The netCDF library supports many versions of HDF5, which handles API
compatibility via a set of API-call-specific macros. netCDF uses
H5Literate(), which was versioned in the 1.12.x maintenance line
in order to better support the virtual object layer (VOL).
h5_test/tst_h_files4.c failed to compile with certain compilers when the
HDF5 library was built using pre-VOL versions of the library- e.g., 1.10,
which can be configured with --with-default-api-version=110. This was due
to the API compatibility macros being used to select the 1.10 version of
H5Literate(), but not its callback function, which was set using a
`H5_VERSION_GE()` macro that does not take the compatibility macros into
consideration.
Fixing the problem involved removing the `H5_VERSION_GE()` macro and
letting the compatibility macros handle the versioning, and using the
`H5_USE_XXX_API_DEFAULT` symbols to protect the H5Oopen_by_addr() call
used in the callback (a new call that wasn't versioned, hence the
different protection mechanism).
Tested w/ HDF5's develop branch w/ both 1.14 and 1.10 API bindings
Fixes#2886 (4118 in HDF5's issue tracker)
Argument 'count' in NetCDF is not exactly the same as the 'count' in
H5Sselect_hyperslabs(space_id, op, start, stride, count, block).
When the argument 'stride' is NULL, NetCDF's 'count' should be used in
argument 'block', for example,
H5Sselect_hyperslabs(space_id, op, start, NULL, ones, count);
where 'one' is an array of all 1s. Although using NULL 'block' below
H5Sselect_hyperslabs(space_id, op, start, NULL, count, NULL);
has the same effect, HDF5 internally stores the space of a subarray as a
list of single elements, instead of a "block", which can affect the
performance.
Mostly just add an explicit cast when calling `malloc` and its
variants. Sometimes instead change the type of a local variable if
this would silence multiple warnings.
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214
The primary change is to support so-called "standard filters".
A standard filter is one that is defined by the following
netcdf-c API:
````
int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params);
int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params);
````
So for example, zstandard would be a standard filter by defining
the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*.
In order to define these functions, we need a new dispatch function:
````
int nc_inq_filter_avail(int ncid, unsigned filterid);
````
This function, combined with the existing filter API can be used
to implement arbitrary standard filters using a simple code pattern.
Note that I would have preferred that this function return a list
of all available filters, but HDF5 does not support that functionality.
So this PR implements the dispatch function and implements
the following standard functions:
+ bzip2
+ zstandard
+ blosc
Specific test cases are also provided for HDF5 and NCZarr.
Over time, other specific standard filters will be defined.
## Primary Changes
* Add nc_inq_filter_avail() to netcdf-c API.
* Add standard filter implementations to test use of *nc_inq_filter_avail*.
* Bump the dispatch table version number and add to all the relevant
dispatch tables (libsrc, libsrcp, etc).
* Create a program to invoke nc_inq_filter_avail so that it is accessible
to shell scripts.
* Cleanup szip support to properly support szip
when HDF5 is disabled. This involves detecting
libsz separately from testing if HDF5 supports szip.
* Integrate shuffle and fletcher32 into the existing
filter API. This means that, for example, nc_def_var_fletcher32
is now a wrapper around nc_def_var_filter.
* Extend the Codec defaulting to allow multiple default shared libraries.
## Misc. Changes
* Modify configure.ac/CMakeLists.txt to look for the relevant
libraries implementing standard filters.
* Modify libnetcdf.settings to list available standard filters
(including deflate and szip).
* Add CMake test modules to locate libbz2 and libzstd.
* Cleanup the HDF5 memory manager function use in the plugins.
* remove unused file include//ncfilter.h
* remove tests for the HDF5 memory operations e.g. H5allocate_memory.
* Add flag to ncdump to force use of _Filter instead of _Deflate
or _Shuffle or _Fletcher32. Used for testing.
