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add some code to support PIO/netCDF integration - ability to change ncid #1483

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add some code to support PIO/netCDF integration - ability to change ncid #1483

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f4d5e4e
now trying to move ncid
edhartnett Aug 22, 2019
57ff363
now able to move an ncid
edhartnett Aug 22, 2019
c18da54
merged master
edhartnett Aug 22, 2019
bec4659
changes
edhartnett Aug 30, 2019
76f91ba
merged master
edhartnett Aug 30, 2019
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1 change: 1 addition & 0 deletions include/nc.h
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,7 @@ extern int add_to_NCList(NC*);
extern void del_from_NCList(NC*);/* does not free object */
extern NC* find_in_NCList(int ext_ncid);
extern NC* find_in_NCList_by_name(const char*);
extern int move_in_NCList(NC *ncp, int new_id);
extern void free_NCList(void);/* reclaim whole list */
extern int count_NCList(void); /* return # of entries in NClist */
extern int iterate_NCList(int i,NC**); /* Walk from 0 ...; ERANGE return => stop */
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1 change: 1 addition & 0 deletions include/nc4internal.h
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Expand Up @@ -388,6 +388,7 @@ int nc4_file_list_add(int ncid, const char *path, int mode,
int nc4_file_list_get(int ncid, char **path, int *mode,
void **dispatchdata);
int nc4_file_list_del(int ncid);
int nc4_file_change_ncid(int ncid, unsigned short new_ncid_index);
int nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims,
NC_VAR_INFO_T **var);
int nc4_var_list_add2(NC_GRP_INFO_T* grp, const char* name,
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66 changes: 25 additions & 41 deletions include/netcdf.h
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Expand Up @@ -21,7 +21,7 @@ See \ref copyright file for more info.
#include <malloc.h>
#endif

/*! The nc_type type is just an int. */
/** The nc_type type is just an int. */
typedef int nc_type;

#if defined(__cplusplus)
Expand Down Expand Up @@ -78,7 +78,8 @@ extern "C" {
#define NC_FILL_STRING ((char *)"")
/**@}*/

/*! Max or min values for a type. Nothing greater/smaller can be
/**
* Max or min values for a type. Nothing greater/smaller can be
* stored in a netCDF file for their associated types. Recall that a C
* compiler may define int to be any length it wants, but a NC_INT is
* *always* a 4 byte signed int. On a platform with 64 bit ints,
Expand Down Expand Up @@ -248,25 +249,16 @@ Use this in mode flags for both nc_create() and nc_open(). */
#define NC_GLOBAL -1

/**
Maximum for classic library.

In the classic netCDF model there are maximum values for the number of
dimensions in the file (\ref NC_MAX_DIMS), the number of global or per
variable attributes (\ref NC_MAX_ATTRS), the number of variables in
the file (\ref NC_MAX_VARS), and the length of a name (\ref
NC_MAX_NAME).

These maximums are enforced by the interface, to facilitate writing
applications and utilities. However, nothing is statically allocated
to these sizes internally.

These maximums are not used for netCDF-4/HDF5 files unless they were
created with the ::NC_CLASSIC_MODEL flag.

As a rule, NC_MAX_VAR_DIMS <= NC_MAX_DIMS.

NOTE: The NC_MAX_DIMS, NC_MAX_ATTRS, and NC_MAX_VARS limits
are *not* enforced after version 4.5.0
* Maximum for classic library.
*
* In the classic netCDF model there are maximum values for the number
* of dimensions in the file (@ref NC_MAX_DIMS), the number of global
* or per variable attributes (@ref NC_MAX_ATTRS), the number of
* variables in the file (@ref NC_MAX_VARS), and the length of a name
* (@ref NC_MAX_NAME).
*
* Only NC_MAX_NAME and NC_MAX_VAR_DIMS are enforced by the library,
* since version 4.5.0.
*/
/**@{*/
#define NC_MAX_DIMS 1024 /* not enforced after 4.5.0 */
Expand All @@ -276,19 +268,20 @@ NOTE: The NC_MAX_DIMS, NC_MAX_ATTRS, and NC_MAX_VARS limits
#define NC_MAX_VAR_DIMS 1024 /**< max per variable dimensions */
/**@}*/

/** This is the max size of an SD dataset name in HDF4 (from HDF4 documentation).*/
/** This is the max size of an SD dataset name in HDF4 (from HDF4
* documentation). */
#define NC_MAX_HDF4_NAME 64

/** In HDF5 files you can set the endianness of variables with
nc_def_var_endian(). This define is used there. */
nc_def_var_endian(). This define is used to specify endianness. */
/**@{*/
#define NC_ENDIAN_NATIVE 0
#define NC_ENDIAN_LITTLE 1
#define NC_ENDIAN_BIG 2
/**@}*/

/** In HDF5 files you can set storage for each variable to be either
* contiguous or chunked, with nc_def_var_chunking(). This define is
* contiguous or chunked, with nc_def_var_chunking(). This define is
* used there. */
/**@{*/
#define NC_CHUNKED 0
Expand All @@ -297,7 +290,7 @@ NOTE: The NC_MAX_DIMS, NC_MAX_ATTRS, and NC_MAX_VARS limits

/** In HDF5 files you can set check-summing for each variable.
Currently the only checksum available is Fletcher-32, which can be set
with the function nc_def_var_fletcher32. These defines are used
with the function nc_def_var_fletcher32. These defines are used
there. */
/**@{*/
#define NC_NOCHECKSUM 0
Expand All @@ -322,14 +315,10 @@ there. */
*/
#define NC_ISSYSERR(err) ((err) > 0)

#define NC_NOERR 0 /**< No Error */
#define NC_NOERR 0 /**< No Error. */
#define NC2_ERR (-1) /**< Returned for all errors in the v2 API. */

/** Not a netcdf id.

The specified netCDF ID does not refer to an
open netCDF dataset. */
#define NC_EBADID (-33)
#define NC_EBADID (-33) /**< Not a netcdf id. */
#define NC_ENFILE (-34) /**< Too many netcdfs open */
#define NC_EEXIST (-35) /**< netcdf file exists && NC_NOCLOBBER */
#define NC_EINVAL (-36) /**< Invalid Argument */
Expand Down Expand Up @@ -358,9 +347,8 @@ larger than the corresponding dimension length will cause an error. */

/** NC_MAX_DIMS exceeded. Max number of dimensions exceeded in a
classic or 64-bit offset file, or an netCDF-4 file with
::NC_CLASSIC_MODEL on. */
#define NC_EMAXDIMS (-41) /* not enforced after 4.5.0 */

::NC_CLASSIC_MODEL on. (Not enforced after 4.5.0.) */
#define NC_EMAXDIMS (-41)
#define NC_ENAMEINUSE (-42) /**< String match to name in use */
#define NC_ENOTATT (-43) /**< Attribute not found */
#define NC_EMAXATTS (-44) /**< NC_MAX_ATTRS exceeded - not enforced after 4.5.0 */
Expand All @@ -370,13 +358,9 @@ ::NC_CLASSIC_MODEL on. */

/** NC_MAX_VARS exceeded. Max number of variables exceeded in a
classic or 64-bit offset file, or an netCDF-4 file with
::NC_CLASSIC_MODEL on. */
#define NC_EMAXVARS (-48) /* not enforced after 4.5.0 */

/** Variable not found.

The variable ID is invalid for the specified netCDF dataset. */
#define NC_ENOTVAR (-49)
::NC_CLASSIC_MODEL on. (Not enforced after 4.5.0.) */
#define NC_EMAXVARS (-48)
#define NC_ENOTVAR (-49) /**< Variable not found. */
#define NC_EGLOBAL (-50) /**< Action prohibited on NC_GLOBAL varid */
#define NC_ENOTNC (-51) /**< Not a netcdf file */
#define NC_ESTS (-52) /**< In Fortran, string too short */
Expand Down
143 changes: 74 additions & 69 deletions include/netcdf_dispatch.h
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Expand Up @@ -135,80 +135,85 @@ struct NC_Dispatch

/* Read-only dispatch layers can use these functions to return
* NC_EPERM to all attempts to modify a file. */

EXTERNL int NC_RO_create(const char *path, int cmode, size_t initialsz, int basepe,
size_t *chunksizehintp, void* parameters,
const NC_Dispatch*, int);
EXTERNL int NC_RO_redef(int ncid);
EXTERNL int NC_RO__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree,
size_t r_align);
EXTERNL int NC_RO_sync(int ncid);
EXTERNL int NC_RO_def_var_fill(int, int, int, const void *);
EXTERNL int NC_RO_rename_att(int ncid, int varid, const char *name,
const char *newname);
EXTERNL int NC_RO_del_att(int ncid, int varid, const char*);
EXTERNL int NC_RO_put_att(int ncid, int varid, const char *name, nc_type datatype,
size_t len, const void *value, nc_type);
EXTERNL int NC_RO_def_var(int ncid, const char *name,
nc_type xtype, int ndims, const int *dimidsp, int *varidp);
EXTERNL int NC_RO_rename_var(int ncid, int varid, const char *name);
EXTERNL int NC_RO_put_vara(int ncid, int varid,
const size_t *start, const size_t *count,
const void *value, nc_type);
EXTERNL int NC_RO_def_dim(int ncid, const char *name, size_t len, int *idp);
EXTERNL int NC_RO_rename_dim(int ncid, int dimid, const char *name);
EXTERNL int NC_RO_set_fill(int ncid, int fillmode, int *old_modep);
#if defined(__cplusplus)
extern "C" {
#endif
EXTERNL int NC_RO_create(const char *path, int cmode, size_t initialsz, int basepe,
size_t *chunksizehintp, void* parameters,
const NC_Dispatch*, int);
EXTERNL int NC_RO_redef(int ncid);
EXTERNL int NC_RO__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree,
size_t r_align);
EXTERNL int NC_RO_sync(int ncid);
EXTERNL int NC_RO_def_var_fill(int, int, int, const void *);
EXTERNL int NC_RO_rename_att(int ncid, int varid, const char *name,
const char *newname);
EXTERNL int NC_RO_del_att(int ncid, int varid, const char*);
EXTERNL int NC_RO_put_att(int ncid, int varid, const char *name, nc_type datatype,
size_t len, const void *value, nc_type);
EXTERNL int NC_RO_def_var(int ncid, const char *name,
nc_type xtype, int ndims, const int *dimidsp, int *varidp);
EXTERNL int NC_RO_rename_var(int ncid, int varid, const char *name);
EXTERNL int NC_RO_put_vara(int ncid, int varid,
const size_t *start, const size_t *count,
const void *value, nc_type);
EXTERNL int NC_RO_def_dim(int ncid, const char *name, size_t len, int *idp);
EXTERNL int NC_RO_rename_dim(int ncid, int dimid, const char *name);
EXTERNL int NC_RO_set_fill(int ncid, int fillmode, int *old_modep);

/* These functions are for dispatch layers that don't implement these
* legacy functions. They return NC_ENOTNC3. */
EXTERNL int NC_NOTNC3_put_varm(int ncid, int varid, const size_t * start,
const size_t *edges, const ptrdiff_t *stride,
const ptrdiff_t *imapp, const void *value0,
nc_type memtype);
EXTERNL int NC_NOTNC3_get_varm(int ncid, int varid, const size_t *start,
const size_t *edges, const ptrdiff_t *stride,
const ptrdiff_t *imapp, void *value0, nc_type memtype);
EXTERNL int NC_NOTNC3_put_varm(int ncid, int varid, const size_t * start,
const size_t *edges, const ptrdiff_t *stride,
const ptrdiff_t *imapp, const void *value0,
nc_type memtype);
EXTERNL int NC_NOTNC3_get_varm(int ncid, int varid, const size_t *start,
const size_t *edges, const ptrdiff_t *stride,
const ptrdiff_t *imapp, void *value0, nc_type memtype);

/* These functions are for dispatch layers that don't implement the
* enhanced model. They return NC_ENOTNC4. */
EXTERNL int NC_NOTNC4_def_var_filter(int, int, unsigned int, size_t,
const unsigned int*);
EXTERNL int NC_NOTNC4_def_grp(int, const char *, int *);
EXTERNL int NC_NOTNC4_rename_grp(int, const char *);
EXTERNL int NC_NOTNC4_def_compound(int, size_t, const char *, nc_type *);
EXTERNL int NC_NOTNC4_insert_compound(int, nc_type, const char *, size_t, nc_type);
EXTERNL int NC_NOTNC4_insert_array_compound(int, nc_type, const char *, size_t,
nc_type, int, const int *);
EXTERNL int NC_NOTNC4_inq_typeid(int, const char *, nc_type *);
EXTERNL int NC_NOTNC4_inq_compound_field(int, nc_type, int, char *, size_t *,
nc_type *, int *, int *);
EXTERNL int NC_NOTNC4_inq_compound_fieldindex(int, nc_type, const char *, int *);
EXTERNL int NC_NOTNC4_def_vlen(int, const char *, nc_type base_typeid, nc_type *);
EXTERNL int NC_NOTNC4_put_vlen_element(int, int, void *, size_t, const void *);
EXTERNL int NC_NOTNC4_get_vlen_element(int, int, const void *, size_t *, void *);
EXTERNL int NC_NOTNC4_def_enum(int, nc_type, const char *, nc_type *);
EXTERNL int NC_NOTNC4_insert_enum(int, nc_type, const char *, const void *);
EXTERNL int NC_NOTNC4_inq_enum_member(int, nc_type, int, char *, void *);
EXTERNL int NC_NOTNC4_inq_enum_ident(int, nc_type, long long, char *);
EXTERNL int NC_NOTNC4_def_opaque(int, size_t, const char *, nc_type *);
EXTERNL int NC_NOTNC4_def_var_deflate(int, int, int, int, int);
EXTERNL int NC_NOTNC4_def_var_fletcher32(int, int, int);
EXTERNL int NC_NOTNC4_def_var_chunking(int, int, int, const size_t *);
EXTERNL int NC_NOTNC4_def_var_endian(int, int, int);
EXTERNL int NC_NOTNC4_set_var_chunk_cache(int, int, size_t, size_t, float);
EXTERNL int NC_NOTNC4_get_var_chunk_cache(int, int, size_t *, size_t *, float *);
EXTERNL int NC_NOTNC4_var_par_access(int, int, int);
EXTERNL int NC_NOTNC4_inq_ncid(int, const char *, int *);
EXTERNL int NC_NOTNC4_inq_grps(int, int *, int *);
EXTERNL int NC_NOTNC4_inq_grpname(int, char *);
EXTERNL int NC_NOTNC4_inq_grpname_full(int, size_t *, char *);
EXTERNL int NC_NOTNC4_inq_grp_parent(int, int *);
EXTERNL int NC_NOTNC4_inq_grp_full_ncid(int, const char *, int *);
EXTERNL int NC_NOTNC4_inq_varids(int, int *, int *);
EXTERNL int NC_NOTNC4_inq_dimids(int, int *, int *, int);
EXTERNL int NC_NOTNC4_inq_typeids(int, int *, int *);
EXTERNL int NC_NOTNC4_inq_user_type(int, nc_type, char *, size_t *,
nc_type *, size_t *, int *);
EXTERNL int NC_NOTNC4_inq_typeid(int, const char *, nc_type *);
EXTERNL int NC_NOTNC4_def_var_filter(int, int, unsigned int, size_t,
const unsigned int*);
EXTERNL int NC_NOTNC4_def_grp(int, const char *, int *);
EXTERNL int NC_NOTNC4_rename_grp(int, const char *);
EXTERNL int NC_NOTNC4_def_compound(int, size_t, const char *, nc_type *);
EXTERNL int NC_NOTNC4_insert_compound(int, nc_type, const char *, size_t, nc_type);
EXTERNL int NC_NOTNC4_insert_array_compound(int, nc_type, const char *, size_t,
nc_type, int, const int *);
EXTERNL int NC_NOTNC4_inq_typeid(int, const char *, nc_type *);
EXTERNL int NC_NOTNC4_inq_compound_field(int, nc_type, int, char *, size_t *,
nc_type *, int *, int *);
EXTERNL int NC_NOTNC4_inq_compound_fieldindex(int, nc_type, const char *, int *);
EXTERNL int NC_NOTNC4_def_vlen(int, const char *, nc_type base_typeid, nc_type *);
EXTERNL int NC_NOTNC4_put_vlen_element(int, int, void *, size_t, const void *);
EXTERNL int NC_NOTNC4_get_vlen_element(int, int, const void *, size_t *, void *);
EXTERNL int NC_NOTNC4_def_enum(int, nc_type, const char *, nc_type *);
EXTERNL int NC_NOTNC4_insert_enum(int, nc_type, const char *, const void *);
EXTERNL int NC_NOTNC4_inq_enum_member(int, nc_type, int, char *, void *);
EXTERNL int NC_NOTNC4_inq_enum_ident(int, nc_type, long long, char *);
EXTERNL int NC_NOTNC4_def_opaque(int, size_t, const char *, nc_type *);
EXTERNL int NC_NOTNC4_def_var_deflate(int, int, int, int, int);
EXTERNL int NC_NOTNC4_def_var_fletcher32(int, int, int);
EXTERNL int NC_NOTNC4_def_var_chunking(int, int, int, const size_t *);
EXTERNL int NC_NOTNC4_def_var_endian(int, int, int);
EXTERNL int NC_NOTNC4_set_var_chunk_cache(int, int, size_t, size_t, float);
EXTERNL int NC_NOTNC4_get_var_chunk_cache(int, int, size_t *, size_t *, float *);
EXTERNL int NC_NOTNC4_var_par_access(int, int, int);
EXTERNL int NC_NOTNC4_inq_ncid(int, const char *, int *);
EXTERNL int NC_NOTNC4_inq_grps(int, int *, int *);
EXTERNL int NC_NOTNC4_inq_grpname(int, char *);
EXTERNL int NC_NOTNC4_inq_grpname_full(int, size_t *, char *);
EXTERNL int NC_NOTNC4_inq_grp_parent(int, int *);
EXTERNL int NC_NOTNC4_inq_grp_full_ncid(int, const char *, int *);
EXTERNL int NC_NOTNC4_inq_varids(int, int *, int *);
EXTERNL int NC_NOTNC4_inq_dimids(int, int *, int *, int);
EXTERNL int NC_NOTNC4_inq_typeids(int, int *, int *);
EXTERNL int NC_NOTNC4_inq_user_type(int, nc_type, char *, size_t *,
nc_type *, size_t *, int *);
EXTERNL int NC_NOTNC4_inq_typeid(int, const char *, nc_type *);
#if defined(__cplusplus)
}
#endif

#endif /* NETCDF_DISPATCH_H */
29 changes: 29 additions & 0 deletions libdispatch/nclistmgr.c
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Expand Up @@ -100,6 +100,35 @@ add_to_NCList(NC* ncp)
return NC_NOERR;
}

/**
* Move an NC in the nc_filelist. This is required by PIO.
*
* @param ncp Pointer to already-allocated and initialized NC struct.
* @param new_id New index in the nc_filelist for this file.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL Invalid input.
* @author Ed Hartnett
*/
int
move_in_NCList(NC *ncp, int new_id)
{
/* If no files in list, error. */
if (!nc_filelist)
return NC_EINVAL;

/* If new slot is already taken, error. */
if (nc_filelist[new_id])
return NC_EINVAL;

/* Move the file. */
nc_filelist[ncp->ext_ncid >> ID_SHIFT] = NULL;
nc_filelist[new_id] = ncp;
ncp->ext_ncid = (new_id << ID_SHIFT);

return NC_NOERR;
}

/**
* Delete an NC struct from the list. This happens when the file is
* closed. Relies on all memory in the NC being deallocated after this
Expand Down
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