Filter support has three goals:
1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled
Detailed usage directions are define in docs/filters.md.
For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.
This is a big change since filters affect many parts of the code.
In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.
### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.
### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.
### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
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.
Primary fixes to get -ansi to work.
1. Convert all '//' C++ style comments to /*...*/ or to use #if 0...#endif
2. It turns out that when -ansi is specified, then a number of
functions no longer are defined in the header -- but they are still
in the .so file.<br>
The big example is strdup(). So, added code to include/ncconfig.h to define
externs for those missing functions that occur in more than one place.
These are enabled if !_WIN32 && __STDC__ == 1 (__STDC__ is supposed to
be the equivalent compile time flag to -ansi). Note that this requires
config.h (which references ncconfig.h) to be included in files where it is
currently not included. Single uses will be only in the file that uses them.
3. Added mmap test for the MAP_ANONYMOUS flag to configure.ac. Apparently
this is not always defined with -ansi.
4. fix some large integer constants in nc_test4/tst_atts3.c and nc_test4/tst_filterparser.c
to avoid compiler complaints.
5. fix a double constant in nc_test4/tst_filterparser.c to avoid compiler complaints.
[Note I suspect #4 and #5 will be a problem on big-endian machines, but we have no way to test]
Misc. Changes:
1. convert more instances of _MSC_VER to _WIN32.
2. added some debugging code to include/nctestserver.h
3. added comment about libdispatch/drc.c always being compiled.
4. modify parser generation in ncgen to remove unneeded files.
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173
Sorry that it is so big, but leak suppression can be complex.
This PR fixes all remaining memory leaks -- as determined by
-fsanitize=address, and with the exceptions noted below.
Unfortunately. there remains a significant leak that I cannot
solve. It involves vlens, and it is unclear if the leak is
occurring in the netcdf-c library or the HDF5 library.
I have added a check_PROGRAM to the ncdump directory to show the
problem. The program is called tst_vlen_demo.c To exercise it,
build the netcdf library with -fsanitize=address enabled. Then
go into ncdump and do a "make clean check". This should build
tst_vlen_demo without actually executing it. Then do the
command "./tst_vlen_demo" to see the output of the memory
checker. Note the the lost malloc is deep in the HDF5 library
(in H5Tvlen.c).
I am temporarily working around this error in the following way.
1. I modified several test scripts to not execute known vlen tests
that fail as described above.
2. Added an environment variable called NC_VLEN_NOTEST.
If set, then those specific tests are suppressed.
This should mean that the --disable-utilities option to
./configure should not need to be set to get a memory leak clean
build. This should allow for detection of any new leaks.
Note: I used an environment variable rather than a ./configure
option to control the vlen tests. This is because it is
temporary (I hope) and because it is a bit tricky for shell
scripts to access ./configure options.
Finally, as before, this only been tested with netcdf-4 and hdf5 support.
This consists of a persistent attribute named
_NCProperties plus two computed attributes
_IsNetcdf4 and _SuperblockVersion.
See the 'Provenance Attributes' section
of docs/attribute_conventions.md for details.
The code for handling character constants
in datalists in ncgen has some problems.
1. It failed on large constants
2. It did not handle e.g. var = 'a', 'b', ...
in the same way that ncgen3 did.
3. The code for generate.c and genchar.c needed
some refactoring to make it a little simpler
(but not simple).
should be under ENABLE_DAP_REMOTE_TESTS.
Fixed to make sure that this is so.
Also attempted to fix ncdap_test/CMakeLists.txt,
but probably got it wrong.
HT to Nico Schlomer.
2. Attempted to reduce the number of conversion errors
when -Wconversion is set. Fixed oc2, but
rest of netcdf remains to be done.
HT to Nico Schlomer.
3. When doing #2, I discovered an error in ncgen.y
that has remained hidden. This required some other
test case fixes.
Ncgen is unable to resolve
ambiguous references to an enum
constant when two different enums
have same econstant name.
Solved by allowing more specific
forms for econstant references.
1. /.../enumname.enumconstname
2. enumname.enumconstname
3. enumconstname
Case 1 is resolved by using the econstant
in the specific enum definition. If none is
found, an error is reported.
Case 2 is resolved by
1. finding an enclosing group with an
enum definition with the specified name
and containing the specified econstant.
If there are more than one, then an error is reported
2. finding all enum definitions in the dataset that have
the specified enum name and contain the specified
econstant. If more than one is found, then an error is reported.
If the above two methods fail, then report an error.
Case 3 is similar to case 2, but all enums, irrespective
of name are used if they contains the specified enum constant.
The ref_tst_econst.cdl test in ncdump is causing ncdump
to fail. So there may be yet some problem.
Primarily focused on memory errors falling into a couple different types:
1) Static overrun errors.
2) Dereference uninitialized memory errors.
make distcheck works after applying these fixes, and coverity no longer sees an issue, so hopefully they are properly resolved.
