Commit Graph

38 Commits

Author SHA1 Message Date
Ward Fisher
ec7cc936fa Adding NC_HAS_BLOSC and NC_HAS_BZ2 to netcdf_meta.h in support of https://github.com/Unidata/netcdf-c/issues/2511 2022-09-20 15:11:23 -06:00
Dennis Heimbigner
f419af9204 Cleanup szip handling some more
re: https://github.com/Unidata/netcdf-c/issues/2420

nc_test4/tst_vars3.c has the wrong conditional
around the szip tests (did I do that?).
Anyway, the current test is
> #ifdef HAVE_SZ

and it should be
> #ifdef HAVE_H5Z_SZIP

because the only thing that matters is that HDF5 lib has szip support.
2022-06-22 16:40:54 -06:00
Edward Hartnett
e723b1d570 added BENCHMARKS to the summary 2022-04-26 06:18:52 -06:00
Edward Hartnett
57365d4b47 added ZSTD to netcdf_meta.h and libnetcdf.settings 2022-04-11 08:03:24 -06:00
Charlie Zender
fb70b4cf46 First draft of Granular BitGroom feature for netcdf-c 2021-10-20 16:00:32 -07:00
Edward Hartnett
2db4311b87
Merge branch 'master' into ejh_quantize_2 2021-08-26 23:05:59 -06:00
Edward Hartnett
9a18689ffa getting ready for next try at quantization code 2021-08-24 00:45:38 -06:00
Edward Hartnett
0218fc6e54 added info about logging to build summary, fixed info about byterange in build summary 2021-08-24 00:17:03 -06:00
Dennis Heimbigner
aeb3ac2809 Mostly revert the filter code to reduce its complexity of use.
re: https://github.com/Unidata/netcdf-c/issues/1836

Revert the internal filter code to simplify it. From the user's
point of view, the only visible changes should be:

1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h
2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter.

Internally,the dispatch table has been modified to get rid of the filter_actions
entry and associated complex structures. It has been replaced with
inq_var_filter_ids and inq_var_filter_info entries and the dispatch table
version has been bumped to 3. Corresponding NOOP and NOTNC4 functions
were added to libdispatch/dnotnc4.c. Also, the filter_action entries
in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2,
etc). This should only impact UDF users.

In the process, it became clear that the form of the filters
field in NC_VAR_INFO_T was format dependent, so I converted it to
be of type void* and pushed its management into the various dispatch
code bases. Specifically libhdf5 and libnczarr now manage the filters
field in their own way.

The auxilliary functions for parsing textual filter specifications
were moved to netcdf_aux.h and were renamed to the following:
* ncaux_h5filterspec_parse
* ncaux_h5filterspec_parselist
* ncaux_h5filterspec_free
* ncaux_h5filter_fix8

Misc. Other Changes:

1. Document NUG/filters.md updated to reflect the changes above.
2. All the old data types (structs and enums)
   used by filter_actions actions were deleted.
   The exception is the NC_H5_Filterspec because it is needed
   by ncaux_h5filterspec_parselist.
3. Clientside filters were removed -- another enhancement
   for which no-one ever asked.
4. The ability to remove filters was itself removed.
5. Some functionality needed by nczarr was moved from libhdf5
   to libsrc4 e.g. nc4_find_default_chunksizes
6. All the filterx code was removed
7. ncfilter.h and nc4filter.c no longer used

Misc. Unrelated Changes:

1. The nczarr_test makefile clean was leaving some directories; so
   add clean-local to take care of them.
2020-09-27 12:43:46 -06:00
Ward Fisher
31dee0c4da
Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
Ward Fisher
16c27ca13f
Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries" 2020-08-17 15:51:01 -06:00
Dennis Heimbigner
6074c8a02d Fix items in netcdf_meta.h 2020-08-04 17:31:24 -06:00
Dennis Heimbigner
59e04ae071 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.
2020-06-28 18:02:47 -06:00
Edward Hartnett
0a0282716d added to libnetcdf.settings and netcdf_meta.h 2020-01-16 09:19:24 -07:00
Edward Hartnett
6a902fe210 further removal of RELAX_COORD_BOUNDS macro 2019-11-26 06:45:26 -07:00
edwardhartnett
a0f984f997 added dispatch version to netcdf_meta.h and libnetcdf.settings 2019-11-15 10:06:46 -07:00
Dennis Heimbigner
0c59e13bf7 Master merge, conflict resolution, cleanup 2019-02-24 16:54:13 -07:00
Dennis Heimbigner
bf2746b8ea Provide byte-range reading of remote datasets
re: issue https://github.com/Unidata/netcdf-c/issues/1251

Assume that you have the URL to a remote dataset
which is a normal netcdf-3 or netcdf-4 file.

This PR allows the netcdf-c to read that dataset's
contents as a netcdf file using HTTP byte ranges
if the remote server supports byte-range access.

Originally, this PR was set up to access Amazon S3 objects,
but it can also access other remote datasets such as those
provided by a Thredds server via the HTTPServer access protocol.
It may also work for other kinds of servers.

Note that this is not intended as a true production
capability because, as is known, this kind of access to
can be quite slow. In addition, the byte-range IO drivers
do not currently do any sort of optimization or caching.

An additional goal here is to gain some experience with
the Amazon S3 REST protocol.

This architecture and its use documented in
the file docs/byterange.dox.

There are currently two test cases:

1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle
   for a remote netcdf-3 file and a remote netcdf-4 file.
2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote
   datasets.

This PR also incorporates significantly changed model inference code
(see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259).

1. It centralizes the code that infers the dispatcher.
2. It adds support for byte-range URLs

Other changes:

1. NC_HDF5_finalize was not being properly called by nc_finalize().
2. Fix minor bug in ncgen3.l
3. fix memory leak in nc4info.c
4. add code to walk the .daprc triples and to replace protocol=
   fragment tag with a more general mode= tag.

Final Note:
Th inference code is still way too complicated. We need to move
to the validfile() model used by netcdf Java, where each
dispatcher is asked if it can process the file. This decentralizes
the inference code. This will be done after all the major new
dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-01 18:27:36 -07:00
Ward Fisher
5be0126920 More standardizing of the copyright stanza. 2018-12-06 14:13:56 -07:00
Wei-keng Liao
48da78e133 Use PnetCDF instead of parallel-netcdf to avoid confusion with
parallel netcdf4. Also, update PnetCDF web page.
2018-09-17 17:18:48 -05:00
Ward Fisher
90d664b9ec Merge branch 'has_parallel4' of https://github.com/wkliao/netcdf-c into pr-aggregation.wif 2018-07-31 11:32:54 -06:00
Wei-keng Liao
d0cb241cfe add NC_HAS_PARALLEL4 to netcdf_meta.h.in 2018-07-14 18:03:42 -05:00
Wei-keng Liao
c8f3a647b6 add NC_RELAX_COORD_BOUND to netcdf_meta.h.in 2018-07-13 16:32:43 -05:00
luz.paz
74fbacdb82 Misc. source comment typos
Some are user-facing. Found via `codespell` and through the downstream FreeCAD.
2018-04-26 23:04:01 -04:00
Ward Fisher
7df45badce Added ERANGE_FILL information to netcdf_meta.h 2018-01-25 12:46:46 -07:00
Ward Fisher
b1ad6b8c2f Updating netcdf_meta.h to include CDF5. 2017-09-26 11:32:12 -06:00
Dennis Heimbigner
3db4f013bf Primary change: add dap4 support
Specific changes:
1. Add dap4 code: libdap4 and dap4_test.
   Note that until the d4ts server problem is solved, dap4 is turned off.
2. Modify various files to support dap4 flags:
	configure.ac, Makefile.am, CMakeLists.txt, etc.
3. Add nc_test/test_common.sh. This centralizes
   the handling of the locations of various
   things in the build tree: e.g. where is
   ncgen.exe located. See nc_test/test_common.sh
   for details.
4. Modify .sh files to use test_common.sh
5. Obsolete separate oc2 by moving it to be part of
   netcdf-c. This means replacing code with netcdf-c
   equivalents.
5. Add --with-testserver to configure.ac to allow
   override of the servers to be used for --enable-dap-remote-tests.
6. There were multiple versions of nctypealignment code. Try to
   centralize in libdispatch/doffset.c and include/ncoffsets.h
7. Add a unit test for the ncuri code because of its complexity.
8. Move the findserver code out of libdispatch and into
   a separate, self contained program in ncdap_test and dap4_test.
9. Move the dispatch header files (nc{3,4}dispatch.h) to
   .../include because they are now shared by modules.
10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts.
11. Make use of MREMAP if available
12. Misc. minor changes e.g.
	- #include <config.h> -> #include "config.h"
	- Add some no-install headers to /include
	- extern -> EXTERNL and vice versa as needed
	- misc header cleanup
	- clean up checking for misc. unix vs microsoft functions
13. Change copyright decls in some files to point to LICENSE file.
14. Add notes to RELEASENOTES.md
2017-03-08 17:01:10 -07:00
Greg Sjaardema
2d3278c58b Update comment
If pnetcdf support is enabled, then  NC_HAS_PARALLEL is defined to 1 even if HDF5 is not enabled.  Fix comment to make this clearer.
2016-02-10 15:07:19 -07:00
Ward Fisher
4826fd73ce Tightened up formatting for generated netcdf_meta.h file. 2014-09-26 13:57:50 -06:00
Ward Fisher
36ca7ca972 Moved previously defined macros out of meta.h and back into netcdf.h, so that we don't break the just-released netcdf-fortran release. 2014-09-24 10:22:40 -06:00
Ward Fisher
4958670b0c Added a new .gitignore specific to include/.
Added netcdf_meta.h to user documentation generated by doxygen.
2014-09-18 15:05:08 -06:00
Ward Fisher
6f4a92f1b6 Updated copyright information for netcdf.h, netcdf_meta.h template. 2014-09-11 15:30:22 -06:00
Ward Fisher
302b8003b7 Added definition of NC_HAVE_META_H to netcdf.h.
Moved NC_HAVE_INQ_FORMAT_EXTENDED, NC_HAVE_RENAME_GRP
to netcdf_meta.h.
2014-09-11 15:19:02 -06:00
Ward Fisher
028d564344 Have finished with autotools-based netcdf_meta.h template. Need to redo cmake-based template to match behavior.
Modified cmake to use the same netcdf_meta template as autotools.

Removed trace of old cmake template file.
2014-09-11 12:32:55 -06:00
Ward Fisher
2368e0ed05 Work in progress. 2014-09-10 13:35:27 -06:00
Ward Fisher
206ebc514c Infrastructure for generating a meta header file dynamically at configure time. 2014-09-10 13:35:27 -06:00
Ward Fisher
bb8077af30 Working woards automatically-generated meta information file. 2014-09-10 13:35:27 -06:00
Ward Fisher
2ddb91205d Initial version of template header file. 2014-09-10 13:35:26 -06:00