2014-08-30 04:51:14 +08:00
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# NetCDF C Configuration Summary
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2014-08-25 06:29:44 +08:00
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==============================
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2014-05-31 03:36:35 +08:00
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2014-08-30 04:51:14 +08:00
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# General
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2014-05-31 03:36:35 +08:00
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-------
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2014-05-31 05:30:58 +08:00
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NetCDF Version: @PACKAGE_VERSION@
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2019-11-20 06:14:26 +08:00
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Dispatch Version: @NC_DISPATCH_VERSION@
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2014-05-31 05:30:58 +08:00
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Configured On: @CONFIG_DATE@
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Host System: @host_cpu@-@host_vendor@-@host_os@
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Build Directory: @abs_top_builddir@
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2019-11-20 06:14:26 +08:00
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Install Prefix: @prefix@
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Support installation of filters into user-specified location
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
2022-04-30 04:31:55 +08:00
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Plugin Install Prefix: @PLUGIN_INSTALL_DIR_SETTING@
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2014-05-31 03:36:35 +08:00
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2014-08-30 04:51:14 +08:00
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# Compiling Options
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2014-05-31 03:36:35 +08:00
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-----------------
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2014-08-25 06:29:44 +08:00
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C Compiler: @CC_VERSION@
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CFLAGS: @CFLAGS@
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CPPFLAGS: @CPPFLAGS@
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LDFLAGS: @LDFLAGS@
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AM_CFLAGS: @AM_CFLAGS@
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AM_CPPFLAGS: @AM_CPPFLAGS@
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AM_LDFLAGS: @AM_LDFLAGS@
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Shared Library: @enable_shared@
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Static Library: @enable_static@
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Extra libraries: @LIBS@
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2021-11-03 05:35:04 +08:00
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XML Parser: @XMLPARSER@
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2014-05-31 03:36:35 +08:00
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2014-08-30 04:51:14 +08:00
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# Features
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2014-08-25 06:29:44 +08:00
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--------
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2023-01-10 04:11:16 +08:00
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Benchmarks: @HAS_BENCHMARKS@
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2014-08-25 06:29:44 +08:00
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NetCDF-2 API: @HAS_NC2@
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HDF4 Support: @HAS_HDF4@
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2018-11-29 06:50:38 +08:00
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HDF5 Support: @HAS_HDF5@
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2015-11-18 07:31:29 +08:00
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NetCDF-4 API: @HAS_NC4@
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2023-01-10 04:11:16 +08:00
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CDF5 Support: @HAS_CDF5@
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2015-08-16 06:26:35 +08:00
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NC-4 Parallel Support: @HAS_PARALLEL4@
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2018-09-18 00:47:40 +08:00
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PnetCDF Support: @HAS_PNETCDF@
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2023-01-10 04:11:16 +08:00
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Upgrade the nczarr code to match Zarr V2
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
2021-04-25 09:48:15 +08:00
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DAP2 Support: @HAS_DAP2@
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2017-03-09 08:01:10 +08:00
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DAP4 Support: @HAS_DAP4@
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2019-02-25 07:54:13 +08:00
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Byte-Range Support: @HAS_BYTERANGE@
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2023-01-10 04:11:16 +08:00
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NCZarr Support: @HAS_NCZARR@
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NCZarr S3 Support: @HAS_NCZARR_S3@
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2014-08-25 06:29:44 +08:00
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Diskless Support: @HAS_DISKLESS@
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MMap Support: @HAS_MMAP@
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JNA Support: @HAS_JNA@
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2018-09-05 01:27:47 +08:00
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ERANGE Fill Support: @HAS_ERANGE_FILL@
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2020-01-25 07:36:29 +08:00
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Relaxed Boundary Check: @RELAX_COORD_BOUND@
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2023-01-10 04:11:16 +08:00
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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
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NCZarr Support: @HAS_NCZARR@
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2020-09-28 02:43:46 +08:00
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Multi-Filter Support: @HAS_MULTIFILTERS@
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2021-08-24 14:45:38 +08:00
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Quantization: @HAS_QUANTIZE@
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2021-08-24 14:19:41 +08:00
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Logging: @HAS_LOGGING@
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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
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SZIP Write Support: @HAS_SZLIB_WRITE@
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Standard Filters: @STD_FILTERS@
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2022-04-26 20:18:52 +08:00
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ZSTD Support: @HAS_ZSTD@
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2023-01-10 04:11:16 +08:00
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Parallel Filters: @HAS_PAR_FILTERS@
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