
}
}
else
{
xtend_size[d2] = (long long unsigned)dim->len;
}
}
#ifdef USE_PARALLEL4
/* Check if anyone wants to extend */
if (extend_possible && h5->parallel &&
NC_COLLECTIVE == var->parallel_access)
{
/* Form consensus opinion among all processes about whether to perform
* collective I/O
*/
if (MPI_SUCCESS != MPI_Allreduce(MPI_IN_PLACE, &need_to_extend, 1,
MPI_INT, MPI_BOR, h5->comm))
BAIL(NC_EMPI);
}
#endif /* USE_PARALLEL4 */
/* If we need to extend it, we also need a new file_spaceid
to reflect the new size of the space. */
if (need_to_extend)
{
LOG((4, "extending dataset"));
#ifdef USE_PARALLEL4
if (h5->parallel)
{
if (NC_COLLECTIVE != var->parallel_access)
BAIL(NC_ECANTEXTEND);
/* Reach consensus about dimension sizes to extend to */
if (MPI_SUCCESS != MPI_Allreduce(MPI_IN_PLACE, xtend_size, var->ndims,
MPI_UNSIGNED_LONG_LONG, MPI_MAX,
h5->comm))
BAIL(NC_EMPI);
}
#endif /* USE_PARALLEL4 */
/* Convert xtend_size back to hsize_t for use with H5Dset_extent */
for (d2 = 0; d2 < var->ndims; d2++)
fdims[d2] = (hsize_t)xtend_size[d2];
if (H5Dset_extent(var->hdf_datasetid, fdims) < 0)
BAIL(NC_EHDFERR);
if (file_spaceid > 0 && H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
if ((file_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, stride, count, NULL) < 0)
BAIL(NC_EHDFERR);
}
}
/* Do we need to convert the data? */
if (need_to_convert)
{
if ((retval = nc4_convert_type(data, bufr, mem_nc_type, var->type_info->hdr.id,
len, &range_error, var->fill_value,
(h5->cmode & NC_CLASSIC_MODEL))))
BAIL(retval);
}
/* Write the data. At last! */
LOG((4, "about to H5Dwrite datasetid 0x%x mem_spaceid 0x%x "
"file_spaceid 0x%x", var->hdf_datasetid, mem_spaceid, file_spaceid));
if (H5Dwrite(var->hdf_datasetid, var->type_info->hdf_typeid,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);
/* Remember that we have written to this var so that Fill Value
* can't be set for it. */
if (!var->written_to)
var->written_to = NC_TRUE;
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
if ((h5->cmode & NC_CLASSIC_MODEL) &&
(var->type_info->hdr.id == NC_UBYTE || var->type_info->hdr.id == NC_BYTE) &&
(mem_nc_type == NC_UBYTE || mem_nc_type == NC_BYTE) &&
range_error)
range_error = 0;
exit:
if (file_spaceid > 0 && H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (mem_spaceid > 0 && H5Sclose(mem_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (xfer_plistid && (H5Pclose(xfer_plistid) < 0))
BAIL2(NC_EPARINIT);
if (need_to_convert && bufr) free(bufr);
/* If there was an error return it, otherwise return any potential
range error value. If none, return NC_NOERR as usual.*/
if (retval)
return retval;
if (range_error)
return NC_ERANGE;
return NC_NOERR;
}
/**
* @internal Read a strided array of data from a variable. This is
* called by nc_get_vars() for netCDF-4 files, as well as all the
* other nc_get_vars_* functions.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices. Must be provided for
* non-scalar vars.
* @param countp Array of counts. Will default to counts of extent of
* dimension if NULL.
* @param stridep Array of strides. Will default to strides of 1 if
* NULL.
* @param data The data to be written.
* @param mem_nc_type The type of the data in memory. (Convert to this
* type from file type.)
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Var not found.
* @returns ::NC_EHDFERR HDF5 function returned error.
* @returns ::NC_EINVALCOORDS Incorrect start.
* @returns ::NC_EEDGE Incorrect start/count.
* @returns ::NC_ENOMEM Out of memory.
* @returns ::NC_EMPI MPI library error (parallel only)
* @returns ::NC_ECANTEXTEND Can't extend dimension for write.
* @returns ::NC_ERANGE Data conversion error.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp,
const ptrdiff_t *stridep, void *data, nc_type mem_nc_type)
{
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
hid_t file_spaceid = 0, mem_spaceid = 0;
hid_t xfer_plistid = 0;
size_t file_type_size;
hsize_t count[NC_MAX_VAR_DIMS];
hsize_t fdims[NC_MAX_VAR_DIMS], fmaxdims[NC_MAX_VAR_DIMS];
hsize_t start[NC_MAX_VAR_DIMS];
hsize_t stride[NC_MAX_VAR_DIMS];
void *fillvalue = NULL;
int no_read = 0, provide_fill = 0;
int fill_value_size[NC_MAX_VAR_DIMS];
int scalar = 0, retval, range_error = 0, i, d2;
void *bufr = NULL;
int need_to_convert = 0;
size_t len = 1;
/* Find info for this file, group, and var. */
if ((retval = nc4_find_grp_h5_var(ncid, varid, &h5, &grp, &var)))
return retval;
assert(h5 && grp && var && var->hdr.id == varid);
LOG((3, "%s: var->hdr.name %s mem_nc_type %d", __func__,
var->hdr.name, mem_nc_type));
/* Check some stuff about the type and the file. Also end define
* mode, if needed. */
if ((retval = check_for_vara(&mem_nc_type, var, h5)))
return retval;
assert(var->hdf_datasetid && (!var->ndims || (startp && countp)));
/* Convert from size_t and ptrdiff_t to hsize_t. Also do sanity
* checks. */
for (i = 0; i < var->ndims; i++)
{
/* If any of the stride values are non-positive, fail. */
if (stridep && stridep[i] <= 0)
return NC_ESTRIDE;
start[i] = startp[i];
count[i] = countp[i];
stride[i] = stridep ? stridep[i] : 1;
/* if any of the count values are zero don't actually read. */
if (count[i] == 0)
no_read++;
}
/* Get file space of data. */
if ((file_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
/* Check to ensure the user selection is
* valid. H5Sget_simple_extent_dims gets the sizes of all the dims
* and put them in fdims. */
if (H5Sget_simple_extent_dims(file_spaceid, fdims, fmaxdims) < 0)
BAIL(NC_EHDFERR);
#ifdef LOGGING
log_dim_info(var, fdims, fmaxdims, start, count);
#endif
/* Check dimension bounds. Remember that unlimited dimensions can
* put data beyond their current length. */
for (d2 = 0; d2 < var->ndims; d2++)
{
hsize_t endindex = start[d2] + stride[d2] * (count[d2] - 1); /* last index read */
dim = var->dim[d2];
assert(dim && dim->hdr.id == var->dimids[d2]);
if (count[d2] == 0)
endindex = start[d2]; /* fixup for zero read count */
if (dim->unlimited)
{
size_t ulen;
/* We can't go beyond the largest current extent of
the unlimited dim. */
if ((retval = NC4_inq_dim(ncid, dim->hdr.id, NULL, &ulen)))
BAIL(retval);
/* Check for out of bound requests. */
#ifdef RELAX_COORD_BOUND
/* Allow start to equal dim size if count is zero. */
if (start[d2] > (hssize_t)ulen ||
(start[d2] == (hssize_t)ulen && count[d2] > 0))
BAIL_QUIET(NC_EINVALCOORDS);
#else
if (start[d2] >= (hssize_t)ulen && ulen > 0)
BAIL_QUIET(NC_EINVALCOORDS);
#endif
if (count[d2] && endindex >= ulen)
BAIL_QUIET(NC_EEDGE);
/* Things get a little tricky here. If we're getting
a GET request beyond the end of this var's
current length in an unlimited dimension, we'll
later need to return the fill value for the
variable. */
if (start[d2] >= (hssize_t)fdims[d2])
fill_value_size[d2] = count[d2];
else if (endindex >= fdims[d2])
fill_value_size[d2] = count[d2] - ((fdims[d2] - start[d2])/stride[d2]);
else
fill_value_size[d2] = 0;
count[d2] -= fill_value_size[d2];
if (fill_value_size[d2])
provide_fill++;
}
else /* Dim is not unlimited. */
{
/* Check for out of bound requests. */
#ifdef RELAX_COORD_BOUND
/* Allow start to equal dim size if count is zero. */
if (start[d2] > (hssize_t)fdims[d2] ||
(start[d2] == (hssize_t)fdims[d2] && count[d2] > 0))
BAIL_QUIET(NC_EINVALCOORDS);
#else
if (start[d2] >= (hssize_t)fdims[d2])
BAIL_QUIET(NC_EINVALCOORDS);
#endif
if (count[d2] && endindex >= fdims[d2])
BAIL_QUIET(NC_EEDGE);
/* Set the fill value boundary */
fill_value_size[d2] = count[d2];
}
}
/* Later on, we will need to know the size of this type in the
* file. */
assert(var->type_info->size);
file_type_size = var->type_info->size;
if (!no_read)
{
/* Now you would think that no one would be crazy enough to write
a scalar dataspace with one of the array function calls, but you
would be wrong. So let's check to see if the dataset is
scalar. If it is, we won't try to set up a hyperslab. */
if (H5Sget_simple_extent_type(file_spaceid) == H5S_SCALAR)
{
if ((mem_spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
scalar++;
}
else
{
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, stride, count, NULL) < 0)
BAIL(NC_EHDFERR);
/* Create a space for the memory, just big enough to hold the slab
we want. */
if ((mem_spaceid = H5Screate_simple(var->ndims, count, NULL)) < 0)
BAIL(NC_EHDFERR);
}
/* Fix bug when reading HDF5 files with variable of type
* fixed-length string. We need to make it look like a
* variable-length string, because that's all netCDF-4 data
* model supports, lacking anonymous dimensions. So
* variable-length strings are in allocated memory that user has
* to free, which we allocate here. */
if (var->type_info->nc_type_class == NC_STRING &&
H5Tget_size(var->type_info->hdf_typeid) > 1 &&
!H5Tis_variable_str(var->type_info->hdf_typeid))
{
hsize_t fstring_len;
if ((fstring_len = H5Tget_size(var->type_info->hdf_typeid)) == 0)
BAIL(NC_EHDFERR);
if (!(*(char **)data = malloc(1 + fstring_len)))
BAIL(NC_ENOMEM);
bufr = *(char **)data;
}
/* Are we going to convert any data? (No converting of compound or
* opaque types.) */
if (mem_nc_type != var->type_info->hdr.id &&
mem_nc_type != NC_COMPOUND && mem_nc_type != NC_OPAQUE)
{
/* We must convert - allocate a buffer. */
need_to_convert++;
if (var->ndims)
for (d2 = 0; d2 < var->ndims; d2++)
len *= countp[d2];
LOG((4, "converting data for var %s type=%d len=%d", var->hdr.name,
var->type_info->hdr.id, len));
/* If we're reading, we need bufr to have enough memory to store
* the data in the file. If we're writing, we need bufr to be
* big enough to hold all the data in the file's type. */
if (len > 0)
if (!(bufr = malloc(len * file_type_size)))
BAIL(NC_ENOMEM);
}
else
if (!bufr)
bufr = data;
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
#ifdef USE_PARALLEL4
/* Set up parallel I/O, if needed. */
if ((retval = set_par_access(h5, var, xfer_plistid)))
BAIL(retval);
#endif
/* Read this hyperslab into memory. */
LOG((5, "About to H5Dread some data..."));
if (H5Dread(var->hdf_datasetid, var->type_info->native_hdf_typeid,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);
/* Convert data type if needed. */
if (need_to_convert)
{
if ((retval = nc4_convert_type(bufr, data, var->type_info->hdr.id, mem_nc_type,
len, &range_error, var->fill_value,
(h5->cmode & NC_CLASSIC_MODEL))))
BAIL(retval);
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
if ((h5->cmode & NC_CLASSIC_MODEL) &&
(var->type_info->hdr.id == NC_UBYTE || var->type_info->hdr.id == NC_BYTE) &&
(mem_nc_type == NC_UBYTE || mem_nc_type == NC_BYTE) &&
range_error)
range_error = 0;
}
} /* endif ! no_read */
else
{
#ifdef USE_PARALLEL4 /* Start block contributed by HDF group. */
/* For collective IO read, some processes may not have any element for reading.
Collective requires all processes to participate, so we use H5Sselect_none
for these processes. */
if (var->parallel_access == NC_COLLECTIVE)
{
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
if ((retval = set_par_access(h5, var, xfer_plistid)))
BAIL(retval);
if (H5Sselect_none(file_spaceid) < 0)
BAIL(NC_EHDFERR);
/* Since no element will be selected, we just get the memory
* space the same as the file space. */
if ((mem_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
if (H5Sselect_none(mem_spaceid) < 0)
BAIL(NC_EHDFERR);
/* Read this hyperslab into memory. */
LOG((5, "About to H5Dread some data..."));
if (H5Dread(var->hdf_datasetid, var->type_info->native_hdf_typeid,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);
}
#endif /* End ifdef USE_PARALLEL4 */
}
/* Now we need to fake up any further data that was asked for,
using the fill values instead. First skip past the data we
just read, if any. */
if (!scalar && provide_fill)
{
void *filldata;
size_t real_data_size = 0;
size_t fill_len;
/* Skip past the real data we've already read. */
if (!no_read)
for (real_data_size = file_type_size, d2 = 0; d2 < var->ndims; d2++)
real_data_size *= (count[d2] - start[d2]);
/* Get the fill value from the HDF5 variable. Memory will be
* allocated. */
if (nc4_get_fill_value(h5, var, &fillvalue) < 0)
BAIL(NC_EHDFERR);
/* How many fill values do we need? */
for (fill_len = 1, d2 = 0; d2 < var->ndims; d2++)
fill_len *= (fill_value_size[d2] ? fill_value_size[d2] : 1);
/* Copy the fill value into the rest of the data buffer. */
filldata = (char *)data + real_data_size;
for (i = 0; i < fill_len; i++)
{
if (var->type_info->nc_type_class == NC_STRING)
{
if (*(char **)fillvalue)
{
if (!(*(char **)filldata = strdup(*(char **)fillvalue)))
BAIL(NC_ENOMEM);
}
else
*(char **)filldata = NULL;
}
else if (var->type_info->nc_type_class == NC_VLEN)
{
if (fillvalue)
{
memcpy(filldata,fillvalue,file_type_size);
} else {
*(char **)filldata = NULL;
}
}
else
memcpy(filldata, fillvalue, file_type_size);
filldata = (char *)filldata + file_type_size;
}
}
exit:
if (file_spaceid > 0)
if (H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (mem_spaceid > 0)
if (H5Sclose(mem_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (xfer_plistid > 0)
if (H5Pclose(xfer_plistid) < 0)
BAIL2(NC_EHDFERR);
if (need_to_convert && bufr)
free(bufr);
if (fillvalue)
{
if (var->type_info->nc_type_class == NC_VLEN)
nc_free_vlen((nc_vlen_t *)fillvalue);
else if (var->type_info->nc_type_class == NC_STRING && *(char **)fillvalue)
free(*(char **)fillvalue);
free(fillvalue);
}
/* If there was an error return it, otherwise return any potential
range error value. If none, return NC_NOERR as usual.*/
if (retval)
return retval;
if (range_error)
return NC_ERANGE;
return NC_NOERR;
}
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