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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.
98 lines
3.6 KiB
C
98 lines
3.6 KiB
C
/*********************************************************************
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* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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* $Id$
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* $Header$
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*********************************************************************/
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/*
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* In order to use any of the netcdf_XXX.h files, it is necessary
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* to include netcdf.h followed by any netcdf_XXX.h files.
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* Various things (like EXTERNL) are defined in netcdf.h
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* to make them available for use by the netcdf_XXX.h files.
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*/
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#ifndef NCAUX_H
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#define NCAUX_H
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#define NCAUX_ALIGN_C 0
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#define NCAUX_ALIGN_UNIFORM 1
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#if defined(__cplusplus)
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extern "C" {
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#endif
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/**
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Reclaim a vector of instances of arbitrary type.
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Intended for use with e.g. nc_get_vara or the input to e.g. nc_put_vara.
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This recursively walks the top-level instances to
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reclaim any nested data such as vlen or strings or such.
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Assumes it is passed a pointer to count instances of xtype.
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Reclaims any nested data.
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WARNING: ncaux_reclaim_data does not reclaim the top-level memory
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because we do not know how it was allocated.
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However ncaux_reclaim_data_all does reclaim top-level memory.
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WARNING: all data blocks below the top-level (e.g. string instances)
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will be reclaimed, so do not call if there is any static data in the instance.
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Should work for any netcdf format.
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WARNING: deprecated in favor the corresponding function in netcdf.h.
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These are just wrappers for nc_reclaim_data and
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nc_reclaim_data_all and nc_copy_data and nc_copy_data_all and
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are here for back compatibilty.
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*/
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EXTERNL int ncaux_reclaim_data(int ncid, int xtype, void* memory, size_t count);
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EXTERNL int ncaux_reclaim_data_all(int ncid, int xtype, void* memory, size_t count);
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/**************************************************/
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/* Capture the id and parameters for a filter
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using the HDF5 unsigned int format
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*/
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typedef struct NC_H5_Filterspec {
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unsigned int filterid; /**< ID for arbitrary filter. */
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size_t nparams; /**< nparams for arbitrary filter. */
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unsigned int* params; /**< Params for arbitrary filter. */
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} NC_H5_Filterspec;
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EXTERNL int ncaux_h5filterspec_parse(const char* txt, unsigned int* idp, size_t* nparamsp, unsigned int** paramsp);
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EXTERNL int ncaux_h5filterspec_parselist(const char* txt0, int* formatp, size_t* nspecsp, struct NC_H5_Filterspec*** vectorp);
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EXTERNL int ncaux_h5filterspec_parse_parameter(const char* txt, size_t* nuiparamsp, unsigned int* uiparams);
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EXTERNL void ncaux_h5filterspec_free(struct NC_H5_Filterspec* f);
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EXTERNL void ncaux_h5filterspec_fix8(unsigned char* mem, int decode);
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/**************************************************/
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/* Wrappers to export selected functions from libnetcdf */
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EXTERNL int ncaux_readfile(const char* filename, size_t* sizep, void** content);
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EXTERNL int ncaux_writefile(const char* filename, size_t size, void* content);
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/**************************************************/
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/* Takes any type */
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EXTERNL int ncaux_type_alignment(int xtype, int ncid, size_t* alignp);
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EXTERNL int ncaux_class_alignment(int ncclass, size_t* alignp);
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/**************************************************/
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/* Takes type classes only */
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/* Build compound types and properly handle offset and alignment */
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EXTERNL int ncaux_class_alignment(int ncclass, size_t* alignp);
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EXTERNL int ncaux_begin_compound(int ncid, const char *name, int alignmode, void** tag);
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EXTERNL int ncaux_end_compound(void* tag, nc_type* xtypeid);
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EXTERNL int ncaux_abort_compound(void* tag);
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EXTERNL int ncaux_add_field(void* tag, const char *name, nc_type field_type,
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int ndims, const int* dimsizes);
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#if defined(__cplusplus)
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}
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#endif
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#endif /*NCAUX_H*/
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