re: https://github.com/Unidata/netcdf-c/issues/2338
re: https://github.com/Unidata/netcdf-c/issues/2294
In issue https://github.com/Unidata/netcdf-c/issues/2338,
Ed Hartnett suggested a better way to install filters to a user
defined location -- for Automake, anyway.
This PR implements that suggestion. It turns out to be more
complicated than it appears, so there are fair number of changes;
mostly to shell scripts. Most of the change is in plugins/Makefile.am.
NOTE: this PR still does NOT address the use of HDF5_PLUGIN_PATH
as the default; this turns out to be complex when dealing with NCZarr.
So this will be addressed in a subsequent post 4.9.0 PR.
## Misc. Changes
1. Record the occurrences of incomplete codecs in libnczarr so that
they can be included in _Codecs attribute correctly. This allows
users to see what missing filters are referenced in the Zarr file.
Primarily affects libnczarr/zfilter.[ch]. Also required creating a
new no-effect filter: H5Zunknown.c.
2. Move the unknown filter test to a separate test file.
3. Incorporates PR https://github.com/Unidata/netcdf-c/pull/2343
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
re: https://github.com/Unidata/netcdf-c/issues/1836
Revert the internal filter code to simplify it. From the user's
point of view, the only visible changes should be:
1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h
2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter.
Internally,the dispatch table has been modified to get rid of the filter_actions
entry and associated complex structures. It has been replaced with
inq_var_filter_ids and inq_var_filter_info entries and the dispatch table
version has been bumped to 3. Corresponding NOOP and NOTNC4 functions
were added to libdispatch/dnotnc4.c. Also, the filter_action entries
in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2,
etc). This should only impact UDF users.
In the process, it became clear that the form of the filters
field in NC_VAR_INFO_T was format dependent, so I converted it to
be of type void* and pushed its management into the various dispatch
code bases. Specifically libhdf5 and libnczarr now manage the filters
field in their own way.
The auxilliary functions for parsing textual filter specifications
were moved to netcdf_aux.h and were renamed to the following:
* ncaux_h5filterspec_parse
* ncaux_h5filterspec_parselist
* ncaux_h5filterspec_free
* ncaux_h5filter_fix8
Misc. Other Changes:
1. Document NUG/filters.md updated to reflect the changes above.
2. All the old data types (structs and enums)
used by filter_actions actions were deleted.
The exception is the NC_H5_Filterspec because it is needed
by ncaux_h5filterspec_parselist.
3. Clientside filters were removed -- another enhancement
for which no-one ever asked.
4. The ability to remove filters was itself removed.
5. Some functionality needed by nczarr was moved from libhdf5
to libsrc4 e.g. nc4_find_default_chunksizes
6. All the filterx code was removed
7. ncfilter.h and nc4filter.c no longer used
Misc. Unrelated Changes:
1. The nczarr_test makefile clean was leaving some directories; so
add clean-local to take care of them.
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
re: https://github.com/Unidata/netcdf-c/issues/1584
Support has been added for multiple filters per variable. This
affects a number of components in netcdf. The new APIs are
documented in NUG/filters.md.
The primary changes are:
* A set of new functions are provided (see __include/netcdf_filter.h__).
- Obtain a list of the filters associated with a variable
- Obtain the parameters for a specific filter.
* The existing __nc_inq_var_filter__ function now returns info
about the first defined filter.
* The utilities (ncgen, ncdump, and nccopy) now support
an extended format for specifying a sequence of filters.
The general form is __<filter>|<filter>..._.
* The ncdump **_Filter** attribute now dumps a list of all the
filters associated with a variable using the above new format.
* Filter specifications can now use a filter name instead of number
for filters known to the netcdf library, which in turn is taken
from the HDF5 filter registration page.
* New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter
is returned if an attempt is made to access an unknown filter.
* Internally, the dispatch table has been extended to add a function
to handle all of the filter functions.
* New, filter-related, tests were added to nc_test4.
* A new plugin was added to the plugins directory to help with testing.
Notes:
1. The shuffle and fletcher32 filters are not part of the multifilter system.
Misc. changes:
1. A debug module was added to libhdf5 to help catch error locations.
re: https://github.com/Unidata/netcdf-c/issues/1347
It turns out that the plugin libraries (bzip2 and misc) were
being installed as part of 'make installed'. This was not intended
behavior. But after some discussion in the above issue, it was decided
to install the bzip2 plugin. However, in order to avoid naming conflicts,
the plugin is installed under the name 'libh5bzip2.so'.
Note that this is automake behavior only; the install does not
(yet) occur using cmake.
Misc. unrelated changes
-----------------------
1. turn off some debug output in ncdump/Makefile.am
re: issue https://github.com/Unidata/netcdf-c/issues/1156
Starting with HDF5 version 1.10.x, the plugin code MUST be
careful when using the standard *malloc()*, *realloc()*, and
*free()* function.
In the event that the code is allocating, reallocating, or
free'ing memory that either came from -- or will be exported to --
the calling HDF5 library, then one MUST use the corresponding
HDF5 functions *H5allocate_memory()*, *H5resize_memory()*,
*H5free_memory()* [5] to avoid memory failures.
Additionally, if your filter code leaks memory, then the HDF5 library
generates a failure something like this.
````
H5MM.c:232: H5MM_final_sanity_check: Assertion `0 == H5MM_curr_alloc_bytes_s' failed.
````
This PR modifies the code in the plugins directory to
conform to these new requirements.
This raises a question about the libhdf5 code where this
same problem may occur. We need to scan especially nc4hdf.c
to look for this problem.
