source: XIOS/dev/branch_openmp/extern/src_netcdf4/nc4internal.h @ 1501

/** \file
  This header file contains the definitions of structs used to hold
  netCDF file metadata in memory.

  Copyright 2005-2011 University Corporation for Atmospheric
  Research/Unidata.
*/

#ifndef _NC4INTERNAL_
#define _NC4INTERNAL_

#include <config.h>
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <stdarg.h>
#include <string.h>
#include <hdf5.h>
#include <ncdimscale.h>
#include <nc_logging.h>

#ifdef USE_PARALLEL
#include <netcdf_par.h>
#else
#define MPI_Info int
#define MPI_Comm int
#include <netcdf.h>
#endif /* USE_PARALLEL */
#include <netcdf_f.h>

#ifdef USE_HDF4
#include <mfhdf.h>
#endif

#define FILE_ID_MASK (0xffff0000)
#define GRP_ID_MASK (0x0000ffff)
#define ID_SHIFT (16)

typedef enum {GET, PUT} NC_PG_T;
typedef enum {VAR, DIM, ATT} NC_OBJ_T;

#define NC_MAX_HDF5_NAME (NC_MAX_NAME + 10)
#define NC_V2_ERR (-1)

/* The name of the root group. */
#define NC_GROUP_NAME "/"

#define MEGABYTE 1048576

/*
 * limits of the external representation
 */
#define X_SCHAR_MIN     (-128)
#define X_SCHAR_MAX     127
#define X_UCHAR_MAX     255U
#define X_SHORT_MIN     (-32768)
#define X_SHRT_MIN      X_SHORT_MIN     /* alias compatible with limits.h */
#define X_SHORT_MAX     32767
#define X_SHRT_MAX      X_SHORT_MAX     /* alias compatible with limits.h */
#define X_USHORT_MAX    65535U
#define X_USHRT_MAX     X_USHORT_MAX    /* alias compatible with limits.h */
#define X_INT_MIN       (-2147483647-1)
#define X_INT_MAX       2147483647
#define X_LONG_MIN      X_INT_MIN
#define X_LONG_MAX      X_INT_MAX
#define X_UINT_MAX      4294967295U
#ifdef WIN32 /* Windows, of course, has to be a *little* different. */
#define X_FLOAT_MAX     3.402823466e+38f
#else
#define X_FLOAT_MAX     3.40282347e+38f
#endif /* WIN32 */
#define X_FLOAT_MIN     (-X_FLOAT_MAX)
#define X_DOUBLE_MAX    1.7976931348623157e+308 
#define X_DOUBLE_MIN    (-X_DOUBLE_MAX)

/* These have to do with creating chuncked datasets in HDF5. */
#define NC_HDF5_UNLIMITED_DIMSIZE (0)
#define NC_HDF5_CHUNKSIZE_FACTOR (10)
#define NC_HDF5_MIN_CHUNK_SIZE (2)

#define NC_EMPTY_SCALE "NC_EMPTY_SCALE"

/* This is an attribute I had to add to handle multidimensional
 * coordinate variables. */
#define COORDINATES "_Netcdf4Coordinates"
#define COORDINATES_LEN (NC_MAX_NAME * 5)

/* This is used when the user defines a non-coordinate variable with
 * same name as a dimension. */
#define NON_COORD_PREPEND "_nc4_non_coord_"

/* An attribute in the HDF5 root group of this name means that the
 * file must follow strict netCDF classic format rules. */
#define NC3_STRICT_ATT_NAME "_nc3_strict"

/* If this attribute is present on a dimscale variable, use the value
 * as the netCDF dimid. */
#define NC_DIMID_ATT_NAME "_Netcdf4Dimid"

/* This is a struct to handle the dim metadata. */
typedef struct NC_DIM_INFO
{
   char *name;
   size_t len;
   int dimid;
   int unlimited;
   int extended;
   struct NC_DIM_INFO *next;
   struct NC_DIM_INFO *prev;
   hid_t hdf_dimscaleid;
   char *old_name; /* only used to rename dim */
   int dirty;
   unsigned char coord_var_in_grp;
   struct NC_VAR_INFO *coord_var; /* The coord var, if it exists. */
   int too_long; /* True if len it too big to fit in local size_t. */
} NC_DIM_INFO_T;

typedef struct NC_ATT_INFO
{
   int len;
   char *name;
   struct NC_ATT_INFO *next;
   struct NC_ATT_INFO *prev;
   int dirty;
   int created;
   nc_type xtype;
   hid_t native_typeid;
   int attnum;
   void *data;
   nc_vlen_t *vldata; /* only used for vlen */
   char **stdata; /* only for string type. */
   int class;
} NC_ATT_INFO_T;

/* This is a struct to handle the var metadata. */
typedef struct NC_VAR_INFO
{
   char *name;
   char *hdf5_name; /* used if different from name */
   int ndims;
   int *dimids;
   NC_DIM_INFO_T **dim;
   int varid;
   int natts;
   struct NC_VAR_INFO *next;
   struct NC_VAR_INFO *prev;
   int dirty;
   int created;
   int written_to;
   int *dimscale_attached;
   struct NC_TYPE_INFO *type_info;
   nc_type xtype;
   hid_t hdf_datasetid;
   NC_ATT_INFO_T *att;
   int no_fill;
   void *fill_value;
   size_t *chunksizes;
   int contiguous;
   int parallel_access;
   int dimscale;
   HDF5_OBJID_T *dimscale_hdf5_objids;
   int deflate;
   int deflate_level;
   int shuffle;
   int fletcher32;
   int options_mask;
   int pixels_per_block;
   size_t chunk_cache_size, chunk_cache_nelems;
   float chunk_cache_preemption;
   /* Stuff below is for hdf4 files. */
   int sdsid;
   int hdf4_data_type;
   /* Stuff below for diskless data files. */
   void *diskless_data;
} NC_VAR_INFO_T;

typedef struct NC_FIELD_INFO
{
   struct NC_FIELD_INFO *next;
   struct NC_FIELD_INFO *prev;
   nc_type nctype;
   hid_t hdf_typeid;
   hid_t native_typeid;
   size_t offset;
   char *name;
   int fieldid;
   int ndims;
   int *dim_size;
} NC_FIELD_INFO_T;

typedef struct NC_ENUM_MEMBER_INFO
{
   struct NC_ENUM_MEMBER_INFO *next;
   struct NC_ENUM_MEMBER_INFO *prev;
   char *name;
   void *value;
} NC_ENUM_MEMBER_INFO_T;

typedef struct NC_TYPE_INFO
{
   struct NC_TYPE_INFO *next;
   struct NC_TYPE_INFO *prev;
   nc_type nc_typeid;
   hid_t hdf_typeid;
   hid_t native_typeid;
   size_t size;
   int committed; /* What the pig is, but the hen isn't, at breakfast. */
   char *name;
   int class; /* NC_VLEN, NC_COMPOUND, NC_OPAQUE, or NC_ENUM */
   int num_enum_members;
   NC_ENUM_MEMBER_INFO_T *enum_member;
   NC_FIELD_INFO_T *field; /* Used for compound types. */
   int num_fields;
   nc_type base_nc_type; /* for VLEN and ENUM only */
   hid_t base_hdf_typeid; /* for VLEN only */
   int close_hdf_typeid; /* True when hdf_typeid must be H5Tclosed. */
   int endianness;
} NC_TYPE_INFO_T;

/* This holds information for one group. Groups reproduce with
 * parthenogenesis. */
typedef struct NC_GRP_INFO
{
   int nc_grpid;
   struct NC_GRP_INFO *parent;
   struct NC_GRP_INFO *children;
   struct NC_GRP_INFO *next; /* points to siblings */
   struct NC_GRP_INFO *prev; /* points to siblings */
   NC_VAR_INFO_T *var;
   NC_DIM_INFO_T *dim;
   NC_ATT_INFO_T *att;
   int nvars;
   int ndims;
   int natts;
   struct NC_FILE_INFO *file;
   char *name;
   hid_t hdf_grpid;
   NC_TYPE_INFO_T *type;
} NC_GRP_INFO_T;

/* These constants apply to the cmode parameter in the
 * HDF5_FILE_INFO_T defined below. */
#define NC_CREAT 2      /* in create phase, cleared by ncendef */
#define NC_INDEF 8      /* in define mode, cleared by ncendef */
#define NC_NSYNC 0x10   /* synchronise numrecs on change */
#define NC_HSYNC 0x20   /* synchronise whole header on change */
#define NC_NDIRTY 0x40  /* numrecs has changed */
#define NC_HDIRTY 0x80  /* header info has changed */

/* This is the metadata we need to keep track of for each
   netcdf-4/HDF5 file. */
typedef struct 
{
   hid_t hdfid;
   int flags;
   int cmode;
   int nvars;
   int ndims;
   int natts;
   int parallel;  /* true if file is open for parallel access */
   int redef;
   char *path;
   int fill_mode;
   int no_write; /* true if nc_open has mode NC_NOWRITE. */
   NC_GRP_INFO_T *root_grp;
   short next_nc_grpid;
   NC_TYPE_INFO_T *type;
   int next_typeid;
   int next_dimid;
   int ignore_creationorder;
   int hdf4;
   int sdid;
} NC_HDF5_FILE_INFO_T;

/* In the nc_file array there will be one entry for each open file.*/

   /* There's an external ncid (ext_ncid) and an internal ncid
    * (int_ncid). The ext_ncid is the ncid returned to the user. If
    * the user has opened or created a netcdf-4 file, then the
    * ext_ncid is the same as the int_ncid. If he has opened or
    * created a netcdf-3 file ext_ncid (which the user sees) is
    * different from the int_ncid, which is the ncid returned by the
    * netcdf-3 layer, which insists on inventing its own ncids,
    * regardless of what is already in use due to previously opened
    * netcdf-4 files. The ext_ncid contains the ncid for the root
    * group (i.e. group zero). */

/* Warning: fields from BEGIN COMMON to END COMMON must be same for:
        1. NCcommon (include/ncdispatch.h)
        2. NC (libsrc/nc.h)
        3. NC_FILE_INFO (libsrc4/nc4internal.h)
        4. whatever libdiskless uses
*/
typedef struct NC_FILE_INFO
{
/*BEGIN COMMON*/
   int ext_ncid;
   int int_ncid;
   struct NC_Dispatch* dispatch;        
   void* dispatchdata;
   char* path;
   int substrate;
/*END COMMON*/

#ifdef USE_PNETCDF
   /* pnetcdf_file will be true if the file is created/opened with the
    * parallel-netcdf library. pnetcdf_access_mode keeps track of
    * whether independpent or collective mode is
    * desired. pnetcdf_ndims keeps track of how many dims each var
    * has, which I need to know to convert start, count, and stride
    * arrays from size_t to MPI_Offset. (I can't use an inq function
    * to find out the number of dims, because these are collective in
    * pnetcdf.) */
   int pnetcdf_file;
   int pnetcdf_access_mode;
   int pnetcdf_ndims[NC_MAX_VARS];
#endif /* USE_PNETCDF */

   /* The nc4_info pointer will remain NULL for netcdf3 files,
    * otherwise it points to information about the netcdf-4 file. */
   NC_HDF5_FILE_INFO_T *nc4_info;
} NC_FILE_INFO_T;

/* These functions only use the netcdf API calls, so they will work on
   both new format and old format files. */
/*int copy_dataset(int ncid_in, int ncid_out);*/


/* These functions convert beteen netcdf and HDF5 types. */
int nc4_get_typelen_mem(NC_HDF5_FILE_INFO_T *h5, nc_type xtype, 
                        int is_long, 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, int src_long,
                     int dest_long);

/* These functions do HDF5 things. */
int nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset);
int pg_var(NC_PG_T pg, NC_FILE_INFO_T *nc, int ncid, int varid, nc_type xtype, int is_long, 
           void *ip);
int nc4_pg_var1(NC_PG_T pg, NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *indexp, 
                nc_type xtype, int is_long, void *ip);
int nc4_put_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, 
                 const size_t *countp, nc_type xtype, int is_long, void *op);
int nc4_get_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, 
                 const size_t *countp, nc_type xtype, int is_long, void *op);
int nc4_pg_varm(NC_PG_T pg, NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, 
                const size_t *countp, const ptrdiff_t *stridep,
                const ptrdiff_t *imapp, nc_type xtype, int is_long, void *op);
int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
int nc4_rec_write_metadata(NC_GRP_INFO_T *grp);
int nc4_rec_write_types(NC_GRP_INFO_T *grp);
int nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5);
int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
int nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T * var);

/* The following functions manipulate the in-memory linked list of
   metadata, without using HDF calls. */
int nc4_find_nc_grp_h5(int ncid, NC_FILE_INFO_T **nc, NC_GRP_INFO_T **grp, 
                       NC_HDF5_FILE_INFO_T **h5);
int nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_HDF5_FILE_INFO_T **h5);
int nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp);
NC_GRP_INFO_T *nc4_find_nc_grp(int ncid);
NC_GRP_INFO_T *nc4_rec_find_grp(NC_GRP_INFO_T *start_grp, int target_nc_grpid);
NC_FILE_INFO_T *nc4_find_nc_file(int ncid);
int nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim, NC_GRP_INFO_T **dim_grp);
int nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len);
int nc4_find_type(NC_HDF5_FILE_INFO_T *h5, int typeid, NC_TYPE_INFO_T **type);
NC_TYPE_INFO_T *nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, hid_t target_nc_typeid);
NC_TYPE_INFO_T *nc4_rec_find_hdf_type(NC_GRP_INFO_T *start_grp, hid_t target_hdf_typeid);
NC_TYPE_INFO_T *nc4_rec_find_named_type(NC_GRP_INFO_T *start_grp, char *name);
NC_TYPE_INFO_T *nc4_rec_find_equal_type(NC_GRP_INFO_T *start_grp, int ncid1, NC_TYPE_INFO_T *type);
int nc4_find_nc_att(int ncid, int varid, const char *name, int attnum,
                    NC_ATT_INFO_T **att);
int nc4_find_g_var_nc(NC_FILE_INFO_T *nc, int ncid, int varid, 
                      NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var);
int nc4_find_grp_att(NC_GRP_INFO_T *grp, int varid, const char *name, int attnum,
                     NC_ATT_INFO_T **att);
int nc4_get_hdf_typeid(NC_HDF5_FILE_INFO_T *h5, nc_type xtype, 
                       hid_t *hdf_typeid, int endianness);
/*int var_info_nc(NC_PG_T pg, hid_t dataset, NC_VAR_INFO_T *var_info);*/

/* These list functions add and delete vars, atts, and files. */
int nc4_file_list_add(NC_FILE_INFO_T**, struct NC_Dispatch*);
void nc4_file_list_free(void);

int nc4_nc4f_list_add(NC_FILE_INFO_T *nc, const char *path, int mode);
int nc4_var_list_add(NC_VAR_INFO_T **list, NC_VAR_INFO_T **var);
int nc4_dim_list_add(NC_DIM_INFO_T **list);
int nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim);
int nc4_att_list_add(NC_ATT_INFO_T **list);
int nc4_type_list_add(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T **new_type);
int nc4_field_list_add(NC_FIELD_INFO_T **list, int fieldid, const char *name,
                       size_t offset, hid_t field_hdf_typeid, hid_t native_typeid, 
                       nc_type xtype, int ndims, const int *dim_sizesp);
void nc4_file_list_del(NC_FILE_INFO_T *nc);
int nc4_att_list_del(NC_ATT_INFO_T **list, NC_ATT_INFO_T *att);
int nc4_grp_list_add(NC_GRP_INFO_T **list, int new_nc_grpid, NC_GRP_INFO_T *parent_grp, 
                     NC_FILE_INFO_T *nc, char *name, NC_GRP_INFO_T **grp);
int nc4_rec_grp_del(NC_GRP_INFO_T **list, NC_GRP_INFO_T *grp);
int nc4_enum_member_add(NC_ENUM_MEMBER_INFO_T **list, size_t size,
                        const char *name, const void *value);

int NC_check_name(const char *name);

/* Check and normalize names. */
int nc4_check_name(const char *name, char *norm_name);
int nc4_normalize_name(const char *name, char *norm_name);

/* Check for name collisions. */
int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *norm_name);

/* Insert and read one element into an already allocated vlen array
 * element (this is for F77). */
/*int nc_put_vlen_element(int ncid, int typeid, void *vlen_element, size_t len, const void *data);
  int nc_get_vlen_element(int ncid, int typeid, const void *vlen_element, size_t *len, void *data);*/

/* This is only included if --enable-logging is used for configure; it
   prints info about the metadata to stderr. */
#ifdef LOGGING
int log_metadata_nc(NC_FILE_INFO_T *nc);
#endif

#endif /* _NETCDF4_ */