netcdf-c/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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Makefile

## This is a automake file, part of Unidata's netCDF package.
# Copyright 2005-2018, see the COPYRIGHT file for more information.
# This is the main automake file for netCDF. It builds the different
# netcdf directories. Not all directories are built, depending on the
# options selected during configure.
# Ed Hartnett, Ward Fisher
# Put together AM_CPPFLAGS and AM_LDFLAGS.
include $(top_srcdir)/lib_flags.am
# This directory stores libtool macros, put there by aclocal.
ACLOCAL_AMFLAGS = -I m4
TESTS_ENVIRONMENT =
TEST_EXTENSIONS = .sh
#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;
##
# Turn off plugin directory during distcheck, see
# comment thread at https://github.com/Unidata/netcdf-c/pull/2348
# for more information.
##
AM_DISTCHECK_CONFIGURE_FLAGS = --without-plugin-dir
# These files get added to the distribution.
EXTRA_DIST = README.md COPYRIGHT INSTALL.md test_prog.c lib_flags.am \
cmake CMakeLists.txt COMPILE.cmake.txt config.h.cmake.in \
cmake_uninstall.cmake.in FixBundle.cmake.in nc-config.cmake.in \
RELEASE_NOTES.md CTestConfig.cmake.in CTestCustom.cmake.in \
libnetcdf.settings.in netCDFConfig.cmake.in CMakeInstallation.cmake \
test-driver-verbose test_common.in fuzz
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = netcdf.pc
# Does the user want to build and run unit tests?
if BUILD_UNIT_TESTS
UNIT_TEST = unit_test
endif # BUILD_UNIT_TESTS
# Does the user want to build the V2 API?
if BUILD_V2
V2_TEST = nctest
endif
# Does the user want to build ncgen/ncdump?
if BUILD_UTILITIES
NCGEN3 = ncgen3
NCGEN = ncgen
NCDUMP = ncdump
endif
# Does the user want to build the examples?
if BUILD_EXAMPLES
EXAMPLES = examples
endif
# Is the user building netCDF-4?
if USE_NETCDF4
LIBSRC4_DIR = libsrc4
endif
# Is the user building with HDF5?
# Note that USE_HDF5 does not imply USE_NETCDF4
if USE_HDF5
H5_TEST_DIR = h5_test
LIBHDF5 = libhdf5
if USE_HDF5
NC_TEST4 = nc_test4
endif
endif
# Build the dap2 client
if ENABLE_DAP
OCLIB = oc2
DAP2 = libdap2
NCDAP2TESTDIR = ncdap_test
endif
if ENABLE_DAP4
DAP4 = libdap4
NCDAP4TESTDIR = dap4_test
XML = libncxml
endif #DAP4
if ENABLE_S3_INTERNAL
XML = libncxml # Internal S3 requires XML
endif #ENABLE_S3_INTERNAL
# Build PnetCDF
if USE_PNETCDF
LIBSRCP = libsrcp
endif
# Build HDF4 if desired.
if USE_HDF4
HDF4_TEST_DIR = hdf4_test
LIBHDF4 = libhdf4
endif
# Build Plugin support
if ENABLE_PLUGINS
NCPOCO = libncpoco
endif
# Build Cloud Storage if desired.
if ENABLE_NCZARR
ZARR_TEST_DIR = nczarr_test
ZARR = libnczarr
endif
# Optionally build test plugins
if ENABLE_PLUGINS
PLUGIN_DIR = plugins
endif
# If benchmarks were turned on, build and run a bunch more tests.
if BUILD_BENCHMARKS
BENCHMARKS_DIR = nc_perf
endif # BUILD_BENCHMARKS
# Define Test directories
if BUILD_TESTSETS
TESTDIRS = $(H5_TEST_DIR)
TESTDIRS += $(UNIT_TEST) $(V2_TEST) nc_test $(NC_TEST4)
TESTDIRS += $(BENCHMARKS_DIR) $(HDF4_TEST_DIR) $(NCDAP2TESTDIR) $(NCDAP4TESTDIR)
TESTDIRS += ${ZARR_TEST_DIR}
endif
# This is the list of subdirs for which Makefiles will be constructed
# and run. ncgen must come before ncdump, because their tests
# depend on it.
SUBDIRS = include ${XML} libdispatch libsrc $(LIBSRC4_DIR) \
$(LIBSRCP) $(LIBHDF4) $(LIBHDF5) $(OCLIB) $(DAP2) ${DAP4} \
${NCPOCO} ${ZARR} liblib \
$(NCGEN3) $(NCGEN) $(NCDUMP) ${PLUGIN_DIR} $(TESTDIRS) docs \
$(EXAMPLES)
# Remove these generated files, for a distclean.
DISTCLEANFILES = VERSION comps.txt test_prog libnetcdf.settings \
test_common.sh
# The nc-config script helps the user build programs with netCDF.
bin_SCRIPTS = nc-config
# install libnetcdf.settings in lib directory.
settingsdir = $(libdir)
settings_DATA = libnetcdf.settings
####
# Provide an entry to rebuild all the m4 generated files
# List of files to create: WARNING leave off the extension
####
MM4= ./nc_test/test_put ./nc_test/test_get ./nc_test/test_write \
./nc_test/test_read ./libsrc/netcdf ./libsrc/putget ./libsrc/ncx \
./libsrc/t_ncxx ./libsrc/attr
mm4::
for m in ${MM4} ; do \
b=`basename $$m` ; d=`dirname $$m`;\
pushd $$d; m4 -s $${b}.m4 > $${b}.c ; popd; done
check_nc_config:
$(CC) `./nc-config --cflags` test_prog.c -o test_prog `./nc-config --libs`
./test_prog
install-data-hook:
@echo ''
@echo '+-------------------------------------------------------------+'
@echo '| Congratulations! You have successfully installed netCDF! |'
@echo '| |'
@echo '| You can use script "nc-config" to find out the relevant |'
@echo '| compiler options to build your application. Enter |'
@echo '| |'
@echo '| nc-config --help |'
@echo '| |'
@echo '| for additional information. |'
@echo '| |'
@echo '| CAUTION: |'
@echo '| |'
@echo '| If you have not already run "make check", then we strongly |'
@echo '| recommend you do so. It does not take very long. |'
@echo '| |'
@echo '| Before using netCDF to store important data, test your |'
@echo '| build with "make check". |'
@echo '| |'
@echo '| NetCDF is tested nightly on many platforms at Unidata |'
@echo '| but your platform is probably different in some ways. |'
@echo '| |'
@echo '| If any tests fail, please see the netCDF web site: |'
@echo '| https://www.unidata.ucar.edu/software/netcdf/ |'
@echo '| |'
@echo '| NetCDF is developed and maintained at the Unidata Program |'
@echo '| Center. Unidata provides a broad array of data and software |'
@echo '| tools for use in geoscience education and research. |'
@echo '| https://www.unidata.ucar.edu |'
@echo '+-------------------------------------------------------------+'
@echo ''
# Create the VERSION file after the build
# in case it is being used by packagers
# Also track the S3 cleanup id
all-local: liblib/libnetcdf.la
echo ${PACKAGE_VERSION} > VERSION
if ENABLE_S3_TESTALL
echo "@TESTUID@" >> ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids
endif
if ENABLE_S3_TESTALL
distclean-local:
rm -f ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids
endif
# Remove the VERSION file
CLEANFILES = VERSION