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6b0feecb05
netcdf-c/libsrc4/nc4var.c
Ed Hartnett 6b0feecb05 some improvements to chunking algorithm
2011-02-09 12:23:09 +00:00

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/*
This file is part of netcdf-4, a netCDF-like interface for HDF5, or a
HDF5 backend for netCDF, depending on your point of view.
This file handles the nc4 variable functions.
Copyright 2003-2006, University Corporation for Atmospheric
Research. See COPYRIGHT file for copying and redistribution
conditions.
$Id: nc4var.c,v 1.148 2010/05/27 21:34:15 dmh Exp $
*/
#include <nc4internal.h>
#include "nc4dispatch.h"
#include <math.h>
#ifdef USE_PNETCDF
#include <pnetcdf.h>
#endif
/* Min and max deflate levels tolerated by HDF5. */
#define MIN_DEFLATE_LEVEL 0
#define MAX_DEFLATE_LEVEL 9
/* This is to track opened HDF5 objects to make sure they are
* closed. */
#ifdef EXTRA_TESTS
extern int num_plists;
#endif /* EXTRA_TESTS */
/* One meg is the minimum buffer size. */
#define ONE_MEG 1048576
/* Szip options. */
#define NC_SZIP_EC_OPTION_MASK 4
#define NC_SZIP_NN_OPTION_MASK 32
#define NC_SZIP_MAX_PIXELS_PER_BLOCK 32
int nc4_get_default_fill_value(NC_TYPE_INFO_T *type_info, void *fill_value);
/* If the HDF5 dataset for this variable is open, then close it and
* reopen it, with the perhaps new settings for chunk caching. */
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;
#ifdef EXTRA_TESTS
num_plists++;
#endif
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->name,
access_pid)) < 0)
return NC_EHDFERR;
if (H5Pclose(access_pid) < 0)
return NC_EHDFERR;
#ifdef EXTRA_TESTS
num_plists--;
#endif
if (var->dimscale)
var->dim[0]->hdf_dimscaleid = var->hdf_datasetid;
}
return NC_NOERR;
}
/* Set chunk cache size for a variable. */
int
NC4_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems,
float preemption)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
int retval;
/* Check input for validity. */
if (preemption < 0 || preemption > 1)
return NC_EINVAL;
/* 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;
/* An attempt to do any of these things on a netCDF-3 file is
* ignored with no error. */
if (!h5)
return NC_NOERR;
assert(nc && grp && h5);
/* Find the var. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
/* Set the values. */
var->chunk_cache_size = size;
var->chunk_cache_nelems = nelems;
var->chunk_cache_preemption = preemption;
if ((retval = nc4_reopen_dataset(grp, var)))
return retval;
return NC_NOERR;
}
/* Need this version for fortran. Accept negative numbers to leave
* settings as they are. */
int
nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems,
int preemption)
{
size_t real_size = H5D_CHUNK_CACHE_NBYTES_DEFAULT;
size_t real_nelems = H5D_CHUNK_CACHE_NSLOTS_DEFAULT;
float real_preemption = H5D_CHUNK_CACHE_W0_DEFAULT;
if (size >= 0)
real_size = size * MEGABYTE;
if (nelems >= 0)
real_nelems = nelems;
if (preemption >= 0)
real_preemption = preemption / 100.;
return nc_set_var_chunk_cache(ncid, varid, real_size, real_nelems,
real_preemption);
}
/* Get chunk cache size for a variable. */
int
NC4_get_var_chunk_cache(int ncid, int varid, size_t *sizep,
size_t *nelemsp, float *preemptionp)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
int retval;
/* 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;
/* Attempting to do any of these things on a netCDF-3 file produces
* an error. */
if (!h5)
return NC_ENOTNC4;
assert(nc && grp && h5);
/* Find the var. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
/* Give the user what they want. */
if (sizep)
*sizep = var->chunk_cache_size;
if (nelemsp)
*nelemsp = var->chunk_cache_nelems;
if (preemptionp)
*preemptionp = var->chunk_cache_preemption;
return NC_NOERR;
}
/* Get chunk cache size for a variable. */
int
nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep,
int *nelemsp, int *preemptionp)
{
size_t real_size, real_nelems;
float real_preemption;
int ret;
if ((ret = nc_get_var_chunk_cache(ncid, varid, &real_size,
&real_nelems, &real_preemption)))
return ret;
if (sizep)
*sizep = real_size / MEGABYTE;
if (nelemsp)
*nelemsp = (int)real_nelems;
if(preemptionp)
*preemptionp = (int)(real_preemption * 100);
return NC_NOERR;
}
/* Check a set of chunksizes to see if they add up to a chunk that is too big. */
static int
check_chunksizes(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, const size_t *chunksizes)
{
NC_TYPE_INFO_T *type_info;
long long total;
size_t type_len;
int d;
int retval;
if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, var->xtype, 0, &type_len)))
return retval;
if ((retval = nc4_find_type(grp->file->nc4_info, var->xtype, &type_info)))
return retval;
if (type_info && type_info->class == NC_VLEN)
total = sizeof(hvl_t);
else
total = type_len;
for (d = 0; d < var->ndims; d++)
{
if (chunksizes[d] < 1)
return NC_EINVAL;
total *= chunksizes[d];
}
if (total > NC_MAX_UINT)
return NC_EBADCHUNK;
return NC_NOERR;
}
/* Find the default chunk nelems (i.e. length of chunk along each
* dimension). */
static int
nc4_find_default_chunksizes(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
int d, max_dim;
size_t type_size, max_len = 0;
float num_values = 1, num_set = 0;
float total_chunk_size;
int retval;
if (var->type_info->nc_typeid == NC_STRING)
type_size = sizeof(char *);
else
type_size = var->type_info->size;
/* Later this will become the total number of bytes in the default
* chunk. */
total_chunk_size = type_size;
/* How many values in the variable (or one record, if there are
* unlimited dimensions); which is the largest dimension, and how
* long is it? */
for (d = 0; d < var->ndims; d++)
{
assert(var->dim[d]);
if (var->dim[d]->len)
num_values *= (float)var->dim[d]->len;
else
num_set++;
if (var->dim[d]->len > max_len)
{
max_len = var->dim[d]->len;
max_dim = d;
}
LOG((4, "d = %d max_dim %d max_len %ld num_values %f", d, max_dim, max_len,
num_values));
}
/* If a dim is several orders of magnitude smaller than the max
* dimension, set it's chunk size to the full extent of the smaller
* dimension. */
#define NC_DIM_MULTIPLIER 1000
for (d = 0; d < var->ndims; d++)
if (var->dim[d]->unlimited)
var->chunksizes[d] = 1;
else if (!var->dim[d]->unlimited && var->dim[d]->len * NC_DIM_MULTIPLIER < max_len)
{
var->chunksizes[d] = var->dim[d]->len;
num_set++;
}
/* 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])
{
size_t suggested_size;
suggested_size = (pow((double)DEFAULT_CHUNK_SIZE/(num_values * type_size),
1/(double)(var->ndims - num_set)) * 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;
total_chunk_size *= var->chunksizes[d];
LOG((4, "nc_def_var_nc4: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", var->name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d]));
}
LOG((4, "total_chunk_size %f", total_chunk_size));
/* But did this add up to 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] /= 2;
}
return NC_NOERR;
}
/* This is called when a new netCDF-4 variable is defined. Break it
* down! */
static int
nc_def_var_nc4(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_HDF5_FILE_INFO_T *h5;
NC_TYPE_INFO_T *type_info;
char norm_name[NC_MAX_NAME + 1];
int new_varid = 0;
int num_unlim = 0;
int d;
size_t num_values = 1;
int retval;
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(grp && h5);
/* If it's not in define mode, strict nc3 files error out,
* otherwise switch to define mode. */
if (!(h5->flags & NC_INDEF))
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_ENOTINDEFINE;
if ((retval = NC4_redef(ncid)))
return retval;
}
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
/* Not a Type is, well, not a type.*/
if (xtype == NC_NAT)
return NC_EBADTYPE;
/* For classic files, only classic types are allowed. */
if (h5->cmode & NC_CLASSIC_MODEL && xtype > NC_DOUBLE)
return NC_ESTRICTNC3;
/* If this is a user defined type, find it. */
if (xtype > NC_STRING)
if ((retval = nc4_find_type(grp->file->nc4_info, xtype, &type_info)))
return NC_EBADTYPE;
/* cast needed for braindead systems with signed size_t */
if((unsigned long) ndims > X_INT_MAX) /* Backward compat */
return NC_EINVAL;
/* Classic model files have a limit on number of vars. */
if(h5->cmode & NC_CLASSIC_MODEL && h5->nvars >= NC_MAX_VARS)
return NC_EMAXVARS;
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
return retval;
/* If the file is read-only, return an error. */
if (h5->no_write)
return NC_EPERM;
/* Get the new varid. */
for (var = grp->var; var; var = var->next)
new_varid++;
/* 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)))
return retval;
if (dim->unlimited)
num_unlim++;
else
num_values *= dim->len;
}
/* These degrubbing messages sure are handy! */
LOG((3, "nc_def_var_nc4: name %s type %d ndims %d", norm_name, xtype, ndims));
#ifdef LOGGING
{
int dd;
for (dd = 0; dd < ndims; dd++)
LOG((4, "dimid[%d] %d", dd, dimidsp[dd]));
}
#endif
/* Add the var to the end of the list. */
if ((retval = nc4_var_list_add(&grp->var, &var)))
return retval;
/* Now fill in the values in the var info structure. */
if (!(var->name = malloc((strlen(norm_name) + 1) * sizeof(char))))
return NC_ENOMEM;
strcpy(var->name, norm_name);
var->varid = grp->nvars++;
var->xtype = xtype;
var->ndims = ndims;
var->dirty++;
/* If this is a user-defined type, there is a type_info stuct with
* all the type information. For atomic types, fake up a type_info
* struct. */
if (xtype > NC_STRING)
var->type_info = type_info;
else
{
if (!(var->type_info = calloc(1, sizeof(NC_TYPE_INFO_T))))
return NC_ENOMEM;
var->type_info->nc_typeid = xtype;
if ((retval = nc4_get_hdf_typeid(h5, var->xtype, &var->type_info->hdf_typeid,
var->type_info->endianness)))
return retval;
if ((var->type_info->native_typeid = H5Tget_native_type(var->type_info->hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0,
&var->type_info->size)))
return retval;
}
if (!num_unlim)
var->contiguous = 1;
/* Allocate space for dimension information. */
if (ndims)
{
if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *))))
return NC_ENOMEM;
if (!(var->dimids = calloc(ndims, sizeof(int))))
return NC_ENOMEM;
}
/* 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? */
for (d = 0; d < ndims; d++)
{
NC_GRP_INFO_T *dim_grp;
if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, &dim_grp)))
return retval;
if (strcmp(dim->name, norm_name) == 0 && dim_grp == grp && d == 0)
{
var->dimscale++;
dim->coord_var = var;
dim->coord_var_in_grp++;
}
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->name));
if (var->ndims)
if (!(var->chunksizes = calloc(var->ndims, sizeof(size_t))))
return NC_ENOMEM;
if ((retval = nc4_find_default_chunksizes(grp, var)))
return retval;
/* Is this a variable with a chunksize greater than the current
* cache size? */
if ((retval = nc4_adjust_var_cache(grp, var)))
return 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. */
for (dim = grp->dim; dim; dim = dim->next)
if (!strcmp(dim->name, norm_name) && dimidsp[0] != dim->dimid)
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
return NC_EMAXNAME;
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(norm_name) + 1) * sizeof(char))))
return 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 (ndims && !(var->dimscale_attached = calloc(ndims, sizeof(int))))
return NC_ENOMEM;
/* Return the varid. */
if (varidp)
*varidp = var->varid;
LOG((4, "new varid %d", var->varid));
return retval;
}
/* Create a new variable to hold user data. This is what it's all
* about baby! */
int
NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims,
const int *dimidsp, int *varidp)
{
NC_FILE_INFO_T *nc;
LOG((2, "nc_def_var: ncid 0x%x name %s xtype %d ndims %d",
ncid, name, xtype, ndims));
/* If there are dimensions, I need their ids. */
if (ndims && !dimidsp)
return NC_EINVAL;
/* Find metadata for this file. */
if (!(nc = nc4_find_nc_file(ncid)))
return NC_EBADID;
#ifdef USE_PNETCDF
/* Take care of files created/opened with parallel-netcdf library. */
if (nc->pnetcdf_file)
{
int ret;
ret = ncmpi_def_var(nc->int_ncid, name, xtype, ndims,
dimidsp, varidp);
nc->pnetcdf_ndims[*varidp] = ndims;
return ret;
}
#endif /* USE_PNETCDF */
/* Netcdf-3 cases handled by dispatch layer. */
assert(nc->nc4_info);
/* Handle netcdf-4 cases. */
return nc_def_var_nc4(ncid, name, xtype, ndims, dimidsp, varidp);
}
/* Get all the information about a variable. Pass NULL for whatever
* you don't care about. This is an internal function, not exposed to
* the user. */
int
NC4_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep,
int *ndimsp, int *dimidsp, int *nattsp,
int *shufflep, int *deflatep, int *deflate_levelp,
int *fletcher32p, int *contiguousp, size_t *chunksizesp,
int *no_fill, void *fill_valuep, int *endiannessp,
int *options_maskp, int *pixels_per_blockp)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_ATT_INFO_T *att;
int natts=0;
size_t type_size;
int d;
int retval;
LOG((2, "nc_inq_var_all: ncid 0x%x varid %d", 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);
#ifdef USE_PNETCDF
/* Take care of files created/opened with parallel-netcdf library. */
if (nc->pnetcdf_file)
return ncmpi_inq_var(nc->int_ncid, varid, name, xtypep, ndimsp,
dimidsp, nattsp);
#endif /* USE_PNETCDF */
/* Walk through the list of vars, and return the info about the one
with a matching varid. If the varid is -1, find the global
atts and call it a day. */
if (varid == NC_GLOBAL)
{
if (nattsp)
{
for (att = grp->att; att; att = att->next)
natts++;
*nattsp = natts;
}
return NC_NOERR;
}
/* Find the var. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
/* Oh no! Maybe we couldn't find it (*sob*)! */
if (!var)
return NC_ENOTVAR;
/* Copy the data to the user's data buffers. */
if (name)
strcpy(name, var->name);
if (xtypep)
*xtypep = var->xtype;
if (ndimsp)
*ndimsp = var->ndims;
if (dimidsp)
for (d = 0; d < var->ndims; d++)
dimidsp[d] = var->dimids[d];
if (nattsp)
{
for (att = var->att; att; att = att->next)
natts++;
*nattsp = natts;
}
/* Chunking stuff. */
if (!var->contiguous && chunksizesp)
for (d = 0; d < var->ndims; d++)
{
chunksizesp[d] = var->chunksizes[d];
LOG((4, "chunksizesp[%d]=%d", d, chunksizesp[d]));
}
if (contiguousp)
*contiguousp = var->contiguous ? NC_CONTIGUOUS : NC_CHUNKED;
/* Filter stuff. */
if (deflatep)
*deflatep = var->deflate;
if (deflate_levelp)
*deflate_levelp = var->deflate_level;
if (shufflep)
*shufflep = var->shuffle;
if (fletcher32p)
*fletcher32p = var->fletcher32;
if (options_maskp)
*options_maskp = var->options_mask;
if (pixels_per_blockp)
*pixels_per_blockp = var->pixels_per_block;
/* Fill value stuff. */
if (no_fill)
*no_fill = var->no_fill;
/* Don't do a thing with fill_valuep if no_fill mode is set for
* this var, or if fill_valuep is NULL. */
if (!var->no_fill && fill_valuep)
{
/* Do we have a fill value for this var? */
if (var->fill_value)
{
if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, var->xtype, 0, &type_size)))
return retval;
memcpy(fill_valuep, var->fill_value, type_size);
}
else
{
if ((retval = nc4_get_default_fill_value(var->type_info, fill_valuep)))
return retval;
}
}
/* Does the user want the endianness of this variable? */
if (endiannessp)
*endiannessp = var->type_info->endianness;
return NC_NOERR;
}
/* This functions sets extra stuff about a netCDF-4 variable which
must be set before the enddef but after the def_var. This is an
internal function, deliberately hidden from the user so that we can
change the prototype of this functions without changing the API. */
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,
int *options_mask, int *pixels_per_block)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
size_t type_size;
int d;
int retval;
LOG((2, "nc_def_var_extra: ncid 0x%x varid %d", 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;
/* Attempting to do any of these things on a netCDF-3 file produces
* an error. */
if (!h5)
return NC_ENOTNC4;
assert(nc && grp && h5);
/* Find the var. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
/* Oh no! Maybe we couldn't find it (*sob*)! */
if (!var)
return NC_ENOTVAR;
/* Can't turn on contiguous and deflate/fletcher32/szip. */
if (contiguous)
if ((*contiguous != NC_CHUNKED && deflate) ||
(*contiguous != NC_CHUNKED && fletcher32) ||
(*contiguous != NC_CHUNKED && options_mask))
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 && options_mask) ||
(deflate && !deflate_level) ||
(options_mask && !pixels_per_block))
return NC_EINVAL;
/* Valid deflate level? */
if (deflate && deflate_level)
{
if (*deflate)
if (*deflate_level < MIN_DEFLATE_LEVEL ||
*deflate_level > MAX_DEFLATE_LEVEL)
return NC_EINVAL;
if (var->options_mask)
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 = 0;
var->deflate = *deflate;
if (*deflate)
var->deflate_level = *deflate_level;
LOG((3, "nc_def_var_extra: *deflate_level %d", *deflate_level));
}
/* Szip in use? */
if (options_mask)
{
#ifndef USE_SZIP
return NC_EINVAL;
#endif
if (var->deflate)
return NC_EINVAL;
if ((*options_mask != NC_SZIP_EC_OPTION_MASK) &&
(*options_mask != NC_SZIP_NN_OPTION_MASK))
return NC_EINVAL;
if ((*pixels_per_block > NC_SZIP_MAX_PIXELS_PER_BLOCK) ||
(var->type_info->nc_typeid >= NC_STRING))
return NC_EINVAL;
var->options_mask = *options_mask;
var->pixels_per_block = *pixels_per_block;
var->contiguous = 0;
}
/* Shuffle filter? */
if (shuffle)
{
var->shuffle = *shuffle;
var->contiguous = 0;
}
/* Fltcher32 checksum error protection? */
if (fletcher32)
{
var->fletcher32 = *fletcher32;
var->contiguous = 0;
}
/* 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 || var->options_mask)
return NC_EINVAL;
for (d = 0; d < var->ndims; d++)
{
if ((retval = nc4_find_dim(grp, var->dimids[d], &dim, NULL)))
return retval;
if (dim->unlimited)
return NC_EINVAL;
}
var->contiguous = NC_CONTIGUOUS;
}
/* Chunksizes anyone? */
if (contiguous && *contiguous == NC_CHUNKED)
{
var->contiguous = 0;
/* 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;
/* 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 == NC_CHUNKED && (chunksizes || deflate || contiguous))
{
/* Determine default chunksizes for this variable. */
if (!var->chunksizes[0])
if ((retval = nc4_find_default_chunksizes(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)
var->no_fill = 1;
else
var->no_fill = 0;
}
/* Are we setting a fill value? */
if (fill_value && !var->no_fill)
{
/* If fill value hasn't been set, allocate space. */
if ((retval = nc4_get_typelen_mem(h5, var->xtype, 0, &type_size)))
return retval;
if (!var->fill_value)
if (!(var->fill_value = malloc(type_size)))
return NC_ENOMEM;
/* Copy the fill_value. */
LOG((4, "Copying fill value into metadata for variable %s",
var->name));
memcpy(var->fill_value, fill_value, type_size);
/* If there's a _FillValue attribute, delete it. */
retval = nc_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->xtype, 1, fill_value)))
return retval;
}
/* Is the user setting the endianness? */
if (endianness)
var->type_info->endianness = *endianness;
return NC_NOERR;
}
/* Set the deflate level for a var, lower is faster, higher is
* better. Must be called after nc_def_var and before nc_enddef or any
* functions which writes data to the file. */
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, NULL, NULL);
}
/* Set checksum for a var. This must be called after the nc_def_var
* but before the nc_enddef. */
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, NULL, NULL);
}
/* Define chunking stuff for a var. This must be done after nc_def_var
and before nc_enddef.
Chunking is required in any dataset with one or more unlimited
dimension in HDF5, or any dataset using a filter.
Where chunksize is a pointer to an array of size ndims, with the
chunksize in each dimension.
*/
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, NULL, NULL);
}
/* Inquire about chunking stuff for a var. This is a private,
* undocumented function, used by the f77 API to avoid size_t
* problems. */
int
nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int *chunksizesp)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
size_t *cs = NULL;
int i, retval;
/* Find this ncid's file info. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(nc);
/* Must be netcdf-4. */
if (!h5)
return NC_ENOTNC4;
/* Find var cause I need the number of dims. */
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
/* 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;
retval = NC4_inq_var_all(ncid, varid, NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, NULL, contiguousp, cs, NULL,
NULL, NULL, NULL, NULL);
/* Copy to size_t array. */
if (*contiguousp == NC_CHUNKED)
for (i = 0; i < var->ndims; i++)
{
chunksizesp[i] = cs[i];
if (cs[i] > NC_MAX_INT)
retval = NC_ERANGE;
}
if (var->ndims)
free(cs);
return retval;
}
/* This function defines the chunking with ints, which works better
* with F77 portability. It is a secret function, which has been
* rendered unmappable, and it is impossible to apparate anywhere in
* this function. */
int
nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizesp)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
size_t *cs = NULL;
int i, retval;
/* Find this ncid's file info. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(nc);
/* Must be netcdf-4. */
if (!h5)
return NC_ENOTNC4;
/* Find var cause I need the number of dims. */
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
/* 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, NULL, NULL);
if (var->ndims)
free(cs);
return retval;
}
/* Define fill value behavior for a variable. This must be done after
nc_def_var and before nc_enddef. */
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, NULL, NULL);
}
/* Define the endianness of a variable. */
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, NULL, NULL);
}
/* Get var id from name. */
int
NC4_inq_varid(int ncid, const char *name, int *varidp)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
char norm_name[NC_MAX_NAME + 1];
int retval;
if (!name)
return NC_EINVAL;
if (!varidp)
return NC_NOERR;
LOG((2, "nc_inq_varid: ncid 0x%x name %s", ncid, 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;
/* Handle netcdf-3. */
assert(h5);
/* Normalize name. */
if ((retval = nc4_normalize_name(name, norm_name)))
return retval;
/* Find var of this name. */
for (var = grp->var; var; var = var->next)
if (!(strcmp(var->name, norm_name)))
{
*varidp = var->varid;
return NC_NOERR;
}
return NC_ENOTVAR;
}
/* Rename a var to "bubba," for example.
According to the netcdf-3.5 docs: If the new name is longer than
the old name, the netCDF dataset must be in define mode. */
int
NC4_rename_var(int ncid, int varid, const char *name)
{
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
int retval = NC_NOERR;
LOG((2, "nc_rename_var: ncid 0x%x varid %d name %s",
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;
#ifdef USE_PNETCDF
/* Take care of files created/opened with parallel-netcdf library. */
if (nc->pnetcdf_file)
return ncmpi_rename_var(nc->int_ncid, varid, name);
#endif /* USE_PNETCDF */
/* Take care of netcdf-3 files. */
assert(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;
/* Is name in use? */
for (var = grp->var; var; var = var->next)
if (!strncmp(var->name, name, NC_MAX_NAME))
return NC_ENAMEINUSE;
/* Find the var. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
/* 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->name) &&
(h5->cmode & NC_CLASSIC_MODEL))
return NC_ENOTINDEFINE;
/* Change the HDF5 file, if this var has already been created
there. */
if (var->created)
{
if (H5Gmove(grp->hdf_grpid, var->name, name) < 0)
BAIL(NC_EHDFERR);
}
/* Now change the name in our metadata. */
free(var->name);
if (!(var->name = malloc((strlen(name) + 1) * sizeof(char))))
return NC_ENOMEM;
strcpy(var->name, name);
exit:
return retval;
}
int
NC4_var_par_access(int ncid, int varid, int par_access)
{
#ifndef USE_PARALLEL
return NC_ENOPAR;
#else
NC_FILE_INFO_T *nc;
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
int retval;
LOG((1, "nc_var_par_access: ncid 0x%x varid %d par_access %d", ncid,
varid, par_access));
if (par_access != NC_INDEPENDENT && par_access != NC_COLLECTIVE)
return NC_EINVAL;
/* 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;
#ifdef USE_PNETCDF
/* Handle files opened/created with parallel-netcdf library. */
if (nc->pnetcdf_file)
{
if (par_access == nc->pnetcdf_access_mode)
return NC_NOERR;
nc->pnetcdf_access_mode = par_access;
if (par_access == NC_INDEPENDENT)
return ncmpi_begin_indep_data(nc->int_ncid);
else
return ncmpi_end_indep_data(nc->int_ncid);
}
#endif /* USE_PNETCDF */
/* This function only for files opened with nc_open_par or nc_create_par. */
if (!h5->parallel)
return NC_ENOPAR;
/* Find the var, and set its preference. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
if (par_access)
var->parallel_access = NC_COLLECTIVE;
else
var->parallel_access = NC_INDEPENDENT;
return NC_NOERR;
#endif /* USE_PARALLEL */
}
static int
nc4_put_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long,
const size_t *startp, const size_t *countp, const void *op)
{
NC_FILE_INFO_T *nc;
LOG((2, "nc4_put_vara_tc: ncid 0x%x varid %d mem_type %d mem_type_is_long %d",
ncid, varid, mem_type, mem_type_is_long));
if (!(nc = nc4_find_nc_file(ncid)))
return NC_EBADID;
#ifdef USE_PNETCDF
/* Handle files opened/created with the parallel-netcdf library. */
if (nc->pnetcdf_file)
{
MPI_Offset mpi_start[NC_MAX_DIMS], mpi_count[NC_MAX_DIMS];
int d;
/* No NC_LONGs for parallel-netcdf library! */
if (mem_type_is_long)
return NC_EINVAL;
/* We must convert the start, count, and stride arrays to
* MPI_Offset type. */
for (d = 0; d < nc->pnetcdf_ndims[varid]; d++)
{
mpi_start[d] = startp[d];
mpi_count[d] = countp[d];
}
if (nc->pnetcdf_access_mode == NC_INDEPENDENT)
{
switch(mem_type)
{
case NC_BYTE:
return ncmpi_put_vara_schar(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_UBYTE:
return ncmpi_put_vara_uchar(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_CHAR:
return ncmpi_put_vara_text(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_SHORT:
return ncmpi_put_vara_short(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_INT:
return ncmpi_put_vara_int(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_FLOAT:
return ncmpi_put_vara_float(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_DOUBLE:
return ncmpi_put_vara_double(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_NAT:
default:
return NC_EBADTYPE;
}
}
else
{
switch(mem_type)
{
case NC_BYTE:
return ncmpi_put_vara_schar_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_UBYTE:
return ncmpi_put_vara_uchar_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_CHAR:
return ncmpi_put_vara_text_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_SHORT:
return ncmpi_put_vara_short_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_INT:
return ncmpi_put_vara_int_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_FLOAT:
return ncmpi_put_vara_float_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_DOUBLE:
return ncmpi_put_vara_double_all(nc->int_ncid, varid, mpi_start, mpi_count, op);
case NC_NAT:
default:
return NC_EBADTYPE;
}
}
}
#endif /* USE_PNETCDF */
/* NetCDF-3 cases handled by dispatch layer. */
assert(nc->nc4_info);
return nc4_put_vara(nc, ncid, varid, startp, countp, mem_type,
mem_type_is_long, (void *)op);
}
int
nc4_get_hdf4_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type mem_nc_type, int is_long, void *data)
{
#ifdef USE_HDF4
NC_GRP_INFO_T *grp, *g;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
int32 start32[NC_MAX_VAR_DIMS], edge32[NC_MAX_VAR_DIMS];
int retval, d;
/* 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 = nc->nc4_info;
assert(grp && h5 && var && var->name);
for (d = 0; d < var->ndims; d++)
{
start32[d] = startp[d];
edge32[d] = countp[d];
}
if (SDreaddata(var->sdsid, start32, NULL, edge32, data))
return NC_EHDFERR;
#endif /* USE_HDF4 */
return NC_NOERR;
}
/* Get an array. */
static int
nc4_get_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long,
const size_t *startp, const size_t *countp, void *ip)
{
NC_FILE_INFO_T *nc;
LOG((2, "nc4_get_vara_tc: ncid 0x%x varid %d mem_type %d mem_type_is_long %d",
ncid, varid, mem_type, mem_type_is_long));
if (!(nc = nc4_find_nc_file(ncid)))
return NC_EBADID;
#ifdef USE_PNETCDF
/* Handle files opened/created with the parallel-netcdf library. */
if (nc->pnetcdf_file)
{
MPI_Offset mpi_start[NC_MAX_VAR_DIMS], mpi_count[NC_MAX_VAR_DIMS];
int d;
/* No NC_LONGs for parallel-netcdf library! */
if (mem_type_is_long)
return NC_EINVAL;
/* We must convert the start, count, and stride arrays to
* MPI_Offset type. */
for (d = 0; d < nc->pnetcdf_ndims[varid]; d++)
{
mpi_start[d] = startp[d];
mpi_count[d] = countp[d];
}
if (nc->pnetcdf_access_mode == NC_INDEPENDENT)
{
switch(mem_type)
{
case NC_BYTE:
return ncmpi_get_vara_schar(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_UBYTE:
return ncmpi_get_vara_uchar(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_CHAR:
return ncmpi_get_vara_text(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_SHORT:
return ncmpi_get_vara_short(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_INT:
return ncmpi_get_vara_int(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_FLOAT:
return ncmpi_get_vara_float(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_DOUBLE:
return ncmpi_get_vara_double(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_NAT:
default:
return NC_EBADTYPE;
}
}
else
{
switch(mem_type)
{
case NC_BYTE:
return ncmpi_get_vara_schar_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_UBYTE:
return ncmpi_get_vara_uchar_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_CHAR:
return ncmpi_get_vara_text_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_SHORT:
return ncmpi_get_vara_short_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_INT:
return ncmpi_get_vara_int_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_FLOAT:
return ncmpi_get_vara_float_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_DOUBLE:
return ncmpi_get_vara_double_all(nc->int_ncid, varid, mpi_start, mpi_count, ip);
case NC_NAT:
default:
return NC_EBADTYPE;
}
}
}
#endif /* USE_PNETCDF */
/* Handle netCDF-3 cases. */
assert(nc->nc4_info);
/* Handle HDF4 cases. */
if (nc->nc4_info->hdf4)
return nc4_get_hdf4_vara(nc, ncid, varid, startp, countp, mem_type,
mem_type_is_long, (void *)ip);
/* Handle HDF5 cases. */
return nc4_get_vara(nc, ncid, varid, startp, countp, mem_type,
mem_type_is_long, (void *)ip);
}
int
NC4_put_vara(int ncid, int varid, const size_t *startp,
const size_t *countp, const void *op, int memtype)
{
return nc4_put_vara_tc(ncid, varid, memtype, 0, startp, countp, op);
}
/* Read an array of values. */
int
NC4_get_vara(int ncid, int varid, const size_t *startp,
const size_t *countp, void *ip, int memtype)
{
return nc4_get_vara_tc(ncid, varid, memtype, 0, startp, countp, ip);
}
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