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netcdf-c/ncdump/Makefile.am
Dennis Heimbigner 8b9253fef2 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.
2022-01-08 18:30:00 -07:00

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Makefile
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## This is a automake file, part of Unidata's netCDF package.
# Copyright 2018, see the COPYRIGHT file for more information.
# This file builds and runs the ncdump program.
# Ed Hartnett, Dennis Heimbigner, Ward Fisher
#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#TESTS_ENVIRONMENT = export SETX=1;
# Put together AM_CPPFLAGS and AM_LDFLAGS.
include $(top_srcdir)/lib_flags.am
LDADD = ${top_builddir}/liblib/libnetcdf.la
noinst_PROGRAMS=
# Note which tests depend on other tests. Necessary for make -j check.
TEST_EXTENSIONS = .sh
XFAIL_TESTS=""
# This is the program we're building, and it's sources.
bin_PROGRAMS = ncdump
ncdump_SOURCES = ncdump.c vardata.c dumplib.c indent.c nctime0.c \
ncdump.h vardata.h dumplib.h indent.h nctime0.h cdl.h utils.h \
utils.c nciter.h nciter.c nccomps.h
# Another utility program that copies any netCDF file using only the
# netCDF API
bin_PROGRAMS += nccopy
nccopy_SOURCES = nccopy.c nciter.c nciter.h chunkspec.h chunkspec.c \
utils.h utils.c dimmap.h dimmap.c list.c list.h
# Wei-keng Liao's (wkliao@eecs.northwestern.edu)
# netcdf-3 validator program
# (https://github.com/Parallel-NetCDF/PnetCDF/blob/master/src/utils/ncvalidator/ncvalidator.c)
# that prints out the structure of a netcdf-3 file.
# This program is built but not installed.
noinst_PROGRAMS += ncvalidator
ncvalidator_SOURCES = ncvalidator.c
# A non-installed utility program to convert paths; similar to cygpath
noinst_PROGRAMS += ncpathcvt
ncpathcvt_SOURCES = ncpathcvt.c
# A simple netcdf-4 metadata -> xml printer. Do not install.
if USE_HDF5
bin_PROGRAMS += nc4print
noinst_PROGRAMS += nc4print
nc4print_SOURCES = nc4print.c nc4printer.c
# Create a helper program for tst_scope.sh
# Program prints out the fqn of the type of
# a specified variable in the .nc file.
noinst_PROGRAMS += printfqn
printfqn_SOURCES = printfqn.c
# A non-installed utility program to return
# the HDF5 Version as an integer of the form XXXYYYZZZ with no newline.
# Where XXX is the major version number, YYY is the minor version number
# and ZZZ is the patch level.
noinst_PROGRAMS += nchdf5version
nchdf5version_SOURCES = nchdf5version.c
endif
# Conditionally build the ocprint program, but do not install
if ENABLE_DAP
bin_PROGRAMS += ocprint
noinst_PROGRAMS += ocprint
ocprint_SOURCES = ocprint.c
endif
# This is the man page.
man_MANS = ncdump.1 nccopy.1
if BUILD_TESTSETS
# C programs needed by shell scripts for classic tests.
check_PROGRAMS = rewrite-scalar ref_ctest ref_ctest64 ncdump tst_utf8 \
bom tst_dimsizes nctrunc tst_rcmerge
# Tests for classic and 64-bit offset files.
TESTS = tst_inttags.sh run_tests.sh tst_64bit.sh ref_ctest \
ref_ctest64 tst_lengths.sh tst_calendars.sh \
run_utf8_tests.sh tst_nccopy3_subset.sh \
tst_charfill.sh tst_iter.sh tst_formatx3.sh tst_bom.sh \
tst_dimsizes.sh run_ncgen_tests.sh tst_ncgen4_classic.sh \
test_radix.sh test_rcmerge.sh
# The tst_nccopy3.sh test uses output from a bunch of other
# tests. This records the dependency so parallel builds work.
tst_nccopy3.log: tst_calendars.log run_utf8_tests.log tst_output.log \
tst_64bit.log run_tests.log tst_lengths.log
TESTS += tst_null_byte_padding.sh
if USE_STRICT_NULL_BYTE_HEADER_PADDING
XFAIL_TESTS += tst_null_byte_padding.sh
endif
if LARGE_FILE_TESTS
TESTS += tst_iter.sh
endif
TESTS += testpathcvt.sh
if USE_HDF5
# HDF5 has some extra C programs to build. These will be run by
# the shell script tests.
check_PROGRAMS += tst_fileinfo tst_create_files tst_h_rdc0 \
tst_group_data tst_enum_data tst_opaque_data tst_string_data \
tst_vlen_data tst_comp tst_comp2 tst_nans tst_special_atts \
tst_unicode tst_fillbug tst_compress tst_chunking tst_h_scalar
check_PROGRAMS += tst_vlen_demo
# Tests for netCDF-4 behavior.
TESTS += tst_fileinfo.sh tst_hdf5_offset.sh tst_inttags4.sh \
tst_netcdf4.sh tst_fillbug.sh \
tst_grp_spec.sh tst_mud.sh tst_h_scalar.sh tst_formatx4.sh \
run_utf8_nc4_tests.sh run_ncgen_nc4_tests.sh \
tst_ncgen4.sh test_scope.sh
# Record interscript dependencies so parallel builds work.
tst_nccopy4.log: run_ncgen_tests.log tst_output.log tst_ncgen4.log \
tst_fillbug.log tst_netcdf4_4.log tst_h_scalar.log tst_netcdf4.log
tst_nccopy5.log: tst_nccopy4.log
endif #USE_HDF5
TESTS += tst_inmemory_nc3.sh tst_nccopy_w3.sh
if USE_HDF5
TESTS += tst_inmemory_nc4.sh tst_nccopy_w4.sh
endif
if USE_HDF5
# Re-activate the ncgen -lc tests
TESTS += tst_ctests.sh
endif
if ENABLE_CDF5
# Test for keywords as identifiers
TESTS += test_keywords.sh
endif
if !ISMINGW
if !ISCYGWIN
TESTS += tst_output.sh
TESTS += tst_nccopy3.sh
TESTS += test_unicode_directory.sh test_unicode_path.sh
if USE_HDF5
TESTS += run_back_comp_tests.sh tst_netcdf4_4.sh
TESTS += tst_nccopy4.sh tst_nccopy5.sh
endif
endif
endif
endif BUILD_TESTSETS
# These files all have to be included with the distribution.
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 \
tst_nccopy3.sh tst_nccopy4.sh tst_nccopy5.sh \
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 \
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 \
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 \
ref_no_ncproperty.nc test_unicode_directory.sh test_unicode_path.sh \
ref_roman_szip_simple.cdl ref_roman_szip_unlim.cdl ref_tst_perdimspecs.cdl \
test_keywords.sh ref_keyword1.cdl ref_keyword2.cdl ref_keyword3.cdl ref_keyword4.cdl \
ref_tst_nofilters.cdl test_scope.sh \
test_rcmerge.sh ref_rcmerge1.txt ref_rcmerge2.txt ref_rcmerge3.txt \
scope_ancestor_only.cdl scope_ancestor_subgroup.cdl scope_group_only.cdl scope_preorder.cdl
# 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
EXTRA_DIST += tst_ctests.sh ref_ctest_small_3.c ref_ctest_small_4.c \
ref_ctest_special_atts_4.c
EXTRA_DIST += testpathcvt.sh ref_pathcvt.txt
# CDL files and Expected results
SUBDIRS = cdl expected
CLEANFILES = tst_*.nc tmp*.nc test*.nc iter.* tmp*.cdl tmp*.txt \
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 \
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 \
inttags4.nc tst_inttags.cdl tst_inttags4.cdl nc4_fileinfo.nc \
hdf5_fileinfo.hdf nccopy3_subset_out.nc c5.nc \
compound_datasize_test.nc compound_datasize_test2.nc ncf199.nc \
tst_c0.cdl tst_c0_4.cdl tst_c0_4c.cdl tst_c0_64.cdl \
tst_compound_datasize_test.cdl tst_compound_datasize_test2.cdl \
tst_ncf199.cdl tst_tst_gattenum.cdl tst_tst_usuffix.cdl ctest.c \
ctest64.c nccopy3_subset_out.nc camrun.c tst_ncf213.cdl tst_ncf213.nc \
tst_radix.nc tmp_radix.cdl ctest_small_3.c ctest_small_4.c \
ctest_special_atts_4.c tst_roman_szip_simple.cdl \
tst_roman_szip_unlim.cdl tst_perdimpspecs.nc tmppds.* \
keyword1.nc keyword2.nc keyword3.nc keyword4.nc \
tmp_keyword1.cdl tmp_keyword2.cdl tmp_keyword3.cdl tmp_keyword4.cdl \
type_*.nc copy_type_*.cdl \
scope_*.nc copy_scope_*.cdl
# Remove directories
clean-local:
rm -fr rcmergedir rchome
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