2010-06-03 21:24:43 +08:00
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## This is a automake file, part of Unidata's netCDF package.
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2018-12-07 06:36:53 +08:00
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# Copyright 2018, see the COPYRIGHT file for more information.
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2010-06-03 21:24:43 +08:00
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# This file builds and runs the ncdump program.
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2017-11-23 03:10:58 +08:00
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# Ed Hartnett, Dennis Heimbigner, Ward Fisher
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2010-06-03 21:24:43 +08:00
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2022-04-30 04:38:18 +08:00
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#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
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#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
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#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
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#TESTS_ENVIRONMENT = export SETX=1;
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2018-03-03 07:55:58 +08:00
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2011-03-22 04:31:56 +08:00
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# Put together AM_CPPFLAGS and AM_LDFLAGS.
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include $(top_srcdir)/lib_flags.am
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2014-08-26 04:30:11 +08:00
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LDADD = ${top_builddir}/liblib/libnetcdf.la
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2018-08-02 04:27:09 +08:00
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noinst_PROGRAMS=
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2017-11-17 23:22:49 +08:00
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# Note which tests depend on other tests. Necessary for make -j check.
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TEST_EXTENSIONS = .sh
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2017-11-21 08:26:06 +08:00
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XFAIL_TESTS=""
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2017-11-17 23:22:49 +08:00
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2011-03-22 04:31:56 +08:00
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# This is the program we're building, and it's sources.
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2014-08-26 04:30:11 +08:00
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bin_PROGRAMS = ncdump
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2017-11-12 07:45:03 +08:00
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ncdump_SOURCES = ncdump.c vardata.c dumplib.c indent.c nctime0.c \
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2020-08-18 09:15:47 +08:00
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ncdump.h vardata.h dumplib.h indent.h nctime0.h cdl.h utils.h \
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2017-11-12 07:45:03 +08:00
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utils.c nciter.h nciter.c nccomps.h
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2011-03-22 04:31:56 +08:00
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# Another utility program that copies any netCDF file using only the
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# netCDF API
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bin_PROGRAMS += nccopy
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2017-11-12 07:45:03 +08:00
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nccopy_SOURCES = nccopy.c nciter.c nciter.h chunkspec.h chunkspec.c \
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2018-07-27 10:16:02 +08:00
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utils.h utils.c dimmap.h dimmap.c list.c list.h
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2011-03-22 04:31:56 +08:00
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2019-03-24 04:02:39 +08:00
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# Wei-keng Liao's (wkliao@eecs.northwestern.edu)
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# netcdf-3 validator program
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# (https://github.com/Parallel-NetCDF/PnetCDF/blob/master/src/utils/ncvalidator/ncvalidator.c)
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# that prints out the structure of a netcdf-3 file.
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2020-03-12 02:49:33 +08:00
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# This program is built but not installed.
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2019-03-24 04:02:39 +08:00
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noinst_PROGRAMS += ncvalidator
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ncvalidator_SOURCES = ncvalidator.c
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2021-09-03 07:04:26 +08:00
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# A non-installed utility program to convert paths; similar to cygpath
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noinst_PROGRAMS += ncpathcvt
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ncpathcvt_SOURCES = ncpathcvt.c
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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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# A non-installed utility program to test if a filter is available
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noinst_PROGRAMS += ncfilteravail
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ncfilteravail_SOURCES = ncfilteravail.c
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2017-11-18 03:29:12 +08:00
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# A simple netcdf-4 metadata -> xml printer. Do not install.
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2018-12-01 23:24:56 +08:00
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if USE_HDF5
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2020-09-16 04:56:12 +08:00
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bin_PROGRAMS += nc4print
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2018-08-02 04:27:09 +08:00
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noinst_PROGRAMS += nc4print
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2020-09-25 04:33:58 +08:00
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nc4print_SOURCES = nc4print.c nc4printer.c
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2021-03-07 05:09:37 +08:00
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# Create a helper program for tst_scope.sh
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# Program prints out the fqn of the type of
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# a specified variable in the .nc file.
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noinst_PROGRAMS += printfqn
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printfqn_SOURCES = printfqn.c
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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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# A non-installed utility program to return
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# the HDF5 Version as an integer of the form XXXYYYZZZ with no newline.
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# Where XXX is the major version number, YYY is the minor version number
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# and ZZZ is the patch level.
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noinst_PROGRAMS += nchdf5version
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nchdf5version_SOURCES = nchdf5version.c
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2017-03-09 08:01:10 +08:00
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endif
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# Conditionally build the ocprint program, but do not install
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if ENABLE_DAP
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2020-09-16 04:56:12 +08:00
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bin_PROGRAMS += ocprint
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2018-08-02 04:19:50 +08:00
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noinst_PROGRAMS += ocprint
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2017-11-12 07:45:03 +08:00
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ocprint_SOURCES = ocprint.c
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2017-03-09 08:01:10 +08:00
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endif
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2011-03-22 04:31:56 +08:00
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# This is the man page.
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man_MANS = ncdump.1 nccopy.1
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2012-04-13 10:41:00 +08:00
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if BUILD_TESTSETS
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2019-09-18 10:27:43 +08:00
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# C programs needed by shell scripts for classic tests.
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2017-11-12 07:45:03 +08:00
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check_PROGRAMS = rewrite-scalar ref_ctest ref_ctest64 ncdump tst_utf8 \
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2022-06-18 04:35:12 +08:00
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bom tst_dimsizes nctrunc tst_rcmerge tst_rcapi
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2016-05-04 11:17:06 +08:00
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2017-11-18 03:29:12 +08:00
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# Tests for classic and 64-bit offset files.
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2017-11-25 22:28:07 +08:00
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TESTS = tst_inttags.sh run_tests.sh tst_64bit.sh ref_ctest \
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2021-11-04 02:49:54 +08:00
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ref_ctest64 tst_lengths.sh tst_calendars.sh \
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run_utf8_tests.sh tst_nccopy3_subset.sh \
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2017-11-25 22:28:07 +08:00
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tst_charfill.sh tst_iter.sh tst_formatx3.sh tst_bom.sh \
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2021-11-04 02:49:54 +08:00
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tst_dimsizes.sh run_ncgen_tests.sh tst_ncgen4_classic.sh \
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test_radix.sh test_rcmerge.sh
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2017-11-18 01:16:17 +08:00
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2017-11-25 22:30:17 +08:00
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# The tst_nccopy3.sh test uses output from a bunch of other
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# tests. This records the dependency so parallel builds work.
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2017-11-18 02:07:24 +08:00
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tst_nccopy3.log: tst_calendars.log run_utf8_tests.log tst_output.log \
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2021-12-24 13:18:56 +08:00
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tst_64bit.log run_tests.log tst_lengths.log
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2016-05-04 11:17:06 +08:00
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2017-11-21 06:06:10 +08:00
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TESTS += tst_null_byte_padding.sh
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2017-11-21 08:26:06 +08:00
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if USE_STRICT_NULL_BYTE_HEADER_PADDING
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XFAIL_TESTS += tst_null_byte_padding.sh
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2017-11-21 06:06:10 +08:00
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endif
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2012-03-16 04:50:28 +08:00
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if LARGE_FILE_TESTS
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TESTS += tst_iter.sh
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endif
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2021-09-03 07:04:26 +08:00
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TESTS += testpathcvt.sh
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2018-12-01 23:24:56 +08:00
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if USE_HDF5
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2020-08-18 09:15:47 +08:00
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# HDF5 has some extra C programs to build. These will be run by
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2017-11-18 03:29:12 +08:00
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# the shell script tests.
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check_PROGRAMS += tst_fileinfo tst_create_files tst_h_rdc0 \
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tst_group_data tst_enum_data tst_opaque_data tst_string_data \
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tst_vlen_data tst_comp tst_comp2 tst_nans tst_special_atts \
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2022-07-18 04:32:31 +08:00
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tst_unicode tst_fillbug tst_compress tst_chunking tst_h_scalar \
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tst_enum_undef
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2017-11-18 03:29:12 +08:00
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2018-11-16 01:00:38 +08:00
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check_PROGRAMS += tst_vlen_demo
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2017-11-18 03:29:12 +08:00
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# Tests for netCDF-4 behavior.
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TESTS += tst_fileinfo.sh tst_hdf5_offset.sh tst_inttags4.sh \
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2021-12-24 13:18:56 +08:00
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tst_netcdf4.sh tst_fillbug.sh \
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tst_grp_spec.sh tst_mud.sh tst_h_scalar.sh tst_formatx4.sh \
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2021-11-04 02:49:54 +08:00
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run_utf8_nc4_tests.sh run_ncgen_nc4_tests.sh \
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2021-03-07 05:09:37 +08:00
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tst_ncgen4.sh test_scope.sh
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2017-11-18 03:29:12 +08:00
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2018-07-27 10:16:02 +08:00
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# Record interscript dependencies so parallel builds work.
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2017-11-25 19:31:58 +08:00
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tst_nccopy4.log: run_ncgen_tests.log tst_output.log tst_ncgen4.log \
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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
|
|
|
tst_fillbug.log tst_netcdf4_4.log tst_h_scalar.log tst_netcdf4.log
|
2018-07-27 10:16:02 +08:00
|
|
|
tst_nccopy5.log: tst_nccopy4.log
|
2021-12-24 13:18:56 +08:00
|
|
|
|
|
|
|
|
endif #USE_HDF5
|
2010-06-03 21:24:43 +08:00
|
|
|
|
2019-03-16 02:05:27 +08:00
|
|
|
TESTS += tst_inmemory_nc3.sh tst_nccopy_w3.sh
|
2018-12-01 23:24:56 +08:00
|
|
|
if USE_HDF5
|
2019-03-16 02:05:27 +08:00
|
|
|
TESTS += tst_inmemory_nc4.sh tst_nccopy_w4.sh
|
2017-11-18 03:29:12 +08:00
|
|
|
endif
|
2012-04-13 10:41:00 +08:00
|
|
|
|
2019-11-01 06:08:57 +08:00
|
|
|
if USE_HDF5
|
|
|
|
|
# Re-activate the ncgen -lc tests
|
2019-11-04 03:03:13 +08:00
|
|
|
TESTS += tst_ctests.sh
|
2019-11-01 06:08:57 +08:00
|
|
|
endif
|
|
|
|
|
|
2020-06-06 07:03:29 +08:00
|
|
|
if ENABLE_CDF5
|
|
|
|
|
# Test for keywords as identifiers
|
|
|
|
|
TESTS += test_keywords.sh
|
|
|
|
|
endif
|
|
|
|
|
|
2021-12-24 13:18:56 +08:00
|
|
|
if !ISMINGW
|
|
|
|
|
if !ISCYGWIN
|
|
|
|
|
TESTS += tst_output.sh
|
|
|
|
|
TESTS += tst_nccopy3.sh
|
2021-11-04 02:49:54 +08:00
|
|
|
if USE_HDF5
|
|
|
|
|
TESTS += run_back_comp_tests.sh tst_netcdf4_4.sh
|
2023-01-19 06:14:28 +08:00
|
|
|
TESTS += tst_nccopy4.sh tst_nccopy5.sh tst_calendars_nc4.sh
|
2021-11-04 02:49:54 +08:00
|
|
|
endif
|
|
|
|
|
endif
|
|
|
|
|
endif
|
|
|
|
|
|
2022-02-09 11:53:30 +08:00
|
|
|
# The unicode tests
|
|
|
|
|
if !ISMINGW
|
|
|
|
|
TESTS += test_unicode_directory.sh test_unicode_path.sh
|
|
|
|
|
endif
|
|
|
|
|
|
2012-04-13 10:41:00 +08:00
|
|
|
endif BUILD_TESTSETS
|
|
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
# These files all have to be included with the distribution.
|
2017-11-18 03:29:12 +08:00
|
|
|
EXTRA_DIST = run_tests.sh tst_64bit.sh tst_output.sh test0.cdl \
|
|
|
|
|
ref_ctest1_nc4.cdl ref_ctest1_nc4c.cdl ref_tst_solar_1.cdl \
|
|
|
|
|
ref_tst_solar_2.cdl tst_netcdf4.sh tst_netcdf4_4.sh ref_tst_small.cdl \
|
|
|
|
|
tst_lengths.sh tst_ncml.cdl ref1.ncml ref_tst_group_data.cdl \
|
|
|
|
|
ref_tst_enum_data.cdl ref_tst_opaque_data.cdl ref_tst_string_data.cdl \
|
|
|
|
|
ref_tst_vlen_data.cdl ref_tst_comp.cdl ref_tst_unicode.cdl \
|
|
|
|
|
ref_tst_nans.cdl small.cdl small2.cdl $(man_MANS) run_utf8_tests.sh \
|
|
|
|
|
ref_tst_utf8.cdl ref_tst_fillbug.cdl tst_fillbug.sh tst_calendars.cdl \
|
|
|
|
|
tst_calendars.sh ref_times.cdl ref_tst_special_atts.cdl \
|
|
|
|
|
ref_tst_noncoord.cdl ref_tst_compounds2.nc ref_tst_compounds2.cdl \
|
|
|
|
|
ref_tst_compounds3.nc ref_tst_compounds3.cdl ref_tst_compounds4.nc \
|
|
|
|
|
ref_tst_compounds4.cdl ref_tst_group_data_v23.cdl tst_mslp.cdl \
|
|
|
|
|
tst_bug321.cdl ref_tst_format_att.cdl ref_tst_format_att_64.cdl \
|
2023-01-19 07:13:37 +08:00
|
|
|
tst_nccopy3.sh tst_nccopy4.sh tst_nccopy5.sh tst_calendars_nc4.sh \
|
2020-07-03 03:59:37 +08:00
|
|
|
ref_nc_test_netcdf4_4_0.nc run_back_comp_tests.sh \
|
|
|
|
|
ref_nc_test_netcdf4.cdl ref_tst_special_atts3.cdl tst_brecs.cdl \
|
|
|
|
|
ref_tst_grp_spec0.cdl ref_tst_grp_spec.cdl tst_grp_spec.sh \
|
|
|
|
|
ref_tst_charfill.cdl tst_charfill.cdl tst_charfill.sh tst_iter.sh \
|
|
|
|
|
tst_mud.sh ref_tst_mud4.cdl ref_tst_mud4-bc.cdl \
|
|
|
|
|
ref_tst_mud4_chars.cdl inttags.cdl inttags4.cdl ref_inttags.cdl \
|
|
|
|
|
ref_inttags4.cdl ref_tst_ncf213.cdl tst_h_scalar.sh \
|
|
|
|
|
run_utf8_nc4_tests.sh tst_formatx3.sh tst_formatx4.sh \
|
|
|
|
|
ref_tst_utf8_4.cdl ref_tst_nc4_utf8_4.cdl tst_inttags.sh \
|
|
|
|
|
tst_inttags4.sh CMakeLists.txt tst_bom.sh tst_inmemory_nc3.sh \
|
|
|
|
|
tst_dimsizes.sh tst_inmemory_nc4.sh tst_fileinfo.sh \
|
|
|
|
|
run_ncgen_tests.sh ref_test_360_day_1900.nc ref_test_365_day_1900.nc \
|
2017-11-26 22:13:10 +08:00
|
|
|
ref_test_366_day_1900.nc ref_test_360_day_1900.cdl \
|
|
|
|
|
ref_test_365_day_1900.cdl ref_test_366_day_1900.cdl \
|
|
|
|
|
tst_hdf5_offset.sh run_ncgen_nc4_tests.sh tst_nccopy3_subset.sh \
|
|
|
|
|
ref_nccopy3_subset.nc ref_test_corrupt_magic.nc tst_ncgen_shared.sh \
|
|
|
|
|
tst_ncgen4.sh tst_ncgen4_classic.sh tst_ncgen4_diff.sh \
|
|
|
|
|
tst_ncgen4_cycle.sh tst_null_byte_padding.sh \
|
2020-07-03 03:59:37 +08:00
|
|
|
ref_null_byte_padding_test.nc ref_tst_irish_rover.nc \
|
|
|
|
|
ref_provenance_v1.nc ref_tst_radix.cdl tst_radix.cdl test_radix.sh \
|
|
|
|
|
ref_nccopy_w.cdl tst_nccopy_w3.sh tst_nccopy_w4.sh \
|
Regularize the scoping of dimensions
This is a follow-on to pull request
````https://github.com/Unidata/netcdf-c/pull/1959````,
which fixed up type scoping.
The primary changes are to _nc\_inq\_dimid()_ and to ncdump.
The _nc\_inq\_dimid()_ function is supposed to allow the name to be
and FQN, but this apparently never got implemented. So if was modified
to support FQNs.
The ncdump program is supposed to output fully qualified dimension names
in its generated CDL file under certain conditions.
Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group
is G. For each dimension id D referenced by V, ncdump needs to determine
whether to print its name as a simple name or as a fully qualified name (FQN).
The algorithm is as follows:
1. Search up the tree of ancestor groups.
2. If one of those ancestor groups contains the dimid, then call it dimgrp.
3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true.
4. If dimgrp is defined and duplicate == false, then we do not need an fqn.
5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate.
6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid.
7. If found, then use the fqn of the first found such dimension location.
8. If not found, then fail.
Test case ncdump/test_scope.sh was modified to test the proper
operation of ncdump and _nc\_inq\_dimid()_.
Misc. Other Changes:
* Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL.
* Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
2021-06-01 05:51:12 +08:00
|
|
|
ref_no_ncproperty.nc test_unicode_directory.sh test_unicode_path.sh \
|
2020-12-08 02:29:12 +08:00
|
|
|
ref_roman_szip_simple.cdl ref_roman_szip_unlim.cdl ref_tst_perdimspecs.cdl \
|
2021-05-28 04:13:14 +08:00
|
|
|
test_keywords.sh ref_keyword1.cdl ref_keyword2.cdl ref_keyword3.cdl ref_keyword4.cdl \
|
Regularize the scoping of dimensions
This is a follow-on to pull request
````https://github.com/Unidata/netcdf-c/pull/1959````,
which fixed up type scoping.
The primary changes are to _nc\_inq\_dimid()_ and to ncdump.
The _nc\_inq\_dimid()_ function is supposed to allow the name to be
and FQN, but this apparently never got implemented. So if was modified
to support FQNs.
The ncdump program is supposed to output fully qualified dimension names
in its generated CDL file under certain conditions.
Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group
is G. For each dimension id D referenced by V, ncdump needs to determine
whether to print its name as a simple name or as a fully qualified name (FQN).
The algorithm is as follows:
1. Search up the tree of ancestor groups.
2. If one of those ancestor groups contains the dimid, then call it dimgrp.
3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true.
4. If dimgrp is defined and duplicate == false, then we do not need an fqn.
5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate.
6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid.
7. If found, then use the fqn of the first found such dimension location.
8. If not found, then fail.
Test case ncdump/test_scope.sh was modified to test the proper
operation of ncdump and _nc\_inq\_dimid()_.
Misc. Other Changes:
* Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL.
* Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
2021-06-01 05:51:12 +08:00
|
|
|
ref_tst_nofilters.cdl test_scope.sh \
|
|
|
|
|
test_rcmerge.sh ref_rcmerge1.txt ref_rcmerge2.txt ref_rcmerge3.txt \
|
2022-06-18 04:35:12 +08:00
|
|
|
scope_ancestor_only.cdl scope_ancestor_subgroup.cdl scope_group_only.cdl scope_preorder.cdl \
|
2023-04-26 07:15:06 +08:00
|
|
|
ref_rcapi.txt ref_tst_enum_undef.cdl tst_calendars_nc4.cdl ref_times_nc4.cdl ref_tst_comp2.cdl
|
re e-support UBS-599337
re pull request https://github.com/Unidata/netcdf-c/pull/405
re pull request https://github.com/Unidata/netcdf-c/pull/446
Notes:
1. This branch is a cleanup of the magic.dmh branch.
2. magic.dmh was originally merged, but caused problems with parallel IO.
It was re-issued as pull request https://github.com/Unidata/netcdf-c/pull/446.
3. This branch + pull request replace any previous pull requests and magic.dmh branch.
Given an otherwise valid netCDF file that has a corrupted header,
the netcdf library currently crashes. Instead, it should return
NC_ENOTNC.
Additionally, the NC_check_file_type code does not do the
forward search required by hdf5 files. It currently only looks
at file position 0 instead of 512, 1024, 2048,... Also, it turns
out that the HDF4 magic number is assumed to always be at the
beginning of the file (unlike HDF5).
The change is localized to libdispatch/dfile.c See
https://support.hdfgroup.org/release4/doc/DSpec_html/DS.pdf
Also, it turns out that the code in NC_check_file_type is duplicated
(mostly) in the function libsrc4/nc4file.c#nc_check_for_hdf.
This branch does the following.
1. Make NC_check_file_type return NC_ENOTNC instead of crashing.
2. Remove nc_check_for_hdf and centralize all file format checking
NC_check_file_type.
3. Add proper forward search for HDF5 files (but not HDF4 files)
to look for the magic number at offsets of 0, 512, 1024...
4. Add test tst_hdf5_offset.sh. This tests that hdf5 files with
an offset are properly recognized. It does so by prefixing
a legal file with some number of zero bytes: 512, 1024, etc.
5. Off-topic: Added -N flag to ncdump to force a specific output dataset name.
2017-10-25 06:25:09 +08:00
|
|
|
|
|
|
|
|
# The L512.bin file is file containing exactly 512 bytes each of value 0.
|
|
|
|
|
# It is used for creating hdf5 files with varying offsets for testing.
|
|
|
|
|
EXTRA_DIST += L512.bin
|
2012-01-10 02:49:15 +08:00
|
|
|
|
2019-11-06 04:43:59 +08:00
|
|
|
EXTRA_DIST += tst_ctests.sh ref_ctest_small_3.c ref_ctest_small_4.c \
|
2023-04-26 07:15:06 +08:00
|
|
|
ref_ctest_special_atts_4.c test_ncdump.sh
|
2019-11-01 06:08:57 +08:00
|
|
|
|
2021-09-03 07:04:26 +08:00
|
|
|
EXTRA_DIST += testpathcvt.sh ref_pathcvt.txt
|
|
|
|
|
|
2014-09-19 08:26:06 +08:00
|
|
|
# CDL files and Expected results
|
2017-11-18 03:29:12 +08:00
|
|
|
SUBDIRS = cdl expected
|
|
|
|
|
|
Upgrade the nczarr code to match Zarr V2
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
|
|
|
CLEANFILES = tst_*.nc tmp*.nc test*.nc iter.* tmp*.cdl tmp*.txt \
|
2018-11-19 05:59:05 +08:00
|
|
|
tst_output_*.cdl tst_output_*.c tst_utf8_*.cdl *.tmp tst_tst8.cdl \
|
|
|
|
|
tst_netcdf4_*.cdl test1_ncdump.cdl test2_ncdump.cdl test1.cdl \
|
|
|
|
|
ctest1.cdl test1_cdf5.cdl test2_cdf5.cdl test1_offset.cdl \
|
2017-11-26 23:50:16 +08:00
|
|
|
test2_offset.cdl ctest0.nc ctest0_64.nc c1.cdl c1_4.cdl ctest1_64.cdl \
|
|
|
|
|
c0.nc c0_4.nc small.nc small2.nc c0tmp.nc c1.ncml utf8.cdl \
|
|
|
|
|
utf8_64.cdl utf8.nc utf8_64.nc nc4_utf8.cdl nc4_utf8.nc \
|
|
|
|
|
tst_unicode.cdl tst_group_data.cdl tst_compounds2.cdl tst_comp.cdl \
|
|
|
|
|
tst_enum_data.cdl tst_small.cdl tst_times.cdl tst_solar_2.cdl \
|
|
|
|
|
tst_string_data.cdl tst_fillbug.cdl tst_opaque_data.cdl \
|
|
|
|
|
tst_compounds4.cdl tst_utf8.cdl tst_compounds3.cdl \
|
|
|
|
|
tst_special_atts.cdl tst_nans.cdl tst_format_att_64.cdl \
|
|
|
|
|
tst_vlen_data.cdl tst_solar_1.cdl tst_format_att.cdl \
|
|
|
|
|
tst_nc_test_netcdf4_4_0.cdl tst_mud4.cdl tst_mud4-bc.cdl \
|
|
|
|
|
tst_ncf213.cdl tst_h_scalar.cdl tst_mud4_chars.cdl inttags.nc \
|
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inttags4.nc tst_inttags.cdl tst_inttags4.cdl nc4_fileinfo.nc \
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hdf5_fileinfo.hdf nccopy3_subset_out.nc c5.nc \
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2017-11-19 05:20:04 +08:00
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compound_datasize_test.nc compound_datasize_test2.nc ncf199.nc \
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tst_c0.cdl tst_c0_4.cdl tst_c0_4c.cdl tst_c0_64.cdl \
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2017-11-12 08:33:51 +08:00
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tst_compound_datasize_test.cdl tst_compound_datasize_test2.cdl \
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2017-11-19 05:20:04 +08:00
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tst_ncf199.cdl tst_tst_gattenum.cdl tst_tst_usuffix.cdl ctest.c \
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2020-07-04 02:56:22 +08:00
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ctest64.c nccopy3_subset_out.nc camrun.c tst_ncf213.cdl tst_ncf213.nc \
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tst_radix.nc tmp_radix.cdl ctest_small_3.c ctest_small_4.c \
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ctest_special_atts_4.c tst_roman_szip_simple.cdl \
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2021-03-07 05:09:37 +08:00
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tst_roman_szip_unlim.cdl tst_perdimpspecs.nc tmppds.* \
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Regularize the scoping of dimensions
This is a follow-on to pull request
````https://github.com/Unidata/netcdf-c/pull/1959````,
which fixed up type scoping.
The primary changes are to _nc\_inq\_dimid()_ and to ncdump.
The _nc\_inq\_dimid()_ function is supposed to allow the name to be
and FQN, but this apparently never got implemented. So if was modified
to support FQNs.
The ncdump program is supposed to output fully qualified dimension names
in its generated CDL file under certain conditions.
Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group
is G. For each dimension id D referenced by V, ncdump needs to determine
whether to print its name as a simple name or as a fully qualified name (FQN).
The algorithm is as follows:
1. Search up the tree of ancestor groups.
2. If one of those ancestor groups contains the dimid, then call it dimgrp.
3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true.
4. If dimgrp is defined and duplicate == false, then we do not need an fqn.
5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate.
6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid.
7. If found, then use the fqn of the first found such dimension location.
8. If not found, then fail.
Test case ncdump/test_scope.sh was modified to test the proper
operation of ncdump and _nc\_inq\_dimid()_.
Misc. Other Changes:
* Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL.
* Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
2021-06-01 05:51:12 +08:00
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keyword1.nc keyword2.nc keyword3.nc keyword4.nc \
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tmp_keyword1.cdl tmp_keyword2.cdl tmp_keyword3.cdl tmp_keyword4.cdl \
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type_*.nc copy_type_*.cdl \
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2023-01-19 07:13:37 +08:00
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scope_*.nc copy_scope_*.cdl keyword5.nc tst_enum_undef.cdl tst_times_nc4.cdl
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2021-04-14 06:56:43 +08:00
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2021-04-26 12:02:29 +08:00
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# Remove directories
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clean-local:
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Mitigate S3 test interference + Unlimited Dimensions in NCZarr
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.
The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.
## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
- "size" with an integer value representing the (current) size of the dimension.
- "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.
For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.
Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.
## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
AWS Transfer Utility mechanism. This is controlled by the
```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
2023-09-27 06:56:48 +08:00
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rm -fr rcmergedir rchome testset_*
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