Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
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/*
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Copyright (c) 1998-2018 University Corporation for Atmospheric Research/Unidata
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See COPYRIGHT for license information.
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*/
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/*
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This file contains various instance operations that operate
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on a deep level rather than the shallow level of e.g. nc_free_vlen_t.
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Currently two operations are defined:
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1. reclaim a vector of instances
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2. copy a vector of instances
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*/
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#include "config.h"
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#include <stdlib.h>
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#include <string.h>
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#include <assert.h>
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#include "netcdf.h"
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#include "nc4internal.h"
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#include "nc4dispatch.h"
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#include "ncoffsets.h"
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#include "ncbytes.h"
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#undef REPORT
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#undef DEBUG
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2022-01-11 06:27:16 +08:00
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Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
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/* It is helpful to have a structure that contains memory and an offset */
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typedef struct Position{char* memory; ptrdiff_t offset;} Position;
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static int type_alignment_initialized = 0;
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/* Forward */
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#ifdef USE_NETCDF4
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static int reclaim_datar(int ncid, nc_type xtype, Position*);
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static int reclaim_compound(int ncid, nc_type xtype, size_t size, size_t nfields, Position* offset);
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static int reclaim_vlen(int ncid, nc_type xtype, nc_type basetype, Position* offset);
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static int reclaim_enum(int ncid, nc_type xtype, nc_type basetype, Position* offset);
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static int reclaim_opaque(int ncid, nc_type xtype, size_t size, Position* offset);
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static int copy_datar(int ncid, nc_type xtype, Position* src, Position* dst);
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static int copy_compound(int ncid, nc_type xtype, size_t size, size_t nfields, Position* src, Position* dst);
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static int copy_vlen(int ncid, nc_type xtype, nc_type basetype, Position* src, Position* dst);
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static int copy_enum(int ncid, nc_type xtype, nc_type basetype, Position* src, Position* dst);
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static int copy_opaque(int ncid, nc_type xtype, size_t size, Position* src,Position* dst);
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static int dump_datar(int ncid, nc_type xtype, Position*, NCbytes* buf);
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static int dump_compound(int ncid, nc_type xtype, size_t size, size_t nfields, Position* offset, NCbytes* buf);
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static int dump_vlen(int ncid, nc_type xtype, nc_type basetype, Position* offset, NCbytes* buf);
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static int dump_enum(int ncid, nc_type xtype, nc_type basetype, Position* offset, NCbytes* buf);
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static int dump_opaque(int ncid, nc_type xtype, size_t size, Position* offset, NCbytes* buf);
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static ptrdiff_t read_align(ptrdiff_t offset, size_t alignment);
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#endif
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2022-01-11 06:27:16 +08:00
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static int NC_inq_any_type(int ncid, nc_type typeid, char *name, size_t *size, nc_type *basetypep, size_t *nfieldsp, int *classp);
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
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/**
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Reclaim a vector of instances of a type. This improves upon
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e.g. nc_free_vlen. This recursively walks the top-level
|
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instances to 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: This needs access to the type metadata of the file, so
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a valid ncid and typeid must be available, which means the file
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must not have been closed or aborted.
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WARNING: DOES NOT RECLAIM THE TOP-LEVEL MEMORY (see the
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|
nc_reclaim_data_all function). The reason is that we do not
|
|
|
|
know how it was allocated (e.g. static vs dynamic); only the
|
|
|
|
caller can know that. But note that it assumes all memory
|
|
|
|
blocks other than the top were dynamically allocated, so they
|
|
|
|
will be free'd.
|
|
|
|
|
|
|
|
Should work for any netcdf format.
|
|
|
|
|
|
|
|
@param ncid root id
|
|
|
|
@param xtype type id
|
|
|
|
@param memory ptr to top-level memory to reclaim
|
|
|
|
@param count number of instances of the type in memory block
|
|
|
|
@return error code
|
|
|
|
*/
|
|
|
|
|
|
|
|
int
|
|
|
|
nc_reclaim_data(int ncid, nc_type xtype, void* memory, size_t count)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t i;
|
|
|
|
Position offset;
|
|
|
|
int isf;
|
|
|
|
|
|
|
|
if(ncid < 0 || xtype <= 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(memory == NULL && count > 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(memory == NULL || count == 0)
|
|
|
|
goto done; /* ok, do nothing */
|
|
|
|
#ifdef REPORT
|
|
|
|
fprintf(stderr,">>> reclaim: memory=%p count=%lu ncid=%d xtype=%d\n",memory,(unsigned long)count,ncid,xtype);
|
|
|
|
#endif
|
|
|
|
|
|
|
|
/* Optimizations */
|
|
|
|
/* 1. Vector of fixed size types */
|
|
|
|
if((stat = NC4_inq_type_fixed_size(ncid,xtype,&isf))) goto done;
|
|
|
|
if(isf) goto done; /* no need to reclaim anything */
|
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
/* 2.Vector of strings */
|
|
|
|
if(xtype == NC_STRING) {
|
|
|
|
char** ss = (char**)memory;
|
|
|
|
for(i=0;i<count;i++) {
|
|
|
|
nullfree(ss[i]);
|
|
|
|
}
|
|
|
|
goto done;
|
|
|
|
}
|
|
|
|
offset.memory = (char*)memory; /* use char* so we can do pointer arithmetic */
|
|
|
|
offset.offset = 0;
|
|
|
|
for(i=0;i<count;i++) {
|
|
|
|
if((stat=reclaim_datar(ncid,xtype,&offset))) /* reclaim one instance */
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
#else
|
|
|
|
stat = NC_EBADTYPE;
|
|
|
|
#endif
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
/* Alternate entry point: includes recovering the top-level memory */
|
|
|
|
int
|
|
|
|
nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
stat = nc_reclaim_data(ncid,xtypeid,memory,count);
|
|
|
|
if(stat == NC_NOERR && memory != NULL)
|
|
|
|
free(memory);
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
/* Recursive type walker: reclaim a single instance */
|
|
|
|
static int
|
|
|
|
reclaim_datar(int ncid, nc_type xtype, Position* offset)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t xsize;
|
|
|
|
nc_type basetype;
|
|
|
|
size_t nfields;
|
|
|
|
int klass, isf;
|
|
|
|
|
|
|
|
if((stat = NC4_inq_type_fixed_size(ncid,xtype,&isf))) goto done;
|
2022-02-09 11:53:30 +08:00
|
|
|
|
|
|
|
/* Get relevant type info */
|
|
|
|
if((stat = NC_inq_any_type(ncid,xtype,NULL,&xsize,&basetype,&nfields,&klass))) goto done;
|
|
|
|
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
if(isf) { /* no need to reclaim anything */
|
|
|
|
offset->offset += xsize;
|
|
|
|
goto done;
|
|
|
|
}
|
|
|
|
|
|
|
|
switch (xtype) {
|
|
|
|
case NC_STRING: {
|
|
|
|
char** sp = (char**)(offset->memory + offset->offset);
|
|
|
|
/* Need to reclaim string */
|
|
|
|
if(*sp != NULL) free(*sp);
|
|
|
|
offset->offset += xsize;
|
|
|
|
} break;
|
|
|
|
default:
|
|
|
|
/* reclaim a user type */
|
|
|
|
switch (klass) {
|
|
|
|
case NC_OPAQUE: stat = reclaim_opaque(ncid,xtype,xsize,offset); break;
|
|
|
|
case NC_ENUM: stat = reclaim_enum(ncid,xtype,basetype,offset); break;
|
|
|
|
case NC_COMPOUND: stat = reclaim_compound(ncid,xtype,xsize,nfields,offset); break;
|
|
|
|
case NC_VLEN:
|
|
|
|
stat = reclaim_vlen(ncid,xtype,basetype,offset);
|
|
|
|
break;
|
|
|
|
default:
|
|
|
|
stat = NC_EINVAL;
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
reclaim_vlen(int ncid, nc_type xtype, nc_type basetype, Position* offset)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t i;
|
|
|
|
nc_vlen_t* vl = (nc_vlen_t*)(offset->memory+offset->offset);
|
|
|
|
|
|
|
|
if(vl->len > 0 && vl->p == NULL)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
|
|
|
|
/* Free up each entry in the vlen list */
|
|
|
|
if(vl->len > 0) {
|
|
|
|
Position voffset;
|
|
|
|
size_t alignment = 0;
|
|
|
|
if((stat = NC_type_alignment(ncid,basetype,&alignment))) goto done;;
|
|
|
|
voffset.memory = vl->p;
|
|
|
|
voffset.offset = 0;
|
|
|
|
for(i=0;i<vl->len;i++) {
|
|
|
|
voffset.offset = read_align(voffset.offset,alignment);
|
|
|
|
if((stat = reclaim_datar(ncid,basetype,&voffset))) goto done;
|
|
|
|
}
|
|
|
|
free(vl->p);
|
|
|
|
}
|
|
|
|
offset->offset += sizeof(nc_vlen_t);
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
reclaim_enum(int ncid, nc_type xtype, nc_type basetype, Position* offset)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
abort();
|
|
|
|
|
|
|
|
/* basically same as an instance of the enum's integer basetype */
|
|
|
|
stat = reclaim_datar(ncid,basetype,offset);
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
reclaim_opaque(int ncid, nc_type xtype, size_t size, Position* offset)
|
|
|
|
{
|
|
|
|
abort();
|
|
|
|
/* basically a fixed size sequence of bytes */
|
|
|
|
offset->offset += size;
|
|
|
|
return NC_NOERR;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
reclaim_compound(int ncid, nc_type xtype, size_t size, size_t nfields, Position* offset)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t fid, i, arraycount;
|
|
|
|
ptrdiff_t saveoffset;
|
|
|
|
int ndims;
|
|
|
|
int dimsizes[NC_MAX_VAR_DIMS];
|
|
|
|
|
|
|
|
saveoffset = offset->offset;
|
|
|
|
|
|
|
|
/* Get info about each field in turn and reclaim it */
|
|
|
|
for(fid=0;fid<nfields;fid++) {
|
|
|
|
size_t fieldalignment;
|
|
|
|
nc_type fieldtype;
|
|
|
|
|
|
|
|
/* Get all relevant info about the field */
|
|
|
|
if((stat = nc_inq_compound_field(ncid,xtype,fid,NULL,&fieldalignment,&fieldtype,&ndims,dimsizes))) goto done;
|
|
|
|
|
|
|
|
if(ndims == 0) {ndims=1; dimsizes[0]=1;} /* fake the scalar case */
|
|
|
|
/* Align to this field */
|
|
|
|
offset->offset = saveoffset + fieldalignment;
|
|
|
|
/* compute the total number of elements in the field array */
|
|
|
|
arraycount = 1;
|
|
|
|
for(i=0;i<ndims;i++) arraycount *= dimsizes[i];
|
|
|
|
for(i=0;i<arraycount;i++) {
|
|
|
|
if((stat = reclaim_datar(ncid, fieldtype, offset))) goto done;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
/* Return to beginning of the compound and move |compound| */
|
|
|
|
offset->offset = saveoffset;
|
|
|
|
offset->offset += size;
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
#endif
|
|
|
|
|
|
|
|
/**************************************************/
|
|
|
|
|
|
|
|
/**
|
|
|
|
Copy a vector of instances of a type. This recursively walks
|
|
|
|
the top-level instances to copy any nested data such as vlen or
|
|
|
|
strings or such.
|
|
|
|
|
|
|
|
Assumes it is passed a pointer to count instances of xtype and a
|
|
|
|
space into which to copy the instance. Copys any nested data.
|
|
|
|
|
|
|
|
WARNING: This needs access to the type metadata of the file, so
|
|
|
|
a valid ncid and typeid must be available, which means the file
|
|
|
|
must not have been closed or aborted.
|
|
|
|
|
|
|
|
WARNING: DOES NOT ALLOCATE THE TOP-LEVEL MEMORY (see the
|
|
|
|
nc_copy_data_all function). Note that all memory blocks other
|
|
|
|
than the top are dynamically allocated.
|
|
|
|
|
|
|
|
Should work for any netcdf format.
|
|
|
|
|
|
|
|
@param ncid root id
|
|
|
|
@param xtype type id
|
|
|
|
@param memory ptr to top-level memory to copy
|
|
|
|
@param count number of instances of the type in memory block
|
|
|
|
@param copy top-level space into which to copy the instance
|
|
|
|
@return error code
|
|
|
|
*/
|
|
|
|
|
|
|
|
int
|
|
|
|
nc_copy_data(int ncid, nc_type xtype, const void* memory, size_t count, void* copy)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t i;
|
|
|
|
Position src;
|
|
|
|
Position dst;
|
|
|
|
size_t xsize;
|
|
|
|
int isf;
|
|
|
|
|
|
|
|
if(ncid < 0 || xtype <= 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(memory == NULL && count > 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(copy == NULL && count > 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(memory == NULL || count == 0)
|
|
|
|
goto done; /* ok, do nothing */
|
|
|
|
|
|
|
|
#ifdef REPORT
|
|
|
|
fprintf(stderr,">>> copy : copy =%p memory=%p count=%lu ncid=%d xtype=%d\n",copy,memory,(unsigned long)count,ncid,xtype);
|
|
|
|
#endif
|
|
|
|
|
|
|
|
/* Get type size */
|
2022-01-11 06:27:16 +08:00
|
|
|
if((stat = NC_inq_any_type(ncid,xtype,NULL,&xsize,NULL,NULL,NULL))) goto done;
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
|
|
|
|
/* Optimizations */
|
|
|
|
/* 1. Vector of fixed sized objects */
|
|
|
|
if((stat = NC4_inq_type_fixed_size(ncid,xtype,&isf))) goto done;
|
|
|
|
if(isf) {
|
|
|
|
memcpy(copy,memory,xsize*count);
|
|
|
|
goto done;
|
|
|
|
}
|
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
src.memory = (char*)memory; /* use char* so we can do pointer arithmetic */
|
|
|
|
src.offset = 0;
|
|
|
|
dst.memory = (char*)copy; /* use char* so we can do pointer arithmetic */
|
|
|
|
dst.offset = 0;
|
|
|
|
for(i=0;i<count;i++) {
|
|
|
|
if((stat=copy_datar(ncid,xtype,&src,&dst))) /* copy one instance copy_datar will increment src and dst*/
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
#else
|
|
|
|
stat = NC_EBADTYPE;
|
|
|
|
#endif
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
/* Alternate entry point: includes recovering the top-level memory */
|
|
|
|
int
|
|
|
|
nc_copy_data_all(int ncid, nc_type xtype, const void* memory, size_t count, void** copyp)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t xsize = 0;
|
|
|
|
void* copy = NULL;
|
|
|
|
|
|
|
|
/* Get type size */
|
2022-01-11 06:27:16 +08:00
|
|
|
if((stat = NC_inq_any_type(ncid,xtype,NULL,&xsize,NULL,NULL,NULL))) goto done;
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
|
|
|
|
/* allocate the top-level */
|
|
|
|
if(count > 0) {
|
|
|
|
if((copy = calloc(xsize,count))==NULL)
|
|
|
|
{stat = NC_ENOMEM; goto done;}
|
|
|
|
}
|
|
|
|
stat = nc_copy_data(ncid,xtype,memory,count,copy);
|
|
|
|
if(copyp) {*copyp = copy; copy = NULL;}
|
|
|
|
|
|
|
|
done:
|
|
|
|
if(copy)
|
|
|
|
stat = nc_reclaim_data_all(ncid,xtype,copy,count);
|
|
|
|
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
/* Recursive type walker: copy a single instance */
|
|
|
|
static int
|
|
|
|
copy_datar(int ncid, nc_type xtype, Position* src, Position* dst)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t xsize;
|
|
|
|
nc_type basetype;
|
|
|
|
size_t nfields;
|
|
|
|
int xclass,isf;
|
|
|
|
|
2022-01-11 06:27:16 +08:00
|
|
|
if((stat = NC_inq_any_type(ncid,xtype,NULL,&xsize,&basetype,&nfields,&xclass))) goto done;
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
|
|
|
|
/* Optimizations */
|
|
|
|
/* 1. Vector of fixed size types */
|
|
|
|
if((stat = NC4_inq_type_fixed_size(ncid,xtype,&isf))) goto done;
|
|
|
|
if(isf) {
|
|
|
|
memcpy(dst->memory+dst->offset,src->memory+src->offset,xsize*1);
|
|
|
|
src->offset += xsize;
|
|
|
|
dst->offset += xsize;
|
|
|
|
goto done;
|
|
|
|
}
|
|
|
|
|
|
|
|
switch (xtype) {
|
|
|
|
case NC_STRING: {
|
|
|
|
char** sp = (char**)(src->memory + src->offset);
|
|
|
|
char* copy = NULL;
|
|
|
|
/* Need to copy string */
|
|
|
|
if(*sp != NULL) {
|
|
|
|
if((copy = strdup(*sp))==NULL) {stat = NC_ENOMEM; goto done;}
|
|
|
|
}
|
|
|
|
memcpy(dst->memory+dst->offset,(void*)©,sizeof(char*));
|
|
|
|
src->offset += xsize;
|
|
|
|
dst->offset += xsize;
|
|
|
|
} break;
|
|
|
|
default:
|
|
|
|
/* copy a user type */
|
|
|
|
switch (xclass) {
|
|
|
|
case NC_OPAQUE: stat = copy_opaque(ncid,xtype,xsize,src,dst); break;
|
|
|
|
case NC_ENUM: stat = copy_enum(ncid,xtype,basetype,src,dst); break;
|
|
|
|
case NC_COMPOUND: stat = copy_compound(ncid,xtype,xsize,nfields,src,dst); break;
|
|
|
|
case NC_VLEN: stat = copy_vlen(ncid,xtype,basetype,src,dst); break;
|
|
|
|
default: stat = NC_EINVAL; break;
|
|
|
|
}
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
copy_vlen(int ncid, nc_type xtype, nc_type basetype, Position* src, Position* dst)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t i, basetypesize;
|
|
|
|
nc_vlen_t* vl = (nc_vlen_t*)(src->memory+src->offset);
|
|
|
|
nc_vlen_t copy = {0,NULL};
|
|
|
|
|
|
|
|
if(vl->len > 0 && vl->p == NULL)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
|
|
|
|
/* Get basetype info */
|
2022-01-11 06:27:16 +08:00
|
|
|
if((stat = NC_inq_any_type(ncid,basetype,NULL,&basetypesize,NULL,NULL,NULL))) goto done;
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
|
|
|
|
/* Make space in the copy vlen */
|
|
|
|
if(vl->len > 0) {
|
|
|
|
copy.len = vl->len;
|
|
|
|
if((copy.p = calloc(copy.len,basetypesize))==NULL) {stat = NC_ENOMEM; goto done;}
|
|
|
|
}
|
|
|
|
/* Copy each entry in the vlen list */
|
|
|
|
if(vl->len > 0) {
|
|
|
|
Position vsrc, vdst;
|
|
|
|
size_t alignment = 0;
|
|
|
|
if((stat = NC_type_alignment(ncid,basetype,&alignment))) goto done;;
|
|
|
|
vsrc.memory = vl->p;
|
|
|
|
vsrc.offset = 0;
|
|
|
|
vdst.memory = copy.p;
|
|
|
|
vdst.offset = 0;
|
|
|
|
for(i=0;i<vl->len;i++) {
|
|
|
|
vsrc.offset= read_align(vsrc.offset,alignment);
|
|
|
|
vdst.offset= read_align(vdst.offset,alignment);
|
|
|
|
if((stat = copy_datar(ncid,basetype,&vsrc,&vdst))) goto done;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
/* Move into place */
|
|
|
|
memcpy(dst->memory+dst->offset,©,sizeof(nc_vlen_t));
|
|
|
|
src->offset += sizeof(nc_vlen_t);
|
|
|
|
dst->offset += sizeof(nc_vlen_t);
|
|
|
|
|
|
|
|
done:
|
|
|
|
if(stat) {
|
|
|
|
nullfree(copy.p);
|
|
|
|
}
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
copy_enum(int ncid, nc_type xtype, nc_type basetype, Position* src, Position* dst)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
abort();
|
|
|
|
/* basically same as an instance of the enum's integer basetype */
|
|
|
|
stat = copy_datar(ncid,basetype,src,dst);
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
copy_opaque(int ncid, nc_type xtype, size_t size, Position* src, Position* dst)
|
|
|
|
{
|
|
|
|
abort();
|
|
|
|
/* basically a fixed size sequence of bytes */
|
|
|
|
memcpy(dst->memory+dst->offset,src->memory+src->offset,size);
|
|
|
|
src->offset += size;
|
|
|
|
dst->offset += size;
|
|
|
|
return NC_NOERR;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
copy_compound(int ncid, nc_type xtype, size_t size, size_t nfields, Position* src, Position* dst)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t fid, i, arraycount;
|
|
|
|
ptrdiff_t savesrcoffset, savedstoffset;
|
|
|
|
int ndims;
|
|
|
|
int dimsizes[NC_MAX_VAR_DIMS];
|
|
|
|
|
|
|
|
savesrcoffset = src->offset;
|
|
|
|
savedstoffset = dst->offset;
|
|
|
|
|
|
|
|
/* Get info about each field in turn and copy it */
|
|
|
|
for(fid=0;fid<nfields;fid++) {
|
|
|
|
size_t fieldoffset;
|
|
|
|
nc_type fieldtype;
|
|
|
|
char name[NC_MAX_NAME];
|
|
|
|
|
|
|
|
/* Get all relevant info about the field */
|
|
|
|
if((stat = nc_inq_compound_field(ncid,xtype,fid,name,&fieldoffset,&fieldtype,&ndims,dimsizes))) goto done;
|
|
|
|
|
|
|
|
if(ndims == 0) {ndims=1; dimsizes[0]=1;} /* fake the scalar case */
|
|
|
|
/* Set offset for this field */
|
|
|
|
#ifdef DEBUG
|
|
|
|
fprintf(stderr,"before: offset = %d after: offset = %d\n",(int)src->offset,(int)(savesrcoffset+fieldoffset));
|
|
|
|
#endif
|
|
|
|
src->offset = savesrcoffset+fieldoffset;
|
|
|
|
dst->offset = savedstoffset+fieldoffset;
|
|
|
|
#ifdef DEBUG
|
|
|
|
fprintf(stderr,"field %s(%d) = %d\n",name,(int)fieldoffset,(int)src->offset);
|
|
|
|
#endif
|
|
|
|
/* compute the total number of elements in the field array */
|
|
|
|
arraycount = 1;
|
|
|
|
for(i=0;i<ndims;i++) arraycount *= dimsizes[i];
|
|
|
|
for(i=0;i<arraycount;i++) {
|
|
|
|
if((stat = copy_datar(ncid, fieldtype, src, dst))) goto done;
|
|
|
|
}
|
|
|
|
#ifdef DEBUG
|
|
|
|
fprintf(stderr,"src=(%d,%p)\n",(int)src->offset,src->memory);
|
|
|
|
#endif
|
|
|
|
}
|
|
|
|
#ifdef DEBUG
|
|
|
|
fprintf(stderr,"\n");
|
|
|
|
#endif
|
|
|
|
/* Return to beginning of the compound and move |compound| */
|
|
|
|
src->offset = savesrcoffset;
|
|
|
|
dst->offset = savedstoffset;
|
|
|
|
src->offset += size;
|
|
|
|
dst->offset += size;
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
#endif
|
|
|
|
|
|
|
|
/**************************************************/
|
|
|
|
/* Alignment functions */
|
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
static ptrdiff_t
|
|
|
|
read_align(ptrdiff_t offset, size_t alignment)
|
|
|
|
{
|
|
|
|
size_t loc_align = (alignment == 0 ? 1 : alignment);
|
|
|
|
size_t delta = (offset % loc_align);
|
|
|
|
if(delta == 0) return offset;
|
|
|
|
return offset + (alignment - delta);
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
/**
|
|
|
|
@param ncid - only needed for a compound type
|
|
|
|
@param xtype - type for which alignment is requested
|
|
|
|
@return 0 if not found
|
|
|
|
*/
|
|
|
|
int
|
|
|
|
NC_type_alignment(int ncid, nc_type xtype, size_t* alignp)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t align = 0;
|
|
|
|
int klass;
|
|
|
|
|
|
|
|
if(!type_alignment_initialized) {
|
|
|
|
NC_compute_alignments();
|
|
|
|
type_alignment_initialized = 1;
|
|
|
|
}
|
|
|
|
if(xtype <= NC_MAX_ATOMIC_TYPE)
|
|
|
|
{stat = NC_class_alignment(xtype,&align); goto done;}
|
|
|
|
else {/* Presumably a user type */
|
2022-01-11 06:27:16 +08:00
|
|
|
if((stat = NC_inq_any_type(ncid,xtype,NULL,NULL,NULL,NULL,&klass))) goto done;
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
switch(klass) {
|
|
|
|
case NC_VLEN: stat = NC_class_alignment(klass,&align); break;
|
|
|
|
case NC_OPAQUE: stat = NC_class_alignment(klass,&align); break;
|
|
|
|
case NC_COMPOUND: {/* get alignment of the first field of the compound */
|
|
|
|
nc_type fieldtype;
|
|
|
|
/* Get all relevant info about the first field */
|
|
|
|
if((stat = nc_inq_compound_field(ncid,xtype,0,NULL,NULL,&fieldtype,NULL,NULL))) goto done;
|
|
|
|
stat = NC_type_alignment(ncid,fieldtype,&align); /* may recurse repeatedly */
|
|
|
|
} break;
|
|
|
|
default: break;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
if(alignp) *alignp = align;
|
|
|
|
|
|
|
|
done:
|
|
|
|
#if 0
|
|
|
|
Why was this here?
|
|
|
|
if(stat == NC_NOERR && align == 0) stat = NC_EINVAL;
|
|
|
|
#endif
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
#endif
|
|
|
|
|
|
|
|
/**************************************************/
|
|
|
|
/* Dump an instance into a bytebuffer
|
|
|
|
|
|
|
|
@param ncid root id
|
|
|
|
@param xtype type id
|
|
|
|
@param memory ptr to top-level memory to dump
|
|
|
|
@param count number of instances of the type in memory block
|
|
|
|
@return error code
|
|
|
|
*/
|
|
|
|
|
|
|
|
int
|
|
|
|
nc_dump_data(int ncid, nc_type xtype, void* memory, size_t count, char** bufp)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t i;
|
|
|
|
Position offset;
|
|
|
|
NCbytes* buf = ncbytesnew();
|
|
|
|
|
|
|
|
if(ncid < 0 || xtype <= 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(memory == NULL && count > 0)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if(memory == NULL || count == 0)
|
|
|
|
goto done; /* ok, do nothing */
|
|
|
|
#ifdef REPORT
|
|
|
|
fprintf(stderr,">>> dump: memory=%p count=%lu ncid=%d xtype=%d\n",memory,(unsigned long)count,ncid,xtype);
|
|
|
|
#endif
|
|
|
|
offset.memory = (char*)memory; /* use char* so we can do pointer arithmetic */
|
|
|
|
offset.offset = 0;
|
|
|
|
for(i=0;i<count;i++) {
|
|
|
|
if(i > 0) ncbytescat(buf," ");
|
|
|
|
if((stat=dump_datar(ncid,xtype,&offset,buf))) /* dump one instance */
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
|
|
|
|
if(bufp) *bufp = ncbytesextract(buf);
|
|
|
|
|
|
|
|
done:
|
|
|
|
ncbytesfree(buf);
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
int
|
|
|
|
nc_print_data(int ncid, nc_type xtype, void* memory, size_t count)
|
|
|
|
{
|
|
|
|
char* s = NULL;
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
if((stat=nc_dump_data(ncid,xtype,memory,count,&s))) return stat;
|
|
|
|
fprintf(stderr,"%s\n",s);
|
|
|
|
nullfree(s)
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
/* Recursive type walker: dump a single instance */
|
|
|
|
static int
|
|
|
|
dump_datar(int ncid, nc_type xtype, Position* offset, NCbytes* buf)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t xsize;
|
|
|
|
nc_type basetype;
|
|
|
|
size_t nfields;
|
|
|
|
int klass;
|
|
|
|
char s[128];
|
|
|
|
|
|
|
|
/* Get relevant type info */
|
2022-01-11 06:27:16 +08:00
|
|
|
if((stat = NC_inq_any_type(ncid,xtype,NULL,&xsize,&basetype,&nfields,&klass))) goto done;
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
|
|
|
|
switch (xtype) {
|
|
|
|
case NC_CHAR:
|
|
|
|
snprintf(s,sizeof(s),"'%c'",*(char*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_BYTE:
|
|
|
|
snprintf(s,sizeof(s),"%d",*(char*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_UBYTE:
|
|
|
|
snprintf(s,sizeof(s),"%u",*(unsigned char*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_SHORT:
|
|
|
|
snprintf(s,sizeof(s),"%d",*(short*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_USHORT:
|
|
|
|
snprintf(s,sizeof(s),"%d",*(unsigned short*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_INT:
|
|
|
|
snprintf(s,sizeof(s),"%d",*(int*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_UINT:
|
|
|
|
snprintf(s,sizeof(s),"%d",*(unsigned int*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_FLOAT:
|
|
|
|
snprintf(s,sizeof(s),"%f",*(float*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_INT64:
|
|
|
|
snprintf(s,sizeof(s),"%lld",*(long long*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_UINT64:
|
|
|
|
snprintf(s,sizeof(s),"%llu",*(unsigned long long*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
case NC_DOUBLE:
|
|
|
|
snprintf(s,sizeof(s),"%lf",*(double*)(offset->memory+offset->offset));
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
break;
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
case NC_STRING: {
|
|
|
|
char* s = *(char**)(offset->memory + offset->offset);
|
|
|
|
ncbytescat(buf,"\"");
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
ncbytescat(buf,"\"");
|
|
|
|
} break;
|
|
|
|
#endif
|
|
|
|
default:
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
/* dump a user type */
|
|
|
|
switch (klass) {
|
|
|
|
case NC_OPAQUE: stat = dump_opaque(ncid,xtype,xsize,offset,buf); break;
|
|
|
|
case NC_ENUM: stat = dump_enum(ncid,xtype,basetype,offset,buf); break;
|
|
|
|
case NC_COMPOUND: stat = dump_compound(ncid,xtype,xsize,nfields,offset,buf); break;
|
|
|
|
case NC_VLEN: stat = dump_vlen(ncid,xtype,basetype,offset,buf); break;
|
|
|
|
default: stat = NC_EBADTYPE; break;
|
|
|
|
}
|
|
|
|
#else
|
|
|
|
stat = NC_EBADTYPE;
|
|
|
|
#endif
|
|
|
|
break;
|
|
|
|
}
|
|
|
|
if(xtype <= NC_MAX_ATOMIC_TYPE)
|
|
|
|
offset->offset += xsize;
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
static int
|
|
|
|
dump_vlen(int ncid, nc_type xtype, nc_type basetype, Position* offset, NCbytes* buf)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t i;
|
|
|
|
nc_vlen_t* vl = (nc_vlen_t*)(offset->memory+offset->offset);
|
|
|
|
char s[128];
|
|
|
|
|
|
|
|
if(vl->len > 0 && vl->p == NULL)
|
|
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
|
|
|
|
snprintf(s,sizeof(s),"{len=%u,p=(",(unsigned)vl->len);
|
|
|
|
ncbytescat(buf,s);
|
|
|
|
/* dump each entry in the vlen list */
|
|
|
|
if(vl->len > 0) {
|
|
|
|
Position voffset;
|
|
|
|
size_t alignment = 0;
|
|
|
|
if((stat = NC_type_alignment(ncid,basetype,&alignment))) goto done;;
|
|
|
|
voffset.memory = vl->p;
|
|
|
|
voffset.offset = 0;
|
|
|
|
for(i=0;i<vl->len;i++) {
|
|
|
|
if(i > 0) ncbytescat(buf," ");
|
|
|
|
voffset.offset = read_align(voffset.offset,alignment);
|
|
|
|
if((stat = dump_datar(ncid,basetype,&voffset,buf))) goto done;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
ncbytescat(buf,")}");
|
|
|
|
offset->offset += sizeof(nc_vlen_t);
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
dump_enum(int ncid, nc_type xtype, nc_type basetype, Position* offset, NCbytes* buf)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
|
|
|
|
/* basically same as an instance of the enum's integer basetype */
|
|
|
|
stat = dump_datar(ncid,basetype,offset,buf);
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
dump_opaque(int ncid, nc_type xtype, size_t size, Position* offset, NCbytes* buf)
|
|
|
|
{
|
|
|
|
size_t i;
|
|
|
|
char sx[16];
|
|
|
|
/* basically a fixed size sequence of bytes */
|
|
|
|
ncbytescat(buf,"|");
|
|
|
|
for(i=0;i<size;i++) {
|
|
|
|
unsigned char x = *(offset->memory+offset->offset+i);
|
|
|
|
snprintf(sx,sizeof(sx),"%2x",x);
|
|
|
|
ncbytescat(buf,sx);
|
|
|
|
}
|
|
|
|
ncbytescat(buf,"|");
|
|
|
|
offset->offset += size;
|
|
|
|
return NC_NOERR;
|
|
|
|
}
|
|
|
|
|
|
|
|
static int
|
|
|
|
dump_compound(int ncid, nc_type xtype, size_t size, size_t nfields, Position* offset, NCbytes* buf)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
|
|
|
size_t fid, i, arraycount;
|
|
|
|
ptrdiff_t saveoffset;
|
|
|
|
int ndims;
|
|
|
|
int dimsizes[NC_MAX_VAR_DIMS];
|
|
|
|
|
|
|
|
saveoffset = offset->offset;
|
|
|
|
|
|
|
|
ncbytescat(buf,"<");
|
|
|
|
|
|
|
|
/* Get info about each field in turn and dump it */
|
|
|
|
for(fid=0;fid<nfields;fid++) {
|
|
|
|
size_t fieldalignment;
|
|
|
|
nc_type fieldtype;
|
|
|
|
char name[NC_MAX_NAME];
|
|
|
|
char sd[128];
|
|
|
|
|
|
|
|
/* Get all relevant info about the field */
|
|
|
|
if((stat = nc_inq_compound_field(ncid,xtype,fid,name,&fieldalignment,&fieldtype,&ndims,dimsizes))) goto done;
|
|
|
|
if(fid > 0) ncbytescat(buf,";");
|
|
|
|
ncbytescat(buf,name);
|
|
|
|
if(ndims > 0) {
|
|
|
|
int j;
|
|
|
|
for(j=0;j<ndims;j++) {
|
|
|
|
snprintf(sd,sizeof(sd),"[%d]",(int)dimsizes[j]);
|
|
|
|
ncbytescat(buf,sd);
|
|
|
|
}
|
|
|
|
}
|
|
|
|
if(ndims == 0) {ndims=1; dimsizes[0]=1;} /* fake the scalar case */
|
|
|
|
/* Align to this field */
|
|
|
|
offset->offset = saveoffset + fieldalignment;
|
|
|
|
/* compute the total number of elements in the field array */
|
|
|
|
arraycount = 1;
|
|
|
|
for(i=0;i<ndims;i++) arraycount *= dimsizes[i];
|
|
|
|
for(i=0;i<arraycount;i++) {
|
|
|
|
if(i > 0) ncbytescat(buf," ");
|
|
|
|
if((stat = dump_datar(ncid, fieldtype, offset,buf))) goto done;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
ncbytescat(buf,">");
|
|
|
|
/* Return to beginning of the compound and move |compound| */
|
|
|
|
offset->offset = saveoffset;
|
|
|
|
offset->offset += size;
|
|
|
|
|
|
|
|
done:
|
|
|
|
return stat;
|
|
|
|
}
|
|
|
|
#endif
|
|
|
|
|
|
|
|
/* Extended version that can handle atomic typeids */
|
2022-01-11 06:27:16 +08:00
|
|
|
int
|
|
|
|
NC_inq_any_type(int ncid, nc_type typeid, char *name, size_t *size,
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
nc_type *basetypep, size_t *nfieldsp, int *classp)
|
|
|
|
{
|
|
|
|
int stat = NC_NOERR;
|
2022-01-11 06:27:16 +08:00
|
|
|
#ifdef USE_NETCDF4
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
if(typeid >= NC_FIRSTUSERTYPEID) {
|
|
|
|
stat = nc_inq_user_type(ncid,typeid,name,size,basetypep,nfieldsp,classp);
|
2022-01-11 06:27:16 +08:00
|
|
|
} else
|
|
|
|
#endif
|
|
|
|
if(typeid > NC_NAT && typeid <= NC_MAX_ATOMIC_TYPE) {
|
Fix various problem around VLEN's
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.
2022-01-09 09:30:00 +08:00
|
|
|
if(basetypep) *basetypep = NC_NAT;
|
|
|
|
if(nfieldsp) *nfieldsp = 0;
|
|
|
|
if(classp) *classp = typeid;
|
|
|
|
stat = NC4_inq_atomic_type(typeid,name,size);
|
|
|
|
} else
|
|
|
|
stat = NC_EBADTYPE;
|
|
|
|
return stat;
|
|
|
|
}
|