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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2018-02-02 23:45:03 +08:00
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# Copyright 2005-2018, see the COPYRIGHT file for more information.
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2010-06-03 21:24:43 +08:00
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# This is the main automake file for netCDF. It builds the different
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# netcdf directories. Not all directories are built, depending on the
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# options selected during configure.
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2018-02-02 23:42:49 +08:00
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2017-11-19 21:56:44 +08:00
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# Ed Hartnett, Ward Fisher
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2010-06-03 21:24:43 +08:00
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2023-04-26 07:15:06 +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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2010-06-03 21:24:43 +08:00
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# This directory stores libtool macros, put there by aclocal.
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ACLOCAL_AMFLAGS = -I m4
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2023-04-26 07:15:06 +08:00
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TESTS_ENVIRONMENT =
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TEST_EXTENSIONS = .sh
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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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2022-06-01 05:50:37 +08:00
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##
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# Turn off plugin directory during distcheck, see
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# comment thread at https://github.com/Unidata/netcdf-c/pull/2348
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# for more information.
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##
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AM_DISTCHECK_CONFIGURE_FLAGS = --without-plugin-dir
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2010-06-03 21:24:43 +08:00
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# These files get added to the distribution.
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2017-11-30 20:29:22 +08:00
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EXTRA_DIST = README.md COPYRIGHT INSTALL.md test_prog.c lib_flags.am \
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cmake CMakeLists.txt COMPILE.cmake.txt config.h.cmake.in \
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cmake_uninstall.cmake.in FixBundle.cmake.in nc-config.cmake.in \
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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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RELEASE_NOTES.md CTestConfig.cmake.in CTestCustom.cmake.in \
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2017-11-30 20:29:22 +08:00
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libnetcdf.settings.in netCDFConfig.cmake.in CMakeInstallation.cmake \
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2024-02-01 03:32:02 +08:00
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test-driver-verbose test_common.in fuzz CITATION.cff
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2010-06-03 21:24:43 +08:00
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2018-02-02 23:42:49 +08:00
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pkgconfigdir = $(libdir)/pkgconfig
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2010-06-03 21:24:43 +08:00
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pkgconfig_DATA = netcdf.pc
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2019-08-09 23:31:24 +08:00
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# Does the user want to build and run unit tests?
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if BUILD_UNIT_TESTS
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UNIT_TEST = unit_test
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endif # BUILD_UNIT_TESTS
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2010-06-03 21:24:43 +08:00
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# Does the user want to build the V2 API?
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if BUILD_V2
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V2_TEST = nctest
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endif
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# Does the user want to build ncgen/ncdump?
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2024-03-19 04:29:24 +08:00
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if NETCDF_BUILD_UTILITIES
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2010-06-03 21:24:43 +08:00
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NCGEN3 = ncgen3
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NCGEN = ncgen
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NCDUMP = ncdump
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endif
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# Does the user want to build the examples?
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if BUILD_EXAMPLES
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EXAMPLES = examples
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endif
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# Is the user building netCDF-4?
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if USE_NETCDF4
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LIBSRC4_DIR = libsrc4
|
2018-11-29 06:48:08 +08:00
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|
endif
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# Is the user building with HDF5?
|
2020-02-17 03:59:33 +08:00
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|
# Note that USE_HDF5 does not imply USE_NETCDF4
|
2018-11-29 06:48:08 +08:00
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|
if USE_HDF5
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|
H5_TEST_DIR = h5_test
|
2018-05-09 01:58:01 +08:00
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|
LIBHDF5 = libhdf5
|
2020-08-18 09:15:47 +08:00
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|
if USE_HDF5
|
2010-06-03 21:24:43 +08:00
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|
NC_TEST4 = nc_test4
|
|
|
|
endif
|
2020-02-17 03:59:33 +08:00
|
|
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endif
|
2010-06-03 21:24:43 +08:00
|
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|
2017-03-09 08:01:10 +08:00
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# Build the dap2 client
|
2024-03-19 04:32:23 +08:00
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|
if NETCDF_ENABLE_DAP
|
2012-08-01 04:34:13 +08:00
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|
OCLIB = oc2
|
2011-05-18 03:14:35 +08:00
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DAP2 = libdap2
|
2017-03-09 08:01:10 +08:00
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|
NCDAP2TESTDIR = ncdap_test
|
2010-06-03 21:24:43 +08:00
|
|
|
endif
|
|
|
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|
2024-03-19 04:32:23 +08:00
|
|
|
if NETCDF_ENABLE_DAP4
|
2017-03-09 08:01:10 +08:00
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|
DAP4 = libdap4
|
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|
NCDAP4TESTDIR = dap4_test
|
2023-04-26 07:15:06 +08:00
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XML = libncxml
|
2017-03-09 08:01:10 +08:00
|
|
|
endif #DAP4
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|
2023-04-26 07:15:06 +08:00
|
|
|
if ENABLE_S3_INTERNAL
|
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XML = libncxml # Internal S3 requires XML
|
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|
endif #ENABLE_S3_INTERNAL
|
|
|
|
|
2018-09-18 00:47:40 +08:00
|
|
|
# Build PnetCDF
|
2013-03-16 04:31:07 +08:00
|
|
|
if USE_PNETCDF
|
2015-08-15 10:38:30 +08:00
|
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|
LIBSRCP = libsrcp
|
2011-09-02 06:32:28 +08:00
|
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|
endif
|
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|
2018-02-08 21:20:58 +08:00
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|
# Build HDF4 if desired.
|
|
|
|
if USE_HDF4
|
2018-03-05 20:53:41 +08:00
|
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|
HDF4_TEST_DIR = hdf4_test
|
2018-02-08 21:20:58 +08:00
|
|
|
LIBHDF4 = libhdf4
|
|
|
|
endif
|
|
|
|
|
2021-09-03 07:04:26 +08:00
|
|
|
# Build Plugin support
|
|
|
|
if ENABLE_PLUGINS
|
|
|
|
NCPOCO = libncpoco
|
|
|
|
endif
|
|
|
|
|
This PR adds EXPERIMENTAL support for accessing data in the
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-29 08:02:47 +08:00
|
|
|
# Build Cloud Storage if desired.
|
|
|
|
if ENABLE_NCZARR
|
|
|
|
ZARR_TEST_DIR = nczarr_test
|
2022-06-01 05:50:37 +08:00
|
|
|
ZARR = libnczarr
|
This PR adds EXPERIMENTAL support for accessing data in the
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-29 08:02:47 +08:00
|
|
|
endif
|
|
|
|
|
2021-09-03 07:04:26 +08:00
|
|
|
# Optionally build test plugins
|
2021-12-24 13:18:56 +08:00
|
|
|
if ENABLE_PLUGINS
|
2018-04-22 10:10:47 +08:00
|
|
|
PLUGIN_DIR = plugins
|
|
|
|
endif
|
|
|
|
|
2019-03-17 22:03:27 +08:00
|
|
|
# If benchmarks were turned on, build and run a bunch more tests.
|
|
|
|
if BUILD_BENCHMARKS
|
|
|
|
BENCHMARKS_DIR = nc_perf
|
|
|
|
endif # BUILD_BENCHMARKS
|
|
|
|
|
2012-04-13 10:41:00 +08:00
|
|
|
# Define Test directories
|
|
|
|
if BUILD_TESTSETS
|
2022-06-01 05:50:37 +08:00
|
|
|
TESTDIRS = $(H5_TEST_DIR)
|
2021-12-24 13:18:56 +08:00
|
|
|
TESTDIRS += $(UNIT_TEST) $(V2_TEST) nc_test $(NC_TEST4)
|
2020-08-18 09:15:47 +08:00
|
|
|
TESTDIRS += $(BENCHMARKS_DIR) $(HDF4_TEST_DIR) $(NCDAP2TESTDIR) $(NCDAP4TESTDIR)
|
|
|
|
TESTDIRS += ${ZARR_TEST_DIR}
|
2012-04-13 10:41:00 +08:00
|
|
|
endif
|
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
# This is the list of subdirs for which Makefiles will be constructed
|
2011-08-11 02:00:32 +08:00
|
|
|
# and run. ncgen must come before ncdump, because their tests
|
2014-07-24 04:26:15 +08:00
|
|
|
# depend on it.
|
2021-12-24 13:18:56 +08:00
|
|
|
SUBDIRS = include ${XML} libdispatch libsrc $(LIBSRC4_DIR) \
|
2021-09-28 08:36:33 +08:00
|
|
|
$(LIBSRCP) $(LIBHDF4) $(LIBHDF5) $(OCLIB) $(DAP2) ${DAP4} \
|
|
|
|
${NCPOCO} ${ZARR} liblib \
|
2021-12-24 13:18:56 +08:00
|
|
|
$(NCGEN3) $(NCGEN) $(NCDUMP) ${PLUGIN_DIR} $(TESTDIRS) docs \
|
2018-05-09 01:58:01 +08:00
|
|
|
$(EXAMPLES)
|
2010-06-03 21:24:43 +08:00
|
|
|
|
|
|
|
# Remove these generated files, for a distclean.
|
2017-11-19 21:56:44 +08:00
|
|
|
DISTCLEANFILES = VERSION comps.txt test_prog libnetcdf.settings \
|
|
|
|
test_common.sh
|
2010-06-03 21:24:43 +08:00
|
|
|
|
|
|
|
# The nc-config script helps the user build programs with netCDF.
|
|
|
|
bin_SCRIPTS = nc-config
|
|
|
|
|
2014-07-24 04:48:36 +08:00
|
|
|
# install libnetcdf.settings in lib directory.
|
2017-11-19 21:56:44 +08:00
|
|
|
settingsdir = $(libdir)
|
|
|
|
settings_DATA = libnetcdf.settings
|
2014-07-24 04:48:36 +08:00
|
|
|
|
2015-08-17 11:44:18 +08:00
|
|
|
####
|
|
|
|
# Provide an entry to rebuild all the m4 generated files
|
|
|
|
# List of files to create: WARNING leave off the extension
|
2015-08-18 03:29:25 +08:00
|
|
|
####
|
|
|
|
|
2017-11-19 21:56:44 +08:00
|
|
|
MM4= ./nc_test/test_put ./nc_test/test_get ./nc_test/test_write \
|
|
|
|
./nc_test/test_read ./libsrc/netcdf ./libsrc/putget ./libsrc/ncx \
|
2015-08-17 11:44:18 +08:00
|
|
|
./libsrc/t_ncxx ./libsrc/attr
|
|
|
|
|
|
|
|
mm4::
|
2015-08-18 03:29:25 +08:00
|
|
|
for m in ${MM4} ; do \
|
|
|
|
b=`basename $$m` ; d=`dirname $$m`;\
|
|
|
|
pushd $$d; m4 -s $${b}.m4 > $${b}.c ; popd; done
|
2015-08-17 11:44:18 +08:00
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
check_nc_config:
|
|
|
|
$(CC) `./nc-config --cflags` test_prog.c -o test_prog `./nc-config --libs`
|
|
|
|
./test_prog
|
|
|
|
|
|
|
|
install-data-hook:
|
2014-11-19 06:33:16 +08:00
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
@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 '| |'
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@echo '| If you have not already run "make check", then we strongly |'
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@echo '| recommend you do so. It does not take very long. |'
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@echo '| |'
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@echo '| Before using netCDF to store important data, test your |'
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@echo '| build with "make check". |'
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@echo '| |'
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@echo '| NetCDF is tested nightly on many platforms at Unidata |'
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@echo '| but your platform is probably different in some ways. |'
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@echo '| |'
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@echo '| If any tests fail, please see the netCDF web site: |'
|
2021-11-12 01:47:49 +08:00
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@echo '| https://www.unidata.ucar.edu/software/netcdf/ |'
|
2010-06-03 21:24:43 +08:00
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@echo '| |'
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@echo '| NetCDF is developed and maintained at the Unidata Program |'
|
2014-07-24 04:26:15 +08:00
|
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@echo '| Center. Unidata provides a broad array of data and software |'
|
2010-06-03 21:24:43 +08:00
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@echo '| tools for use in geoscience education and research. |'
|
2021-11-12 01:47:49 +08:00
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@echo '| https://www.unidata.ucar.edu |'
|
2010-06-03 21:24:43 +08:00
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@echo '+-------------------------------------------------------------+'
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@echo ''
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2022-10-10 09:32:20 +08:00
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# Create the VERSION file after the build
|
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# in case it is being used by packagers
|
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
|
|
|
# Also track the S3 cleanup id
|
2022-10-10 09:32:20 +08:00
|
|
|
all-local: liblib/libnetcdf.la
|
|
|
|
echo ${PACKAGE_VERSION} > VERSION
|
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
|
|
|
if ENABLE_S3_TESTALL
|
2023-10-09 01:22:52 +08:00
|
|
|
rm -f ${abs_top_builddir}/tmp_@PLATFORMUID@.uids
|
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
|
|
|
echo "@TESTUID@" >> ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids
|
2023-10-09 01:22:52 +08:00
|
|
|
cat ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids | sort | uniq > ${abs_top_builddir}/tmp_@PLATFORMUID@.uids
|
|
|
|
rm -f ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids
|
|
|
|
mv ${abs_top_builddir}/tmp_@PLATFORMUID@.uids ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids
|
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
|
|
|
endif
|
|
|
|
|
|
|
|
if ENABLE_S3_TESTALL
|
|
|
|
distclean-local:
|
|
|
|
rm -f ${abs_top_builddir}/s3cleanup_@PLATFORMUID@.uids
|
|
|
|
endif
|
|
|
|
|
2022-10-10 09:32:20 +08:00
|
|
|
# Remove the VERSION file
|
|
|
|
CLEANFILES = VERSION
|