2018-12-07 06:27:32 +08:00
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# Copyright 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
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# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014,
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2019-03-18 22:09:46 +08:00
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# 2015, 2016, 2017, 2018, 2019
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2018-12-07 06:27:32 +08:00
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# University Corporation for Atmospheric Research/Unidata.
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# See netcdf-c/COPYRIGHT file for more info.
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2019-03-18 22:09:46 +08:00
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# This is the cmake build file for the nc_test4 directory.
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# Ward Fisher, Ed Hartnett
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2021-09-03 07:04:26 +08:00
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SET(srcdir ${CMAKE_CURRENT_SOURCE_DIR})
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2012-08-07 07:07:40 +08:00
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# Some extra tests
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2017-10-26 18:49:57 +08:00
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SET(NC4_TESTS tst_dims tst_dims2 tst_dims3 tst_files tst_files4
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tst_vars tst_varms tst_unlim_vars tst_converts tst_converts2
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tst_grps tst_grps2 tst_compounds tst_compounds2 tst_compounds3
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tst_opaques tst_strings tst_strings2 tst_interops tst_interops4
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2019-11-14 03:51:34 +08:00
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tst_interops6 tst_interops_dims tst_enums tst_coords tst_coords2 tst_coords3 tst_vars3
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2017-10-26 18:49:57 +08:00
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tst_vars4 tst_chunks tst_chunks2 tst_utf8 tst_fills tst_fills2
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tst_fillbug tst_xplatform2 tst_endian_fill tst_atts t_type
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cdm_sea_soundings tst_vl tst_atts1 tst_atts2 tst_vars2 tst_files5
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tst_files6 tst_sync tst_h_strbug tst_h_refs tst_h_scalar tst_rename
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2019-02-02 20:53:45 +08:00
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tst_rename2 tst_rename3 tst_h5_endians tst_atts_string_rewrite tst_put_vars_two_unlim_dim
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2018-04-23 17:19:11 +08:00
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tst_hdf5_file_compat tst_fill_attr_vanish tst_rehash tst_types tst_bug324
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2022-03-15 05:02:02 +08:00
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tst_atts3 tst_put_vars tst_elatefill tst_udf tst_bug1442 tst_broken_files
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2023-03-09 18:11:42 +08:00
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tst_quantize tst_h_transient_types)
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2017-11-14 02:15:02 +08:00
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2022-01-30 06:27:52 +08:00
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IF(HAS_PAR_FILTERS)
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SET(NC4_tests $NC4_TESTS tst_alignment)
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ENDIF()
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2017-11-14 02:15:02 +08:00
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2013-07-21 09:08:39 +08:00
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# Note, renamegroup needs to be compiled before run_grp_rename
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2016-09-01 05:48:10 +08:00
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IF(BUILD_UTILITIES)
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2016-09-01 05:53:34 +08:00
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SET(NC4_TESTS ${NC4_TESTS} tst_xplatform)
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2016-09-01 05:48:10 +08:00
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build_bin_test(renamegroup)
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add_sh_test(nc_test4 run_grp_rename)
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2021-04-17 08:54:35 +08:00
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build_bin_test(tst_charvlenbug)
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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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build_bin_test(tst_vlenstr)
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2016-09-01 05:48:10 +08:00
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ADD_SH_TEST(nc_test4 tst_misc)
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2020-09-13 04:49:59 +08:00
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build_bin_test(tst_fillonly)
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ADD_SH_TEST(nc_test4 test_fillonly)
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2022-07-30 04:47:07 +08:00
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ADD_SH_TEST(nc_test4 tst_fixedstring)
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Enhance/Fix filter support
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.
2022-03-15 02:39:37 +08:00
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IF(USE_HDF5 AND ENABLE_FILTER_TESTING)
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2020-05-11 23:42:31 +08:00
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build_bin_test(tst_filterparser)
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2018-01-17 02:00:09 +08:00
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build_bin_test(test_filter)
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build_bin_test(test_filter_misc)
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2020-02-17 03:59:33 +08:00
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build_bin_test(tst_multifilter)
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build_bin_test(test_filter_order)
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2020-05-11 23:42:31 +08:00
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build_bin_test(test_filter_repeat)
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2023-06-22 04:46:22 +08:00
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build_bin_test(tst_filter_vlen)
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2018-01-17 02:00:09 +08:00
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ADD_SH_TEST(nc_test4 tst_filter)
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2021-09-03 07:04:26 +08:00
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ADD_SH_TEST(nc_test4 tst_specific_filters)
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2022-07-13 05:19:07 +08:00
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ADD_SH_TEST(nc_test4 tst_bloscfail)
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2023-06-22 04:46:22 +08:00
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ADD_SH_TEST(nc_test4 tst_filter_vlen)
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2022-11-16 07:15:32 +08:00
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IF(FALSE)
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# This test is too dangerous to run in a parallel make environment.
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# It causes race conditions. So suppress and only test by hand.
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ADD_SH_TEST(nc_test4 tst_unknown)
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2023-06-22 04:46:22 +08:00
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# The tst_filterinstall test can only be run after an install
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# occurred with --with-plugin-dir enabled. So there is no point
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#in running it via make check. It is kept here so it can be
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# manually invoked if desired
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ADD_SH_TEST(nc_test4 tst_filterinstall)
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2022-11-16 07:15:32 +08:00
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ENDIF(FALSE)
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Enhance/Fix filter support
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.
2022-03-15 02:39:37 +08:00
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ENDIF(USE_HDF5 AND ENABLE_FILTER_TESTING)
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2018-01-24 08:18:53 +08:00
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2016-09-01 05:48:10 +08:00
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ENDIF(BUILD_UTILITIES)
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2013-07-21 09:08:39 +08:00
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2020-09-15 00:06:34 +08:00
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IF(${HDF5_VERSION} VERSION_GREATER "1.10.0")
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SET(NC4_TESTS ${NC4_TESTS} tst_virtual_datasets)
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ENDIF(${HDF5_VERSION} VERSION_GREATER "1.10.0")
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2016-02-20 01:16:42 +08:00
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##
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# The shell script, run_empty_vlen_test.sh,
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# depends on the 'tst_empty_vlen_unlim' binary.
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##
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BUILD_BIN_TEST(tst_empty_vlen_unlim)
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ADD_SH_TEST(nc_test4 run_empty_vlen_test)
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2012-09-15 05:35:25 +08:00
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IF(NOT MSVC)
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2014-04-22 01:15:33 +08:00
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SET(NC4_TESTS ${NC4_TESTS} tst_interops5 tst_camrun)
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2012-09-15 05:35:25 +08:00
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ENDIF()
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2014-04-04 00:45:22 +08:00
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# If the v2 API was built, add the test program.
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IF(ENABLE_V2_API)
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build_bin_test(tst_v2)
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ENDIF()
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2013-02-13 06:22:54 +08:00
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IF(LARGE_FILE_TESTS)
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2014-04-22 01:15:33 +08:00
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SET(NC4_TESTS ${NC4_TESTS} tst_large tst_large2)
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2013-02-13 06:22:54 +08:00
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ENDIF()
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2014-04-22 01:15:33 +08:00
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2013-02-13 06:22:54 +08:00
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Enhance/Fix filter support
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.
2022-03-15 02:39:37 +08:00
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IF(HAVE_H5Z_SZIP)
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2017-08-31 02:06:23 +08:00
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BUILD_BIN_TEST(test_szip)
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BUILD_BIN_TEST(h5testszip)
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IF(BUILD_UTILITIES)
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add_sh_test(nc_test4 tst_szip)
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ENDIF()
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2017-08-28 05:51:45 +08:00
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ENDIF()
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2021-09-03 07:04:26 +08:00
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2012-08-08 04:21:44 +08:00
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# Copy some test files from current source dir to out-of-tree build dir.
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2018-03-05 20:03:46 +08:00
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FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/ref_bzip2.c ${CMAKE_CURRENT_SOURCE_DIR}/*.sh ${CMAKE_CURRENT_SOURCE_DIR}/*.h5 ${CMAKE_CURRENT_SOURCE_DIR}/*.cdl)
|
2012-08-07 07:07:40 +08:00
|
|
|
FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
|
2013-02-22 07:56:15 +08:00
|
|
|
IF(MSVC)
|
2014-04-22 01:15:33 +08:00
|
|
|
FILE(COPY ${COPY_FILES} DESTINATION ${RUNTIME_OUTPUT_DIRECTORY}/)
|
2013-02-22 07:56:15 +08:00
|
|
|
ENDIF()
|
|
|
|
|
|
2013-01-16 06:43:09 +08:00
|
|
|
FOREACH(CTEST ${NC4_TESTS})
|
2012-09-15 05:53:08 +08:00
|
|
|
add_bin_test(nc_test4 ${CTEST})
|
2021-09-03 07:04:26 +08:00
|
|
|
SET_TESTS_PROPERTIES(nc_test4_${CTEST} PROPERTIES ENVIRONMENT srcdir=${CMAKE_CURRENT_SOURCE_DIR})
|
2012-08-07 07:07:40 +08:00
|
|
|
ENDFOREACH()
|
|
|
|
|
|
2016-06-10 03:21:28 +08:00
|
|
|
IF(TEST_PARALLEL4)
|
2014-06-12 05:51:31 +08:00
|
|
|
build_bin_test(tst_mpi_parallel)
|
2014-04-22 01:15:33 +08:00
|
|
|
build_bin_test(tst_parallel)
|
|
|
|
|
build_bin_test(tst_parallel3)
|
|
|
|
|
build_bin_test(tst_parallel4)
|
2018-05-14 22:11:32 +08:00
|
|
|
build_bin_test(tst_parallel5)
|
2022-05-03 00:40:22 +08:00
|
|
|
build_bin_test(tst_parallel6)
|
2019-12-20 00:20:20 +08:00
|
|
|
build_bin_test(tst_parallel_zlib)
|
2020-02-06 08:40:31 +08:00
|
|
|
build_bin_test(tst_parallel_compress)
|
2014-04-22 01:15:33 +08:00
|
|
|
build_bin_test(tst_nc4perf)
|
2016-02-05 03:12:15 +08:00
|
|
|
build_bin_test(tst_mode)
|
2016-06-10 01:26:06 +08:00
|
|
|
build_bin_test(tst_simplerw_coll_r)
|
2021-09-03 00:18:42 +08:00
|
|
|
build_bin_test(tst_quantize_par)
|
2014-04-22 01:15:33 +08:00
|
|
|
add_sh_test(nc_test4 run_par_test)
|
2014-06-12 05:51:31 +08:00
|
|
|
ENDIF()
|
