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Re-implement the nc_get/put_vars operations for netcdf-4 using the corresponding HDF5 operations. #1001

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merged 4 commits into from
Jun 8, 2018
Merged

Re-implement the nc_get/put_vars operations for netcdf-4 using the corresponding HDF5 operations. #1001

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ee509ff
Re-Implement the nc_get/put_vars operations for netcdf-4 using the
DennisHeimbigner May 22, 2018
2f1daaa
Merge branch 'master' into vars.dmh
DennisHeimbigner May 30, 2018
df4942d
Merge branch 'master' into vars.dmh
WardF Jun 8, 2018
1d789d9
Additional reconciliation
WardF Jun 8, 2018
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1 change: 1 addition & 0 deletions RELEASE_NOTES.md
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Expand Up @@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release

## 4.7.0 - TBD

* [Enhancement] Improved the performance of the nc_get/put_vars operations by using the equivalent slab capabilities of hdf5. Result is a significant speedup of these operations. See [GitHub #1001](https://github.com/Unidata/netcdf-c/pull/1001) for more information.
* [Enhancement] Expanded the capabilities of `NC_INMEMORY` to support writing and accessing the final modified memory. See [GitHub #879](https://github.com/Unidata/netcdf-c/pull/879) for more information.
* [Enhancement] Made CDF5 support enabled by default. See [Github #931](https://github.com/Unidata/netcdf-c/issues/931) for more information.
* [Bug Fix] Corrected a number of memory issues identified in `ncgen`. See [GitHub #558 for more information](https://github.com/Unidata/netcdf-c/pull/558).
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10 changes: 10 additions & 0 deletions include/nc4dispatch.h
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Expand Up @@ -147,6 +147,16 @@ NC4_get_vara(int ncid, int varid,
const size_t *start, const size_t *count,
void *value, nc_type);

extern int
NC4_put_vars(int ncid, int varid,
const size_t *start, const size_t *count, const ptrdiff_t* stride,
const void *value, nc_type);

extern int
NC4_get_vars(int ncid, int varid,
const size_t *start, const size_t *count, const ptrdiff_t* stride,
void *value, nc_type);

/* End _var */

/* netCDF4 API only */
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15 changes: 11 additions & 4 deletions include/nc4internal.h
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Expand Up @@ -105,7 +105,7 @@ typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP} NC_SORT;
#define HDF5_DIMSCALE_NAME_ATT_NAME "NAME"

/** This is the number of netCDF atomic types. */
#define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE + 1)
#define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE + 1)

/* Boolean type, to make the code easier to read */
typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
Expand Down Expand Up @@ -351,17 +351,24 @@ int nc4_get_typelen_mem(NC_HDF5_FILE_INFO_T *h5, nc_type xtype, size_t *len);
int nc4_convert_type(const void *src, void *dest,
const nc_type src_type, const nc_type dest_type,
const size_t len, int *range_error,
const void *fill_value, int strict_nc3);
const void *fill_value, int strict_nc3, int src_long,
int dest_long);

/* These functions do HDF5 things. */
int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
int rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
int delete_existing_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim);
int nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset);
int nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type xtype, void *op);
const size_t *countp, nc_type xtype, int is_long, void *op);
int nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type xtype, void *op);
const size_t *countp, nc_type xtype, int is_long, void *op);
int nc4_put_vars(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
nc_type xtype, int is_long, void *op);
int nc4_get_vars(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
nc_type xtype, int is_long, void *op);
int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
int nc4_rec_detect_need_to_preserve_dimids(NC_GRP_INFO_T *grp, nc_bool_t *bad_coord_orderp);
int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order);
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2 changes: 1 addition & 1 deletion libhdf4/hdf4var.c
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Expand Up @@ -96,7 +96,7 @@ NC_HDF4_get_vara(int ncid, int varid, const size_t *startp,
if (var->type_info->hdr.id != memtype)
{
if ((retval = nc4_convert_type(data, ip, var->type_info->hdr.id, memtype, nelem,
&range_error, NULL, 0)))
&range_error, NULL, 0, 0, 0)))
return retval;
free(data);
if (range_error)
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2 changes: 1 addition & 1 deletion libhdf5/hdf5attr.c
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Expand Up @@ -581,7 +581,7 @@ NC4_put_att(int ncid, int varid, const char *name, nc_type file_type,
/* Data types are like religions, in that one can convert. */
if ((retval = nc4_convert_type(data, att->data, mem_type, file_type,
len, &range_error, NULL,
(h5->cmode & NC_CLASSIC_MODEL))))
(h5->cmode & NC_CLASSIC_MODEL), 0, 0)))
BAIL(retval);
}
}
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