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Fix 1D variables with an unlimited dimension taking DEFAULT_CHUNK_SIZE (4MiB), by default, in netCDF-4 files

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Russ Rew 2015-09-29 13:58:51 -06:00
parent 8515ece987
commit d3d442537d
1 changed files with 18 additions and 4 deletions
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22
libsrc4/nc4var.c
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@ -266,8 +266,22 @@ nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
var->chunksizes[d] = 1; /* overwritten below, if all dims are unlimited */
}
}
if (var->ndims > 0 && var->ndims == num_unlim) { /* all dims 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 */
#define DEFAULT_1D_UNLIM_SIZE (4096) /* TODO: make build-time parameter? */
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->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++)
{
@ -878,7 +892,7 @@ nc_def_var_extra(int ncid, int varid, int *shuffle, int *deflate,
var->contiguous = NC_FALSE;
}
/* Fltcher32 checksum error protection? */
/* Fletcher32 checksum error protection? */
if (fletcher32)
{
var->fletcher32 = *fletcher32;
@ -995,7 +1009,7 @@ NC4_def_var_fletcher32(int ncid, int varid, int fletcher32)
and before nc_enddef.
Chunking is required in any dataset with one or more unlimited
dimension in HDF5, or any dataset using a filter.
dimensions 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.