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Update the following documentation files:

## docs/FAQ.md
* Discuss the use of UTF-8 names under Windows 10+.

## docs/filters.md
* Add documentation about NCzarr filters.
  * Specifically Codec support and HDF5 <-> Codec translation
* Add documentation about standard filters

## docs/dispatch.md
* Convert from .dox format to .md (markdown) format.
* Add discussion about the user defined dispatch tables.
* Update the example.
* Abbreviate the NC_infermodel documentation and move the more detailed discusion to the companion *dinternal.md* documenation.

## docs/internal.md

This is a (mostly) new file that attempts to provide detailed
descriptions about how various features are implemented inside
the netcdf-c library. The topics currently covered the
following.

### Including C++ Code in the netcdf-c Library {#intern_c++}

The state of C compiler technology has reached the point where
it is possible to include C++ code into the netcdf-c library
code base. The document describes how to do this.

### Managing instances of complex data types

The document describes how to properly handle instances of
complex types (those with variable length).  This involves
having functions that can recursively walk instances of such
types to perform various actions on them.  These new functions
are intended to replace the *nc_free_vlen*, *nc_free_vlens* and
*nc_free_string* functions in *netcdf.h*.

### Inferring File Types

As described in the companion document -- docs/dispatch.md --
when *nc\_create()* or *nc\_open()* is called, the library must
figure out what kind of file is being created or opened.  Once it
has figured out the file kind, the appropriate "dispatch table"
can be used to process that file.

As a result of the introduction of remote data access to the netcdf-c
library, the path arguments to *nc\_open()* and *nc\_create()* have
been extended to support URLs as paths. Processing URLs requires
some significant changes to the file inference algorithm. The
details of that processing are recorded in the document.
This commit is contained in:
Dennis Heimbigner 2022-03-16 12:38:00 -06:00
parent e0a2236b5a
commit f1eaefd91e
7 changed files with 1594 additions and 293 deletions
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name: Run MSYS2, MinGW64-based Tests
on: [ pull_request ]
on: [pull_request]
jobs:

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@abs_top_srcdir@/docs/COPYRIGHT.md \
@abs_top_srcdir@/docs/credits.md \
@abs_top_srcdir@/docs/tutorial.dox \
@abs_top_srcdir@/docs/internal.dox \
@abs_top_srcdir@/docs/internal.md \
@abs_top_srcdir@/docs/dispatch.md \
@abs_top_srcdir@/docs/inmeminternal.dox \
@abs_top_srcdir@/docs/indexing.dox \
@abs_top_srcdir@/docs/testserver.dox \

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@ -1079,9 +1079,22 @@ and writable by programs that used older versions of the libraries.
However, programs linked to older library versions will not be able to
create new data objects with the new less-restrictive names.
How difficult is it to convert my application to handle arbitrary netCDF-4 files? {#How-difficult-is-it-to-convert-my-application-to-handle-arbitrary-netCDF-4-files}
Can I use UTF-8 File Names with Windows? {#Can-I-use-UTF-8-File-Names-with-Windows}
-----------------
Starting with Windows 10 build 17134, Windows can support use of
the UTF-8 character set. We strongly encourage Windows users to
enable this feature. This requires the following steps.
1. In the "run" toolbar, execute the command "intl.cpl".
2. Move to the Administrative tab.
3. Move to "Change system locale"
4. Check the box at the bottom labeled something like
"Beta: Use Unicode UTF-8 for worldwide language support"
How difficult is it to convert my application to handle arbitrary netCDF-4 files? {#How-difficult-is-it-to-convert-my-application-to-handle-arbitrary-netCDF-4-files}
-----------------
Modifying an application to fully support the new enhanced data model
may be relatively easy or arbitrarily difficult :-), depending on what

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# These files will be included with the dist.
EXTRA_DIST = netcdf.m4 DoxygenLayout.xml Doxyfile.in footer.html \
mainpage.dox tutorial.dox \
architecture.dox internal.dox windows-binaries.md \
architecture.dox internal.md windows-binaries.md dispatch.md \
building-with-cmake.md CMakeLists.txt groups.dox notes.md \
install-fortran.md all-error-codes.md credits.md auth.md filters.md \
obsolete/fan_utils.html indexing.dox \

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Internal Dispatch Table Architecture
============================
<!-- double header is needed to workaround doxygen bug -->
# Internal Dispatch Table Architecture
\tableofcontents
# Introduction {#dispatch_intro}
The netcdf-c library uses an internal dispatch mechanism
as the means for wrapping the netcdf-c API around a wide variety
of underlying storage and stream data formats.
As of last check, the following formats are supported and each
has its own dispatch table.
Warning: some of the listed function signatures may be out of date
and the specific code should be consulted to see the actual parameters.
<table>
<tr><th>Format<td>Directory<th>NC_FORMATX Name
<tr><td>NetCDF-classic<td>libsrc<td>NC_FORMATX_NC3
<tr><td>NetCDF-enhanced<td>libhdf5<td>NC_FORMATX_NC_HDF5
<tr><td>HDF4<td>libhdf4<td>NC_FORMATX_NC_HDF4
<tr><td>PNetCDF<td>libsrcp<td>NC_FORMATX_PNETCDF
<tr><td>DAP2<td>libdap2<td>NC_FORMATX_DAP2
<tr><td>DAP4<td>libdap4<td>NC_FORMATX_DAP4
<tr><td>UDF0<td>N.A.<td>NC_FORMATX_UDF0
<tr><td>UDF1<td>N.A.<td>NC_FORMATX_UDF1
<tr><td>NCZarr<td>libnczarr<td>NC_FORMATX_NCZARR
</table>
Note that UDF0 and UDF1 allow for user-defined dispatch tables to
be implemented.
The idea is that when a user opens or creates a netcdf file, a
specific dispatch table is chosen. A dispatch table is a struct
containing an entry for (almost) every function in the netcdf-c API.
During execution, netcdf API calls are channeled through that
dispatch table to the appropriate function for implementing that
API call. The functions in the dispatch table are not quite the
same as those defined in *netcdf.h*. For simplicity and
compactness, some netcdf.h API calls are mapped to the same
dispatch table function. In addition to the functions, the first
entry in the table defines the model that this dispatch table
implements. It will be one of the NC_FORMATX_XXX values.
The second entry in the table is the version of the dispatch table.
The rule is that previous entries may not be removed, but new entries
may be added, and adding new entries increases the version number.
The dispatch table represents a distillation of the netcdf API down to
a minimal set of internal operations. The format of the dispatch table
is defined in the file *libdispatch/ncdispatch.h*. Every new dispatch
table must define this minimal set of operations.
# Adding a New Dispatch Table
In order to make this process concrete, let us assume we plan to add
an in-memory implementation of netcdf-3.
## Defining configure.ac flags
Define a *–-enable* flag option for *configure.ac*. For our
example, we assume the option "--enable-ncm" and the
internal corresponding flag "enable_ncm". If you examine the existing
*configure.ac* and see how, for example, *--enable_dap2* is
defined, then it should be clear how to do it for your code.
## Defining a "name space"
Choose some prefix of characters to identify the new dispatch
system. In effect we are defining a name-space. For our in-memory
system, we will choose "NCM" and "ncm". NCM is used for non-static
procedures to be entered into the dispatch table and ncm for all other
non-static procedures. Note that the chosen prefix should probably start
with "nc" or "NC" in order to avoid name conflicts outside the netcdf-c library.
## Extend include/netcdf.h
Modify the file *include/netcdf.h* to add an NC_FORMATX_XXX flag
by adding a flag for this dispatch format at the appropriate places.
````
#define NC_FORMATX_NCM 7
````
Add any format specific new error codes.
````
#define NC_ENCM (?)
````
## Extend include/ncdispatch.h
Modify the file *include/ncdispatch.h* to
add format specific data and initialization functions;
note the use of our NCM namespace.
````
#ifdef ENABLE_NCM
extern NC_Dispatch* NCM_dispatch_table;
extern int NCM_initialize(void);
#endif
````
## Define the dispatch table functions
Define the functions necessary to fill in the dispatch table. As a
rule, we assume that a new directory is defined, *libsrcm*, say. Within
this directory, we need to define *Makefile.am* and *CMakeLists.txt*.
We also need to define the source files
containing the dispatch table and the functions to be placed in the
dispatch table -– call them *ncmdispatch.c* and *ncmdispatch.h*. Look at
*libsrc/nc3dispatch.[ch]* or *libnczarr/zdispatch.[ch]* for examples.
Similarly, it is best to take existing *Makefile.am* and *CMakeLists.txt*
files (from *libsrcp* for example) and modify them.
## Adding the dispatch code to libnetcdf
Provide for the inclusion of this library in the final libnetcdf
library. This is accomplished by modifying *liblib/Makefile.am* by
adding something like the following.
````
if ENABLE_NCM
libnetcdf_la_LIBADD += $(top_builddir)/libsrcm/libnetcdfm.la
endif
````
## Extend library initialization
Modify the *NC_initialize* function in *liblib/nc_initialize.c* by adding
appropriate references to the NCM dispatch function.
````
#ifdef ENABLE_NCM
extern int NCM_initialize(void);
#endif
...
int NC_initialize(void)
{
...
#ifdef ENABLE_NCM
if((stat = NCM_initialize())) return stat;
#endif
...
}
````
Finalization is handled in an analogous fashion.
## Testing the new dispatch table
Add a directory of tests: *ncm_test*, say. The file *ncm_test/Makefile.am*
will look something like this.
````
# These files are created by the tests.
CLEANFILES = ...
# These are the tests which are always run.
TESTPROGRAMS = test1 test2 ...
test1_SOURCES = test1.c ...
...
# Set up the tests.
check_PROGRAMS = $(TESTPROGRAMS)
TESTS = $(TESTPROGRAMS)
# Any extra files required by the tests
EXTRA_DIST = ...
````
# Top-Level build of the dispatch code
Provide for *libnetcdfm* to be constructed by adding the following to
the top-level *Makefile.am*.
````
if ENABLE_NCM
NCM=libsrcm
NCMTESTDIR=ncm_test
endif
...
SUBDIRS = ... $(DISPATCHDIR) $(NCM) ... $(NCMTESTDIR)
````
# Choosing a Dispatch Table
The dispatch table is ultimately chosen by the function
NC_infermodel() in libdispatch/dinfermodel.c. This function is
invoked by the NC_create and the NC_open procedures. This can
be, unfortunately, a complex process. The detailed operation of
NC_infermodel() is defined in the companion document in docs/dinternal.md.
In any case, the choice of dispatch table is currently based on the following
pieces of information.
1. The mode argument – this can be used to detect, for example, what kind
of file to create: netcdf-3, netcdf-4, 64-bit netcdf-3, etc.
Using a mode flag is the most common mechanism, in which case
*netcdf.h* needs to be modified to define the relevant mode flag.
2. The file path – this can be used to detect, for example, a DAP url
versus a normal file system file. If the path looks like a URL, then
the fragment part of the URL is examined to determine the specific
dispatch function.
3. The file contents - when the contents of a real file are available,
the contents of the file can be used to determine the dispatch table.
As a rule, this is likely to be useful only for *nc_open*.
4. If the file is being opened vs being created.
5. Is parallel IO available?
The *NC_infermodel* function returns two values.
1. model - this is used by nc_open and nc_create to choose the dispatch table.
2. newpath - in some case, usually URLS, the path may be rewritten to include extra information for use by the dispatch functions.
# Special Dispatch Table Signatures.
The entries in the dispatch table do not necessarily correspond
to the external API. In many cases, multiple related API functions
are merged into a single dispatch table entry.
## Create/Open
The create table entry and the open table entry in the dispatch table
have the following signatures respectively.
````
int (*create)(const char *path, int cmode,
size_t initialsz, int basepe, size_t *chunksizehintp,
int useparallel, void* parameters,
struct NC_Dispatch* table, NC* ncp);
int (*open)(const char *path, int mode,
int basepe, size_t *chunksizehintp,
int use_parallel, void* parameters,
struct NC_Dispatch* table, NC* ncp);
````
The key difference is that these are the union of all the possible
create/open signatures from the include/netcdfXXX.h files. Note especially the last
three parameters. The parameters argument is a pointer to arbitrary data
to provide extra info to the dispatcher.
The table argument is included in case the create
function (e.g. *NCM_create_) needs to invoke other dispatch
functions. The very last argument, ncp, is a pointer to an NC
instance. The raw NC instance will have been created by *libdispatch/dfile.c*
and is passed to e.g. open with the expectation that it will be filled in
by the dispatch open function.
## Accessing Data with put_vara() and get_vara()
````
int (*put_vara)(int ncid, int varid, const size_t *start, const size_t *count,
const void *value, nc_type memtype);
````
````
int (*get_vara)(int ncid, int varid, const size_t *start, const size_t *count,
void *value, nc_type memtype);
````
Most of the parameters are similar to the netcdf API parameters. The
last parameter, however, is the type of the data in
memory. Additionally, instead of using an "int islong" parameter, the
memtype will be either ::NC_INT or ::NC_INT64, depending on the value
of sizeof(long). This means that even netcdf-3 code must be prepared
to encounter the ::NC_INT64 type.
## Accessing Attributes with put_attr() and get_attr()
````
int (*get_att)(int ncid, int varid, const char *name,
void *value, nc_type memtype);
````
````
int (*put_att)(int ncid, int varid, const char *name, nc_type datatype, size_t len,
const void *value, nc_type memtype);
````
Again, the key difference is the memtype parameter. As with
put/get_vara, it used ::NC_INT64 to encode the long case.
## Pre-defined Dispatch Functions
It is sometimes not necessary to implement all the functions in the
dispatch table. Some pre-defined functions are available which may be
used in many cases.
## Inquiry Functions
Many of The netCDF inquiry functions operate from an in-memory model of
metadata. Once a file is opened, or a file is created, this
in-memory metadata model is kept up to date. Consequenty the inquiry
functions do not depend on the dispatch layer code. These functions
can be used by all dispatch layers which use the internal netCDF
enhanced data model.
- NC4_inq
- NC4_inq_type
- NC4_inq_dimid
- NC4_inq_dim
- NC4_inq_unlimdim
- NC4_inq_att
- NC4_inq_attid
- NC4_inq_attname
- NC4_get_att
- NC4_inq_varid
- NC4_inq_var_all
- NC4_show_metadata
- NC4_inq_unlimdims
- NC4_inq_ncid
- NC4_inq_grps
- NC4_inq_grpname
- NC4_inq_grpname_full
- NC4_inq_grp_parent
- NC4_inq_grp_full_ncid
- NC4_inq_varids
- NC4_inq_dimids
- NC4_inq_typeids
- NC4_inq_type_equal
- NC4_inq_user_type
- NC4_inq_typeid
## NCDEFAULT get/put Functions
The mapped (varm) get/put functions have been
implemented in terms of the array (vara) functions. So dispatch layers
need only implement the vara functions, and can use the following
functions to get the and varm functions:
- NCDEFAULT_get_varm
- NCDEFAULT_put_varm
For the netcdf-3 format, the strided functions (nc_get/put_vars)
are similarly implemented in terms of the vara functions. So the following
convenience functions are available.
- NCDEFAULT_get_vars
- NCDEFAULT_put_vars
For the netcdf-4 format, the vars functions actually exist, so
the default vars functions are not used.
## Read-Only Functions
Some dispatch layers are read-only (ex. HDF4). Any function which
writes to a file, including nc_create(), needs to return error code
::NC_EPERM. The following read-only functions are available so that
these don't have to be re-implemented in each read-only dispatch layer:
- NC_RO_create
- NC_RO_redef
- NC_RO__enddef
- NC_RO_sync
- NC_RO_set_fill
- NC_RO_def_dim
- NC_RO_rename_dim
- NC_RO_rename_att
- NC_RO_del_att
- NC_RO_put_att
- NC_RO_def_var
- NC_RO_rename_var
- NC_RO_put_vara
- NC_RO_def_var_fill
## Classic NetCDF Only Functions
There are two functions that are only used in the classic code. All
other dispatch layers (except PnetCDF) return error ::NC_ENOTNC3 for
these functions. The following functions are provided for this
purpose:
- NOTNC3_inq_base_pe
- NOTNC3_set_base_pe
# HDF4 Dispatch Layer as a Simple Example
The HDF4 dispatch layer is about the simplest possible dispatch
layer. It is read-only, classic model. It will serve as a nice, simple
example of a dispatch layer.
Note that the HDF4 layer is optional in the netCDF build. Not all
users will have HDF4 installed, and those users will not build with
the HDF4 dispatch layer enabled. For this reason HDF4 code is guarded
as follows.
````
#ifdef USE_HDF4
...
#endif /*USE_HDF4*/
````
Code in libhdf4 is only compiled if HDF4 is
turned on in the build.
### The netcdf.h File
In the main netcdf.h file, we have the following:
````
#define NC_FORMATX_NC_HDF4 (3)
````
### The ncdispatch.h File
In ncdispatch.h we have the following:
````
#ifdef USE_HDF4
extern NC_Dispatch* HDF4_dispatch_table;
extern int HDF4_initialize(void);
extern int HDF4_finalize(void);
#endif
````
### The netcdf_meta.h File
The netcdf_meta.h file allows for easy determination of what features
are in use. For HDF4, It contains the following, set by configure:
````
...
#define NC_HAS_HDF4 0 /*!< HDF4 support. */
...
````
### The hdf4dispatch.h File
The file *hdf4dispatch.h* contains prototypes and
macro definitions used within the HDF4 code in libhdf4. This include
file should not be used anywhere except in libhdf4.
### Initialization Code Changes in liblib Directory
The file *nc_initialize.c* is modified to include the following:
````
#ifdef USE_HDF4
extern int HDF4_initialize(void);
extern int HDF4_finalize(void);
#endif
````
### Changes to libdispatch/dfile.c
In order for a dispatch layer to be used, it must be correctly
determined in functions *NC_open()* or *NC_create()* in *libdispatch/dfile.c*.
HDF4 has a magic number that is detected in
*NC_interpret_magic_number()*, which allows *NC_open* to automatically
detect an HDF4 file.
Once HDF4 is detected, the *model* variable is set to *NC_FORMATX_NC_HDF4*,
and later this is used in a case statement:
````
case NC_FORMATX_NC_HDF4:
dispatcher = HDF4_dispatch_table;
break;
````
This sets the dispatcher to the HDF4 dispatcher, which is defined in
the libhdf4 directory.
### Dispatch Table in libhdf4/hdf4dispatch.c
The file *hdf4dispatch.c* contains the definition of the HDF4 dispatch
table. It looks like this:
````
/* This is the dispatch object that holds pointers to all the
* functions that make up the HDF4 dispatch interface. */
static NC_Dispatch HDF4_dispatcher = {
NC_FORMATX_NC_HDF4,
NC_DISPATCH_VERSION,
NC_RO_create,
NC_HDF4_open,
NC_RO_redef,
NC_RO__enddef,
NC_RO_sync,
...
NC_NOTNC4_set_var_chunk_cache,
NC_NOTNC4_get_var_chunk_cache,
...
};
````
Note that most functions use some of the predefined dispatch
functions. Functions that start with NC_RO* are read-only, they return
::NC_EPERM. Functions that start with NOTNC4* return ::NC_ENOTNC4.
Only the functions that start with NC_HDF4* need to be implemented for
the HDF4 dispatch layer. There are 6 such functions:
- NC_HDF4_open
- NC_HDF4_abort
- NC_HDF4_close
- NC_HDF4_inq_format
- NC_HDF4_inq_format_extended
- NC_HDF4_get_vara
### HDF4 Reading Code
The code in *hdf4file.c* opens the HDF4 SD dataset, and reads the
metadata. This metadata is stored in the netCDF internal metadata
model, allowing the inq functions to work.
The code in *hdf4var.c* does an *nc_get_vara()* on the HDF4 SD
dataset. This is all that is needed for all the nc_get_* functions to
work.
# Point of Contact {#filters_poc}
*Author*: Dennis Heimbigner<br>
*Email*: dmh at ucar dot edu<br>
*Initial Version*: 12/22/2021<br>
*Last Revised*: 12/22/2021

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Notes On the Internals of the NetCDF-C Library
============================
<!-- double header is needed to workaround doxygen bug -->
# Notes On the Internals of the NetCDF-C Library {#intern_head}
\tableofcontents
This document attempts to record important information about
the internal architecture and operation of the netcdf-c library.
# 1. Including C++ Code in the netcdf-c Library {#intern_c++}
The state of C compiler technology has reached the point where
it is possible to include C++ code into the netcdf-c library
code base. Two examples are:
1. The AWS S3 SDK wrapper *libdispatch/ncs3sdk.cpp* file.
2. The TinyXML wrapper *ncxml\_tinyxml2.cpp* file.
However there are some consequences that must be handled for this to work.
Specifically, the compiler must be told that the C++ runtime is needed
in the following ways.
## Modifications to *lib\_flags.am*
Suppose we have a flag *ENABLE\_XXX* where that XXX
feature entails using C++ code. Then the following must be added
to *lib\_flags.am*
````
if ENABLE_XXX
AM_LDFLAGS += -lstdc++
endif
````
## Modifications to *libxxx/Makefile.am*
The Makefile in which the C++ code is included and compiled
(assumed here to be the *libxxx* directory) must have this set.
````
AM_CXXFLAGS = -std=c++11
````
It is possible that other values (e.g. *-std=c++14*) may also work.
# 2. Managing instances of complex data types
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.
The term complex type refers to any type that directly or
recursively 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.
Two deep walking operations are provided by the netcdf-c library
to aid in managing instances of complex structures.
* free'ing an instance of the complex type
* copying an instance of the complex type.
Previously The netcdf-c library only did shallow free and shallow copy of
complex types. This meant that only the top level was properly
free'd or copied, but deep internal blocks in the instance were
not touched. This led to a host of memory leaks and failures
when the deep data was effectively shared between the netcdf-c library
internally and the user's data.
Note that the term "vector" is 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. Note that computing the size of the vector
may be tricky because the strides must be taken into account.
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. They are marked in the description as
deprecated in favor of the newer recursive function.
## nc\_put\_vars
Suppose one is writing a vector of instances using nc\_put\_vars
(or nc\_put\_vara or nc\_put\_var, etc.). These functions will
write the contents of the vector to the specified variable.
Note that internally, the data passed to the nc\_put\_xxx function is
immediately written so there is no need to copy it internally. But the
caller may need to reclaim the vector of data that was created and passed
in to the nc\_put\_xxx function.
After writing this vector of instances, and assuming it was dynamically
created, at some point it will be necessary to reclaim that data.
So again, the recursive reclaim function can be used
to walk the returned instance vector and do a deep reclaim of
the data.
## 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. Note that this copying behavior is different from
writing to a variable, where the data is written immediately.
Again, the code inside the netcdf library used to use only shallow copying
rather than deep copy. As a result, one saw 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() as in the
nc\_put\_xxx functions (previously described).
## 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 used to only do shallow copying
rather than deep copy. So this could lead to memory leaks and errors
because the deep data was shared between the library and the user.
## New Instance Walking API
Proper recursive functions were added to the netcdf-c library to
provide reclaim and copy functions and use those as needed.
These 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. This 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 the bugs are found and fixed, all this code will be removed.
## Optimizations
In order to make these functions as efficient as possible, it is
desirable to classify all types as to whether or not they contain
variable-size data. If a type is fixed sized (i.e. does not contain
variable-size data) then it can be freed or copied as a single chunk.
This significantly increases the performance for such types.
For variable-size types, it is necessary to walk each instance of the type
and recursively reclaim or copy it. As another optimization,
if the type is a vector of strings, then the per-instance walk can be
sped up by doing the reclaim or copy inline.
The rules for classifying types as fixed or variable size are as follows.
1. All atomic types, except string, are fixed size.
2. All enum type and opaque types are fixed size.
3. All string types and VLEN types are variable size.
4. A compound type is fixed size if all of the types of its
fields are fixed size. Otherwise it has variable size.
The classification of types can be made at the time the type is defined
or is read in from some existing file. The reclaim and copy functions
use this information to speed up the handling of fixed size types.
# Warnings
1. The new API functions require that the type information be
accessible. This means that you cannot use these functions
after the file has been closed. After the file is closed, you
are on your own.
2. There is still one known failure that has not been solved; it is
possibly an HDF5 memory leak. 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}, _ ;
}
````
# 3. Inferring File Types
As described in the companion document -- docs/dispatch.md --
when nc\_create() or nc\_open() is called, it must figure out what
kind of file is being created or opened. Once it has figured out
the file kind, the appropriate "dispatch table" can be used
to process that file.
## The Role of URLs
Figuring out the kind of file is referred to as model inference
and is, unfortunately, a complicated process. The complication
is mostly a result of allowing a path argument to be a URL.
Inferring the file kind from a URL requires deep processing of
the URL structure: the protocol, the host, the path, and the fragment
parts in particular. The query part is currently not used because
it usually contains information to be processed by the server
receiving the URL.
The "fragment" part of the URL may be unfamiliar.
The last part of a URL may optionally contain a fragment, which
is syntactically of this form in this pseudo URL specification.
````
<protocol>://<host>/<path>?<query>#<fragment>
````
The form of the fragment is similar to a query and takes this general form.
````
'#'<key>=<value>&<key>=<value>&...
````
The key is a simple name, the value is any sequence of characters,
although URL special characters such as '&' must be URL encoded in
the '%XX' form where each X is a hexadecimal digit.
An example might look like this non-sensical example:
````
https://host.com/path#mode=nczarr,s3&bytes
````
It is important to note that the fragment part is not intended to be
passed to the server, but rather is processed by the client program.
It is this property that allows the netcdf-c library to use it to
pass information deep into the dispatch table code that is processing the
URL.
## Model Inference Inputs
The inference algorithm is given the following information
from which it must determine the kind of file being accessed.
### Mode
The mode is a set of flags that are passed as the second
argument to nc\_create and nc\_open. The set of flags is define in
the netcdf.h header file. Generally it specifies the general
format of the file: netcdf-3 (classic) or netcdf-4 (enhanced).
Variants of these can also be specified, e.g. 64-bit netcdf-3 or
classic netcdf-4.
In the case where the path argument is a simple file path,
using a mode flag is the most common mechanism for specifying
the model.
### Path
The file path, the first argument to nc\_create and nc\_open,
Can be either a simple file path or a URL.
If it is a URL, then it will be deeply inspected to determine
the model.
### File Contents
When the contents of a real file are available,
the contents of the file can be used to determine the dispatch table.
As a rule, this is likely to be useful only for *nc\_open*.
It also requires access to functions that can open and read at least
the initial part of the file.
As a rule, the initial small prefix of the file is read
and examined to see if it matches any of the so-called
"magic numbers" that indicate the kind of file being read.
### Open vs Create
Is the file being opened or is it being created?
### Parallelism
Is parallel IO available?
## Model Inference Outputs
The inferencing algorithm outputs two pieces of information.
1. model - this is used by nc\_open and nc\_create to choose the dispatch table.
2. newpath - in some case, usually URLS, the path may be rewritten to include extra information for use by the dispatch functions.
The model output is actually a struct containing two fields:
1. implementation - this is a value from the NC\_FORMATX\_xxx
values in netcdf.h. It generally determines the dispatch
table to use.
2. format -- this is an NC\_FORMAT\_xxx value defining, in effect,
the netcdf-format to which the underlying format is to be
translated. Thus it can tell the netcdf-3 dispatcher that it
should actually implement CDF5 rather than standard netcdf classic.
## The Inference Algorithm
The construction of the model is primarily carried out by the function
*NC\_infermodel()* (in *libdispatch/dinfermodel.c).
It is given the following parameters:
1. path -- (IN) absolute file path or URL
2. modep -- (IN/OUT) the set of mode flags given to *NC\_open* or *NC\_create*.
3. iscreate -- (IN) distinguish open from create.
4. useparallel -- (IN) indicate if parallel IO can be used.
5. params -- (IN/OUT) arbitrary data dependent on the mode and path.
6. model -- (IN/OUT) place to store inferred model.
7. newpathp -- (OUT) the canonical rewrite of the path argument.
As a rule, these values are used in the this order of preference
to infer the model.
1. file contents -- highest precedence
2. url (if it is one) -- using the "mode=" key in the fragment (see below).
3. mode flags
4. default format -- lowest precedence
The sequence of steps is as follows.
### URL processing -- processuri()
If the path appears to be a URL, then it is parsed
and processed by the processuri function as follows.
1. Protocol --
The protocol is extracted and tested against the list of
legal protocols. If not found, then it is an error.
If found, then it is replaced by a substitute -- if specified.
So, for example, the protocol "dods" is replaced the protocol "http"
(note that at some point "http" will be replaced with "https").
Additionally, one or more "key=value" strings is appended
to the existing fragment of the url. So, again for "dods",
the fragment is extended by the string "mode=dap2".
Thus replacing "dods" does not lose information, but rather transfers
it to the fragment for later use.
2. Fragment --
After the protocol is processed, the initial fragment processing occurs
by converting it to a list data structure of the form
````
{<key>,<value>,<key>,<value>,<key>,<value>....}
````
### Macro Processing -- processmacros()
If the fragment list produced by processuri() is non-empty, then
it is processed for "macros". Notice that if the original path
was not a URL, then the fragment list is empty and this
processing will be bypassed. In any case, It is convenient to
allow some singleton fragment keys to be expanded into larger
fragment components. In effect, those singletons act as
macros. They can help to simplify the user's URL. The term
singleton means a fragment key with no associated value:
"#bytes", for example.
The list of fragments is searched looking for keys whose
value part is NULL or the empty string. Then the table
of macros is searched for that key and if found, then
a key and values is appended to the fragment list and the singleton
is removed.
### Mode Inference -- processinferences()
This function just processes the list of values associated
with the "mode" key. It is similar to a macro in that
certain mode values are added or removed based on tables
of "inferences" and "negations".
Again, the purpose is to allow users to provide simplified URL fragments.
The list of mode values is repeatedly searched and whenever a value
is found that is in the "modeinferences" table, then the associated inference value
is appended to the list of mode values. This process stops when no changes
occur. This form of inference allows the user to specify "mode=zarr"
and have it converted to "mode=nczarr,zarr". This avoids the need for the
dispatch table code to do the same inference.
After the inferences are made, The list of mode values is again
repeatedly searched and whenever a value
is found that is in the "modenegations" table, then the associated negation value
is removed from the list of mode values, assuming it is there. This process stops when no changes
occur. This form of inference allows the user to make sure that "mode=bytes,nczarr"
has the bytes mode take precedence by removing the "nczarr" value. Such illegal
combinations can occur because of previous processing steps.
### Fragment List Normalization
As the fragment list is processed, duplicates appear with the same key.
A function -- cleanfragments() -- is applied to clean up the fragment list
by coalesing the values of duplicate keys and removing duplicate key values.
### S3 Rebuild
If the URL is determined to be a reference to a resource on the Amazon S3 cloud,
then the URL needs to be converted to what is called "path format".
There are four S3 URL formats:
1. Virtual -- ````https://<bucket>.s3.<region>.amazonaws.com/<path>````
2. Path -- ````https://s3.<region>.amazonaws.com/<bucket>/<path>````
3. S3 -- ````s3://<bucket>/<path>````
4. Other -- ````https://<host>/<bucket>/<path>````
The S3 processing converts all of these to the Path format. In the "S3" format case
it is necessary to find or default the region from examining the ".aws" directory files.
### File Rebuild
If the URL protocol is "file" and its path is a relative file path,
then it is made absolute by prepending the path of the current working directory.
In any case, after S3 or File rebuilds, the URL is completely
rebuilt using any modified protocol, host, path, and
fragments. The query is left unchanged in the current algorithm.
The resulting rebuilt URL is passed back to the caller.
### Mode Key Processing
The set of values of the fragment's "mode" key are processed one by one
to see if it is possible to determine the model.
There is a table for format interpretations that maps a mode value
to the model's implementation and format. So for example,
if the mode value "dap2" is encountered, then the model
implementation is set to NC\_FORMATX\_DAP2 and the format
is set to NC\_FORMAT\_CLASSIC.
### Non-Mode Key Processing
If processing the mode does not tell us the implementation, then
all other fragment keys are processed to see if the implementaton
(and format) can be deduced. Currently this does nothing.
### URL Defaults
If the model is still not determined and the path is a URL, then
the implementation is defaulted to DAP2. This is for back
compatibility when all URLS implied DAP2.
### Mode Flags
In the event that the path is not a URL, then it is necessary
to use the mode flags and the isparallel arguments to choose a model.
This is just a straight forward flag checking exercise.
### Content Inference -- check\_file\_type()
If the path is being opened (as opposed to created), then
it may be possible to actually read the first few bytes of the
resource specified by the path and use that to determine the
model. If this succeeds, then it takes precedence over
all other model inferences.
### Flag Consistency
Once the model is known, then the set of mode flags
is modified to be consistent with that information.
So for example, if DAP2 is the model, then all netcdf-4 mode flags
and some netcdf-3 flags are removed from the set of mode flags
because DAP2 provides only a standard netcdf-classic format.
# 4. Adding a Standard Filter
The standard filter system extends the netcdf-c library API to
support a fixed set of "standard" filters. This is similar to the
way that deflate and szip are currently supported.
For background, the file filter.md should be consulted.
In general, the API for a standard filter has the following prototypes.
The case of zstandard (libzstd) is used as an example.
````
int nc_def_var_zstandard(int ncid, int varid, int level);
int nc_inq_var_zstandard(int ncid, int varid, int* has_filterp, int* levelp);
````
So generally the API has the ncid and the varid as fixed, and then
a list of parameters specific to the filter -- level in this case.
For the inquire function, there is an additional argument -- has_filterp --
that is set to 1 if the filter is defined for the given variable
and is 0 if not.
The remainder of the inquiry parameters are pointers to memory
into which the parameters are stored -- levelp in this case.
It is important to note that including a standard filter still
requires three supporting objects:
1. The implementing library for the filter. For example,
libzstd must be installed in order to use the zstandard
API.
2. A HDF5 wrapper for the filter must be installed in the
directory pointed to by the HDF5_PLUGIN_PATH environment
variable.
3. (Optional) An NCZarr Codec implementation must be installed
in the the HDF5_PLUGIN_PATH directory.
## Adding a New Standard Filter
The implementation of a standard filter must be loaded from one
of several locations.
1. It can be part of libnetcdf.so (preferred),
2. it can be loaded as part of the client code,
3. or it can be loaded as part of an external library such as libccr.
However, the three objects listed above need to be
stored in the HDF5_PLUGIN_DIR directory, so adding a standard
filter still requires modification to the netcdf build system.
This limitation may be lifted in the future.
### Build Changes
In order to detect a standard library, the following changes
must be made for Automake (configure.ac/Makefile.am)
and CMake (CMakeLists.txt)
#### Configure.ac
Configure.ac must have a block that similar to this that locates
the implementing library.
````
# See if we have libzstd
AC_CHECK_LIB([zstd],[ZSTD_compress],[have_zstd=yes],[have_zstd=no])
if test "x$have_zstd" = "xyes" ; then
AC_SEARCH_LIBS([ZSTD_compress],[zstd zstd.dll cygzstd.dll], [], [])
AC_DEFINE([HAVE_ZSTD], [1], [if true, zstd library is available])
fi
AC_MSG_CHECKING([whether libzstd library is available])
AC_MSG_RESULT([${have_zstd}])
````
Note the the entry point (*ZSTD_compress*) is library dependent
and is used to see if the library is available.
#### Makefile.am
It is assumed you have an HDF5 wrapper for zstd. If you want it
to be built as part of the netcdf-c library then you need to
add the following to *netcdf-c/plugins/Makefile.am*.
````
if HAVE_ZSTD
noinst_LTLIBRARIES += libh5zstd.la
libh5szip_la_SOURCES = H5Zzstd.c H5Zzstd.h
endif
````
# Need our version of szip if libsz available and we are not using HDF5
if HAVE_SZ
noinst_LTLIBRARIES += libh5szip.la
libh5szip_la_SOURCES = H5Zszip.c H5Zszip.h
endif
#### CMakeLists.txt
In an analog to *configure.ac*, a block like
this needs to be in *netcdf-c/CMakeLists.txt*.
````
FIND_PACKAGE(Zstd)
set_std_filter(Zstd)
````
The FIND_PACKAGE requires a CMake module for the filter
in the cmake/modules directory.
The *set_std_filter* function is a macro.
An entry in the file config.h.cmake.in will also be needed.
````
/* Define to 1 if zstd library available. */
#cmakedefine HAVE_ZSTD 1
````
### Implementation Template
As a template, here is the implementation for zstandard.
It can be used as the template for adding other standard filters.
It is currently located in *netcdf-d/libdispatch/dfilter.c*, but
could be anywhere as indicated above.
````
#ifdef HAVE_ZSTD
int
nc_def_var_zstandard(int ncid, int varid, int level)
{
int stat = NC_NOERR;
unsigned ulevel;
if((stat = nc_inq_filter_avail(ncid,H5Z_FILTER_ZSTD))) goto done;
/* Filter is available */
/* Level must be between -131072 and 22 on Zstandard v. 1.4.5 (~202009)
Earlier versions have fewer levels (especially fewer negative levels) */
if (level < -131072 || level > 22)
return NC_EINVAL;
ulevel = (unsigned) level; /* Keep bit pattern */
if((stat = nc_def_var_filter(ncid,varid,H5Z_FILTER_ZSTD,1,&ulevel))) goto done;
done:
return stat;
}
int
nc_inq_var_zstandard(int ncid, int varid, int* hasfilterp, int *levelp)
{
int stat = NC_NOERR;
size_t nparams;
unsigned params = 0;
int hasfilter = 0;
if((stat = nc_inq_filter_avail(ncid,H5Z_FILTER_ZSTD))) goto done;
/* Filter is available */
/* Get filter info */
stat = nc_inq_var_filter_info(ncid,varid,H5Z_FILTER_ZSTD,&nparams,NULL);
if(stat == NC_ENOFILTER) {stat = NC_NOERR; hasfilter = 0; goto done;}
if(stat != NC_NOERR) goto done;
hasfilter = 1;
if(nparams != 1) {stat = NC_EFILTER; goto done;}
if((stat = nc_inq_var_filter_info(ncid,varid,H5Z_FILTER_ZSTD,&nparams,&params))) goto done;
done:
if(levelp) *levelp = (int)params;
if(hasfilterp) *hasfilterp = hasfilter;
return stat;
}
#endif /*HAVE_ZSTD*/
````
# Point of Contact {#intern_poc}
*Author*: Dennis Heimbigner<br>
*Email*: dmh at ucar dot edu<br>
*Initial Version*: 12/22/2021<br>
*Last Revised*: 01/25/2022