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8b9253fef2
re: https://github.com/Unidata/netcdf-c/issues/541 re: https://github.com/Unidata/netcdf-c/issues/1208 re: https://github.com/Unidata/netcdf-c/issues/2078 re: https://github.com/Unidata/netcdf-c/issues/2041 re: https://github.com/Unidata/netcdf-c/issues/2143 For a long time, there have been known problems with the management of complex types containing VLENs. This also involves the string type because it is stored as a VLEN of chars. This PR (mostly) fixes this problem. But note that it adds new functions to netcdf.h (see below) and this may require bumping the .so number. These new functions can be removed, if desired, in favor of functions in netcdf_aux.h, but netcdf.h seems the better place for them because they are intended as alternatives to the nc_free_vlen and nc_free_string functions already in netcdf.h. The term complex type refers to any type that directly or transitively references a VLEN type. So an array of VLENS, a compound with a VLEN field, and so on. In order to properly handle instances of these complex types, it is necessary to have function that can recursively walk instances of such types to perform various actions on them. The term "deep" is also used to mean recursive. At the moment, the two operations needed by the netcdf library are: * free'ing an instance of the complex type * copying an instance of the complex type. The current library does only shallow free and shallow copy of complex types. This means that only the top level is properly free'd or copied, but deep internal blocks in the instance are not touched. Note that the term "vector" will be used to mean a contiguous (in memory) sequence of instances of some type. Given an array with, say, dimensions 2 X 3 X 4, this will be stored in memory as a vector of length 2*3*4=24 instances. The use cases are primarily these. ## nc_get_vars Suppose one is reading a vector of instances using nc_get_vars (or nc_get_vara or nc_get_var, etc.). These functions will return the vector in the top-level memory provided. All interior blocks (form nested VLEN or strings) will have been dynamically allocated. After using this vector of instances, it is necessary to free (aka reclaim) the dynamically allocated memory, otherwise a memory leak occurs. So, the recursive reclaim function is used to walk the returned instance vector and do a deep reclaim of the data. Currently functions are defined in netcdf.h that are supposed to handle this: nc_free_vlen(), nc_free_vlens(), and nc_free_string(). Unfortunately, these functions only do a shallow free, so deeply nested instances are not properly handled by them. Note that internally, the provided data is immediately written so there is no need to copy it. But the caller may need to reclaim the data it passed into the function. ## nc_put_att Suppose one is writing a vector of instances as the data of an attribute using, say, nc_put_att. Internally, the incoming attribute data must be copied and stored so that changes/reclamation of the input data will not affect the attribute. Again, the code inside the netcdf library does only shallow copying rather than deep copy. As a result, one sees effects such as described in Github Issue https://github.com/Unidata/netcdf-c/issues/2143. Also, after defining the attribute, it may be necessary for the user to free the data that was provided as input to nc_put_att(). ## nc_get_att Suppose one is reading a vector of instances as the data of an attribute using, say, nc_get_att. Internally, the existing attribute data must be copied and returned to the caller, and the caller is responsible for reclaiming the returned data. Again, the code inside the netcdf library does only shallow copying rather than deep copy. So this can lead to memory leaks and errors because the deep data is shared between the library and the user. # Solution The solution is to build properly recursive reclaim and copy functions and use those as needed. These recursive functions are defined in libdispatch/dinstance.c and their signatures are defined in include/netcdf.h. For back compatibility, corresponding "ncaux_XXX" functions are defined in include/netcdf_aux.h. ```` int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy); int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp); ```` There are two variants. The first two, nc_reclaim_data() and nc_copy_data(), assume the top-level vector is managed by the caller. For reclaim, this is so the user can use, for example, a statically allocated vector. For copy, it assumes the user provides the space into which the copy is stored. The second two, nc_reclaim_data_all() and nc_copy_data_all(), allows the functions to manage the top-level. So for nc_reclaim_data_all, the top level is assumed to be dynamically allocated and will be free'd by nc_reclaim_data_all(). The nc_copy_data_all() function will allocate the top level and return a pointer to it to the user. The user can later pass that pointer to nc_reclaim_data_all() to reclaim the instance(s). # Internal Changes The netcdf-c library internals are changed to use the proper reclaim and copy functions. It turns out that the places where these functions are needed is quite pervasive in the netcdf-c library code. Using these functions also allows some simplification of the code since the stdata and vldata fields of NC_ATT_INFO are no longer needed. Currently this is commented out using the SEPDATA \#define macro. When any bugs are largely fixed, all this code will be removed. # Known Bugs 1. There is still one known failure that has not been solved. All the failures revolve around some variant of this .cdl file. The proximate cause of failure is the use of a VLEN FillValue. ```` netcdf x { types: float(*) row_of_floats ; dimensions: m = 5 ; variables: row_of_floats ragged_array(m) ; row_of_floats ragged_array:_FillValue = {-999} ; data: ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32}, {40, 41}, _ ; } ```` When a solution is found, I will either add it to this PR or post a new PR. # Related Changes * Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data. * Remove the --enable-unfixed-memory-leaks option. * Remove the NC_VLENS_NOTEST code that suppresses some vlen tests. * Document this change in docs/internal.md * Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh. * Mark types as fixed size or not (transitively) to optimize the reclaim and copy functions. # Misc. Changes * Make Doxygen process libdispatch/daux.c * Make sure the NC_ATT_INFO_T.container field is set.
210 lines
6.0 KiB
C
210 lines
6.0 KiB
C
/*! \file
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Functions for VLEN Types
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Copyright 2018 University Corporation for Atmospheric
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Research/Unidata. See \ref copyright file for more info. */
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#include "ncdispatch.h"
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/** \name Variable Length Array Types
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Functions to create and learn about VLEN types. */
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/*! \{ */ /* All these functions are part of this named group... */
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/**
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\ingroup user_types
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Free memory in a VLEN object.
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When you read VLEN type the library will actually allocate the storage
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space for the data. This storage space must be freed, so pass the
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pointer back to this function, when you're done with the data, and it
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will free the vlen memory.
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The function nc_free_vlens() is more useful than this function,
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because it can free an array of VLEN objects.
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WARNING: this code is incorrect because it will only
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work if the basetype of the vlen is
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- atomic (excluding string basetype)
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- + enum
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- + opaque
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The reason is that to operate properly, it needs to recurse when
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the basetype is a complex object such as another vlen or compound.
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This function is deprecated in favor of the function "nc_reclaim_data".
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See include/netcdf.h.
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\param vl pointer to the vlen object.
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\returns ::NC_NOERR No error.
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*/
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int
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nc_free_vlen(nc_vlen_t *vl)
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{
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free(vl->p);
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return NC_NOERR;
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}
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/**
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\ingroup user_types
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Free an array of vlens given the number of elements and an array.
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When you read VLEN type the library will actually allocate the storage
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space for the data. This storage space must be freed, so pass the
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pointer back to this function, when you're done with the data, and it
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will free the vlen memory.
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WARNING: this code is incorrect because it will only
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work if the basetype of the vlen is
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- atomic
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- + enum
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- + opaque
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- excluding string basetype,
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The reason is that to operate properly, it needs to recurse when
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the basetype is a complex object such as another vlen or compound.
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This function is deprecated in favor of the function "nc_reclaim_data".
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See include/netcdf.h.
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\param len number of elements in the array.
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\param vlens pointer to the vlen object.
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\returns ::NC_NOERR No error.
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*/
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int
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nc_free_vlens(size_t len, nc_vlen_t vlens[])
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{
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int ret;
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size_t i;
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for(i = 0; i < len; i++)
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if ((ret = nc_free_vlen(&vlens[i])))
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return ret;
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return NC_NOERR;
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}
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/**
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\ingroup user_types
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Use this function to define a variable length array type.
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\param ncid \ref ncid
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\param name \ref object_name of new type.
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\param base_typeid The typeid of the base type of the VLEN. For
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example, for a VLEN of shorts, the base type is ::NC_SHORT. This can be
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a user defined type.
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\param xtypep A pointer to an nc_type variable. The typeid of the new
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VLEN type will be set here.
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\returns ::NC_NOERR No error.
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\returns ::NC_EBADID Bad \ref ncid.
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\returns ::NC_EBADTYPE Bad type id.
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\returns ::NC_ENOTNC4 Not an netCDF-4 file, or classic model enabled.
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\returns ::NC_EHDFERR An error was reported by the HDF5 layer.
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\returns ::NC_ENAMEINUSE That name is in use.
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\returns ::NC_EMAXNAME Name exceeds max length NC_MAX_NAME.
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\returns ::NC_EBADNAME Name contains illegal characters.
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\returns ::NC_EPERM Attempt to write to a read-only file.
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\returns ::NC_ENOTINDEFINE Not in define mode.
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*/
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int
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nc_def_vlen(int ncid, const char *name, nc_type base_typeid, nc_type *xtypep)
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{
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NC* ncp;
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int stat = NC_check_id(ncid,&ncp);
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if(stat != NC_NOERR) return stat;
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return ncp->dispatch->def_vlen(ncid,name,base_typeid,xtypep);
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}
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/** \ingroup user_types
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Learn about a VLEN type.
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\param ncid \ref ncid
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\param xtype The type of the VLEN to inquire about.
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\param name \ref object_name of the type. \ref ignored_if_null.
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\param datum_sizep A pointer to a size_t, this will get the size of
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one element of this vlen. \ref ignored_if_null.
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\param base_nc_typep Pointer to get the base type of the VLEN. \ref
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ignored_if_null.
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\returns ::NC_NOERR No error.
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\returns ::NC_EBADID Bad \ref ncid.
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\returns ::NC_EBADTYPE Bad type id.
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\returns ::NC_ENOTNC4 Not an netCDF-4 file, or classic model enabled.
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\returns ::NC_EHDFERR An error was reported by the HDF5 layer.
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*/
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int
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nc_inq_vlen(int ncid, nc_type xtype, char *name, size_t *datum_sizep, nc_type *base_nc_typep)
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{
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int class = 0;
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int stat = nc_inq_user_type(ncid,xtype,name,datum_sizep,base_nc_typep,NULL,&class);
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if(stat != NC_NOERR) return stat;
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if(class != NC_VLEN) stat = NC_EBADTYPE;
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return stat;
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}
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/*! \} */ /* End of named group ...*/
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/** \internal
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\ingroup user_types
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Put a VLEN element. This function writes an element of a VLEN for the
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Fortran APIs.
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\param ncid \ref ncid
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\param typeid1 Typeid of the VLEN.
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\param vlen_element Pointer to the element of the VLEN.
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\param len Length of the VLEN element.
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\param data VLEN data.
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\returns ::NC_NOERR No error.
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\returns ::NC_EBADID Bad \ref ncid.
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\returns ::NC_EBADTYPE Bad type id.
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\returns ::NC_ENOTNC4 Not an netCDF-4 file, or classic model enabled.
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\returns ::NC_EHDFERR An error was reported by the HDF5 layer.
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\returns ::NC_EPERM Attempt to write to a read-only file.
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*/
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int
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nc_put_vlen_element(int ncid, int typeid1, void *vlen_element, size_t len, const void *data)
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{
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NC* ncp;
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int stat = NC_check_id(ncid,&ncp);
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if(stat != NC_NOERR) return stat;
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return ncp->dispatch->put_vlen_element(ncid,typeid1,vlen_element,len,data);
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}
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/**
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\internal
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\ingroup user_types
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Get a VLEN element. This function reads an element of a VLEN for the
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Fortran APIs.
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\param ncid \ref ncid
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\param typeid1 Typeid of the VLEN.
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\param vlen_element Pointer to the element of the VLEN.
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\param len Length of the VLEN element.
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\param data VLEN data.
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\returns ::NC_NOERR No error.
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\returns ::NC_EBADID Bad \ref ncid.
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\returns ::NC_EBADTYPE Bad type id.
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\returns ::NC_ENOTNC4 Not an netCDF-4 file, or classic model enabled.
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\returns ::NC_EHDFERR An error was reported by the HDF5 layer.
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*/
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int
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nc_get_vlen_element(int ncid, int typeid1, const void *vlen_element,
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size_t *len, void *data)
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{
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NC *ncp;
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int stat = NC_check_id(ncid,&ncp);
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if(stat != NC_NOERR) return stat;
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return ncp->dispatch->get_vlen_element(ncid, typeid1, vlen_element,
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len, data);
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}
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