mirror/netcdf-c
2
0
Fork 0
mirror of https://github.com/Unidata/netcdf-c.git synced 2024-11-27 07:30:33 +08:00
Code Issues Packages Projects Releases Wiki Activity

moved put and get vars functions from nc4hdf5.c to hdf5var.c

Browse Source
This commit is contained in:
Ed Hartnett 2018-08-09 06:44:38 -06:00
parent 5e9ffcaab3
commit 2e7a7ea94e
2 changed files with 827 additions and 826 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

827
libhdf5/hdf5var.c
View File

@ -1248,3 +1248,830 @@ NC4_get_vars(int ncid, int varid, const size_t *startp,
return nc4_get_vars(nc, ncid, varid, startp, countp, stridep, memtype,
(void *)ip);
}
/**
* @internal Do some common check for nc4_put_vara and
* nc4_get_vara. 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.
*
* @param nc Pointer to the file NC struct.
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices. Will default to starts of 0
* if NULL.
* @param countp Array of counts. Will default to counts of 1 if NULL.
* @param stridep Array of strides. Will default to strides of 1 if
* NULL.
* @param mem_nc_type The type of the data in memory.
* @param data The data to be written.
*
* @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(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
nc_type mem_nc_type, void *data)
{
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];
char *name_to_use;
int need_to_extend = 0;
#ifdef USE_PARALLEL4
int extend_possible = 0;
#endif
int retval = NC_NOERR, 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 our metadata for this file, group, and var. */
assert(nc);
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
h5 = NC4_DATA(nc);
assert(grp && h5 && var && var->hdr.name);
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;
/* 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 == NULL ? 0 : startp[i]);
count[i] = (countp == NULL ? 1 : countp[i]);
stride[i] = (stridep == NULL ? 1 : stridep[i]);
/* Check to see if any counts are zero. */
if (!count[i])
zero_count++;
}
/* Open this dataset if necessary, also checking for a weird case:
* a non-coordinate (and non-scalar) variable that has the same
* name as a dimension. */
if (var->hdf5_name && strlen(var->hdf5_name) >= strlen(NON_COORD_PREPEND) &&
strncmp(var->hdf5_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)) == 0 &&
var->ndims)
name_to_use = var->hdf5_name;
else
name_to_use = var->hdr.name;
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, name_to_use, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
/* 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 = 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.
*
* @param nc Pointer to the file NC struct.
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices. Will default to starts of 0
* if NULL.
* @param countp Array of counts. Will default to counts of 1 if NULL.
* @param stridep Array of strides. Will default to strides of 1 if
* NULL.
* @param mem_nc_type The type of the data in memory. (Convert to this
* type from file type.)
* @param data The data to be written.
*
* @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(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
nc_type mem_nc_type, void *data)
{
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 *xtend_size = NULL, 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];
char *name_to_use;
void *fillvalue = NULL;
int no_read = 0, provide_fill = 0;
int fill_value_size[NC_MAX_VAR_DIMS];
int scalar = 0, retval = NC_NOERR, range_error = 0, i, d2;
void *bufr = NULL;
int need_to_convert = 0;
size_t len = 1;
/* Find our metadata for this file, group, and var. */
assert(nc);
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
h5 = NC4_DATA(nc);
assert(grp && h5 && var && var->hdr.name);
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 ((retval = check_for_vara(&mem_nc_type, var, h5)))
return retval;
/* 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 == NULL ? 0 : startp[i]);
count[i] = (countp == NULL ? 1 : countp[i]);
stride[i] = (stridep == NULL ? 1 : stridep[i]);
/* if any of the count values are zero don't actually read. */
if (count[i] == 0)
no_read++;
}
/* Open this dataset if necessary, also checking for a weird case:
* a non-coordinate (and non-scalar) variable that has the same
* name as a dimension. */
if (var->hdf5_name && strlen(var->hdf5_name) >= strlen(NON_COORD_PREPEND) &&
strncmp(var->hdf5_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)) == 0 &&
var->ndims)
name_to_use = var->hdf5_name;
else
name_to_use = var->hdr.name;
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, name_to_use, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
/* 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 != NULL)
free(bufr);
if (xtend_size)
free(xtend_size);
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;
}

826
libhdf5/nc4hdf.c
View File

@ -531,106 +531,6 @@ exit:
return retval;
}
/**
* @internal Do some common check for nc4_put_vara and
* nc4_get_vara. 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 an attribute.
*
@ -3598,729 +3498,3 @@ NC4_walk(hid_t gid, int* countp)
return ncstat;
}
/**
* @internal Write a strided array of data to a variable.
*
* @param nc Pointer to the file NC struct.
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices. Will default to starts of 0
* if NULL.
* @param countp Array of counts. Will default to counts of 1 if NULL.
* @param stridep Array of strides. Will default to strides of 1 if
* NULL.
* @param mem_nc_type The type of the data in memory.
* @param data The data to be written.
*
* @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(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
nc_type mem_nc_type, void *data)
{
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];
char *name_to_use;
int need_to_extend = 0;
#ifdef USE_PARALLEL4
int extend_possible = 0;
#endif
int retval = NC_NOERR, 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 our metadata for this file, group, and var. */
assert(nc);
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
h5 = NC4_DATA(nc);
assert(grp && h5 && var && var->hdr.name);
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;
/* 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 == NULL ? 0 : startp[i]);
count[i] = (countp == NULL ? 1 : countp[i]);
stride[i] = (stridep == NULL ? 1 : stridep[i]);
/* Check to see if any counts are zero. */
if (!count[i])
zero_count++;
}
/* Open this dataset if necessary, also checking for a weird case:
* a non-coordinate (and non-scalar) variable that has the same
* name as a dimension. */
if (var->hdf5_name && strlen(var->hdf5_name) >= strlen(NON_COORD_PREPEND) &&
strncmp(var->hdf5_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)) == 0 &&
var->ndims)
name_to_use = var->hdf5_name;
else
name_to_use = var->hdr.name;
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, name_to_use, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
/* 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 = 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.
*
* @param nc Pointer to the file NC struct.
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices. Will default to starts of 0
* if NULL.
* @param countp Array of counts. Will default to counts of 1 if NULL.
* @param stridep Array of strides. Will default to strides of 1 if
* NULL.
* @param mem_nc_type The type of the data in memory. (Convert to this
* type from file type.)
* @param data The data to be written.
*
* @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(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
nc_type mem_nc_type, void *data)
{
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 *xtend_size = NULL, 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];
char *name_to_use;
void *fillvalue = NULL;
int no_read = 0, provide_fill = 0;
int fill_value_size[NC_MAX_VAR_DIMS];
int scalar = 0, retval = NC_NOERR, range_error = 0, i, d2;
void *bufr = NULL;
int need_to_convert = 0;
size_t len = 1;
/* Find our metadata for this file, group, and var. */
assert(nc);
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
h5 = NC4_DATA(nc);
assert(grp && h5 && var && var->hdr.name);
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 ((retval = check_for_vara(&mem_nc_type, var, h5)))
return retval;
/* 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 == NULL ? 0 : startp[i]);
count[i] = (countp == NULL ? 1 : countp[i]);
stride[i] = (stridep == NULL ? 1 : stridep[i]);
/* if any of the count values are zero don't actually read. */
if (count[i] == 0)
no_read++;
}
/* Open this dataset if necessary, also checking for a weird case:
* a non-coordinate (and non-scalar) variable that has the same
* name as a dimension. */
if (var->hdf5_name && strlen(var->hdf5_name) >= strlen(NON_COORD_PREPEND) &&
strncmp(var->hdf5_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)) == 0 &&
var->ndims)
name_to_use = var->hdf5_name;
else
name_to_use = var->hdr.name;
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, name_to_use, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
/* 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 != NULL)
free(bufr);
if (xtend_size)
free(xtend_size);
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;
}