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netcdf-c/ncdump/Makefile.am
Dennis Heimbigner df3636b959 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.
2023-09-26 16:56:48 -06:00

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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 non-installed utility program to test if a filter is available
noinst_PROGRAMS += ncfilteravail
ncfilteravail_SOURCES = ncfilteravail.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 tst_rcapi
# 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 \
tst_enum_undef
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
if USE_HDF5
TESTS += run_back_comp_tests.sh tst_netcdf4_4.sh
TESTS += tst_nccopy4.sh tst_nccopy5.sh tst_calendars_nc4.sh
endif
endif
endif
# The unicode tests
if !ISMINGW
TESTS += test_unicode_directory.sh test_unicode_path.sh
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 tst_calendars_nc4.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 \
ref_rcapi.txt ref_tst_enum_undef.cdl tst_calendars_nc4.cdl ref_times_nc4.cdl ref_tst_comp2.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 test_ncdump.sh
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 keyword5.nc tst_enum_undef.cdl tst_times_nc4.cdl
# Remove directories
clean-local:
rm -fr rcmergedir rchome testset_*
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