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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
# This is part of Unidata's netCDF package. Copyright 2018, see the
# COPYRIGHT file for more information.
# Build the ZARR dispatch layer.
# Dennis Heimbigner
# Get AM_CPPFLAGS and AM_LDFLAGS
include $(top_srcdir)/lib_flags.am
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
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
AM_CPPFLAGS += -D_LARGEFILE_SOURCE
Add filter support to NCZarr Filter support has three goals: 1. Use the existing HDF5 filter implementations, 2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr, 3. Allow filters to be used even when HDF5 is disabled Detailed usage directions are define in docs/filters.md. For now, the existing filter API is left in place. So filters are defined using ''nc_def_var_filter'' using the HDF5 style where the id and parameters are unsigned integers. This is a big change since filters affect many parts of the code. In the following, the terms "compressor" and "filter" and "codec" are generally used synonomously. ### Filter-Related Changes: * In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms. * Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h. * Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out. * Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h. * Add a number of new test to test the new nczarr filters. * Let ncgen parse _Codecs attribute, although it is ignored. ### Plugin directory changes: * Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file * Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip * Add a Codec defaulter (see docs/filters.md) for the big four filters. * Make plugins work with windows by properly adding __declspec declaration. ### Misc. Non-Filter Changes * Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5. * Improve support for caching * More fixes for path conversion code * Fix misc. memory leaks * Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath. * Add a number of new test to test the non-filter fixes. * Update the parsers * Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-03 07:04:26 +08:00
AM_CPPFLAGS += -I$(top_srcdir)/libsrc4 -I$(top_srcdir)/libncpoco
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
libnczarr_la_CPPFLAGS = ${AM_CPPFLAGS}
AM_CXXFLAGS =
libnczarr_la_LIBADD =
libnczarr_la_LDFLAGS =
Replace ENABLE_NCZARR with NETCDF_ENABLE_NCZARR
2024-03-19 04:37:39 +08:00
# Remember NETCDF_ENABLE_NCZARR implies USE_NETCDF4
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
# We may have to add to these later.
DISTCLEANFILES =
MAINTAINERCLEANFILES =
CLEANFILES =
EXTRA_DIST =
LDADD=
# This is our output. The ZARR convenience library.
noinst_LTLIBRARIES = libnczarr.la
# The source files.
libnczarr_la_SOURCES = \
zarr.c \
zattr.c \
Provide a Number of fixes/improvements to NCZarr Primary changes: * Add an improved cache system to speed up performance. * Fix NCZarr to properly handle scalar variables. Misc. Related Changes: * Added unit tests for extendible hash and for the generic cache. * Add config parameter to set size of the NCZarr cache. * Add initial performance tests but leave them unused. * Add CRC64 support. * Move location of ncdumpchunks utility from /ncgen to /ncdump. * Refactor auth support. Misc. Unrelated Changes: * More cleanup of the S3 support * Add support for S3 authentication in .rc files: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY. * Remove the hashkey from the struct OBJHDR since it is never used.
2020-11-20 08:01:04 +08:00
zxcache.c \
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
zchunking.c \
zclose.c \
zcreate.c \
zcvt.c \
zdim.c \
zdispatch.c \
zfile.c \
zgrp.c \
zinternal.c \
zmap.c \
Add zip file support The primary change is to support the use of a zip file as a storage format. Simultaneously the .nz4 support is made obsolete Use of zip requires the libzip support library, so a number of changes to the build files (Makefile.am, CMakeLists.txt) are necessary to locate and incorporate libzip. The nczarr_tests tests are also changed to add zip testing. Other changes: * Make sure distcheck leaves no files around. * Add some functions to netcdf_aux to export some functions of libnetcdf. * Add a new error NC_EFOUND as the complement of NC_EEMPTY. * Add tracing support to nclog and use it in libnczarr. * Modify the zmap interface to support the writeonce semantics of zip. * Create a new s3util.c to support a variety of S3 auxilliary functions. * EXTERNL'ize a number of functions so they can be used in s3util. * Add support for the S3 ListObjects CommonPrefixes mechanism to improve search. * Add experimental support for running nczarr X s3 tests against the actual Amazon S3 cloud.
2021-01-29 11:11:01 +08:00
zmap_file.c \
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
zodom.c \
zopen.c \
zprov.c \
zsync.c \
ztype.c \
zutil.c \
zvar.c \
zwalk.c \
zdebug.c \
zarr.h \
zcache.h \
zchunking.h \
zdispatch.h \
zincludes.h \
zinternal.h \
zmap.h \
zodom.h \
zprovenance.h \
ckp
2024-10-01 04:39:48 +08:00
zplugins.h \
Add filter support to NCZarr Filter support has three goals: 1. Use the existing HDF5 filter implementations, 2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr, 3. Allow filters to be used even when HDF5 is disabled Detailed usage directions are define in docs/filters.md. For now, the existing filter API is left in place. So filters are defined using ''nc_def_var_filter'' using the HDF5 style where the id and parameters are unsigned integers. This is a big change since filters affect many parts of the code. In the following, the terms "compressor" and "filter" and "codec" are generally used synonomously. ### Filter-Related Changes: * In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms. * Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h. * Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out. * Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h. * Add a number of new test to test the new nczarr filters. * Let ncgen parse _Codecs attribute, although it is ignored. ### Plugin directory changes: * Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file * Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip * Add a Codec defaulter (see docs/filters.md) for the big four filters. * Make plugins work with windows by properly adding __declspec declaration. ### Misc. Non-Filter Changes * Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5. * Improve support for caching * More fixes for path conversion code * Fix misc. memory leaks * Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath. * Add a number of new test to test the non-filter fixes. * Update the parsers * Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-03 07:04:26 +08:00
zfilter.h \
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
zdebug.h
Replace ENABLE_NCZARR with NETCDF_ENABLE_NCZARR
2024-03-19 04:37:39 +08:00
if NETCDF_ENABLE_NCZARR_ZIP
Add zip file support The primary change is to support the use of a zip file as a storage format. Simultaneously the .nz4 support is made obsolete Use of zip requires the libzip support library, so a number of changes to the build files (Makefile.am, CMakeLists.txt) are necessary to locate and incorporate libzip. The nczarr_tests tests are also changed to add zip testing. Other changes: * Make sure distcheck leaves no files around. * Add some functions to netcdf_aux to export some functions of libnetcdf. * Add a new error NC_EFOUND as the complement of NC_EEMPTY. * Add tracing support to nclog and use it in libnczarr. * Modify the zmap interface to support the writeonce semantics of zip. * Create a new s3util.c to support a variety of S3 auxilliary functions. * EXTERNL'ize a number of functions so they can be used in s3util. * Add support for the S3 ListObjects CommonPrefixes mechanism to improve search. * Add experimental support for running nczarr X s3 tests against the actual Amazon S3 cloud.
2021-01-29 11:11:01 +08:00
libnczarr_la_SOURCES += zmap_zip.c
endif
Replace ENABLE_NCZARR with NETCDF_ENABLE_NCZARR
2024-03-19 04:37:39 +08:00
if NETCDF_ENABLE_NCZARR_FILTERS
ckp
2024-10-01 04:39:48 +08:00
libnczarr_la_SOURCES += zfilter.c zplugins.c
Support MSYS2/Mingw platform re: The current netcdf-c release has some problems with the mingw platform on windows. Mostly they are path issues. Changes to support mingw+msys2: ------------------------------- * Enable option of looking into the windows registry to find the mingw root path. In aid of proper path handling. * Add mingw+msys as a specific platform in configure.ac and move testing of the platform to the front so it is available early. * Handle mingw X libncpoco (dynamic loader) properly even though mingw does not yet support it. * Handle mingw X plugins properly even though mingw does not yet support it. * Alias pwd='pwd -W' to better handle paths in shell scripts. * Plus a number of other minor compile irritations. * Disallow the use of multiple nc_open's on the same file for windows (and mingw) because windows does not seem to handle these properly. Not sure why we did not catch this earlier. * Add mountpoint info to dpathmgr.c to help support mingw. * Cleanup dpathmgr conversions. Known problems: --------------- * I have not been able to get shared libraries to work, so plugins/filters must be disabled. * There is some kind of problem with libcurl that I have not solved, so all uses of libcurl (currently DAP+Byterange) must be disabled. Misc. other fixes: ------------------ * Cleanup the relationship between ENABLE_PLUGINS and various other flags in CMakeLists.txt and configure.ac. * Re-arrange the TESTDIRS order in Makefile.am. * Add pseudo-breakpoint to nclog.[ch] for debugging. * Improve the documentation of the path manager code in ncpathmgr.h * Add better support for relative paths in dpathmgr.c * Default the mode args to NCfopen to include "b" (binary) for windows. * Add optional debugging output in various places. * Make sure that everything builds with plugins disabled. * Fix numerous (s)printf inconsistencies betweenb the format spec and the arguments.
2021-12-24 13:18:56 +08:00
endif
Replace ENABLE_S3 with NETCDF_ENABLE_S3
2024-03-19 04:40:19 +08:00
if NETCDF_ENABLE_S3
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
libnczarr_la_SOURCES += zmap_s3sdk.c
Replace ENABLE_S3 with NETCDF_ENABLE_S3
2024-03-19 04:40:19 +08:00
if NETCDF_ENABLE_S3_AWS
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
AM_CXXFLAGS += -std=c++11
endif
Improve S3 Documentation and Support ## Improvements to S3 Documentation * Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths. * Modify *nczarr.md* to remove most of the S3 related text. * Move the S3 text from *nczarr.md* to a new document *cloud.md*. * Add some S3-related text to the *byterange.md* document. Hopefully, this will make it easier for users to find the information they want. ## Rebuild NCZarr Testing In order to avoid problems with running make check in parallel, two changes were made: 1. The *nczarr_test* test system was rebuilt. Now, for each test. any generated files are kept in a test-specific directory, isolated from all other test executions. 2. Similarly, since the S3 test bucket is shared, any generated S3 objects are isolated using a test-specific key path. ## Other S3 Related Changes * Add code to ensure that files created on S3 are reclaimed at end of testing. * Used the bash "trap" command to ensure S3 cleanup even if the test fails. * Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former. * Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket. * Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in. * Merge partial S3 support into dhttp.c. * Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it. * Move some definitions from ncrc.h to ncs3sdk.h ## Other Changes * Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
2023-04-26 07:15:06 +08:00
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
# For now, ignore these
IGNORED=ztype.c
# Package this for cmake build.
EXTRA_DIST += CMakeLists.txt
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