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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/* Copyright 2018-2018 University Corporation for Atmospheric
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Research/Unidata. */
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/**
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* @file
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* @internal Includes prototypes for libzarr dispatch functions.
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*
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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#ifndef ZDISPATCH_H
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#define ZDISPATCH_H
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#include "zincludes.h"
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#if defined(__cplusplus)
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extern "C" {
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#endif
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EXTERNL int NCZ_create(const char *path, int cmode, size_t initialsz, int basepe, size_t *chunksizehintp, void* parameters, const NC_Dispatch*, int);
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EXTERNL int NCZ_open(const char *path, int mode, int basepe, size_t *chunksizehintp, void* parameters, const NC_Dispatch*, int);
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EXTERNL int NCZ_redef(int ncid);
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EXTERNL int NCZ__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree, size_t r_align);
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EXTERNL int NCZ_sync(int ncid);
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EXTERNL int NCZ_abort(int ncid);
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EXTERNL int NCZ_close(int ncid,void*);
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EXTERNL int NCZ_set_fill(int ncid, int fillmode, int *old_modep);
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EXTERNL int NCZ_set_base_pe(int ncid, int pe);
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EXTERNL int NCZ_inq_base_pe(int ncid, int *pe);
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EXTERNL int NCZ_inq_format(int ncid, int *formatp);
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EXTERNL int NCZ_inq_format_extended(int ncid, int *formatp, int *modep);
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EXTERNL int NCZ_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp);
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EXTERNL int NCZ_inq_type(int, nc_type, char *, size_t *);
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/* Begin _dim */
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EXTERNL int NCZ_def_dim(int ncid, const char *name, size_t len, int *idp);
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EXTERNL int NCZ_inq_dimid(int ncid, const char *name, int *idp);
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EXTERNL int NCZ_inq_dim(int ncid, int dimid, char *name, size_t *lenp);
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EXTERNL int NCZ_inq_unlimdim(int ncid, int *unlimdimidp);
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EXTERNL int NCZ_rename_dim(int ncid, int dimid, const char *name);
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/* End _dim */
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/* Begin _att */
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EXTERNL int NCZ_inq_att(int ncid, int varid, const char *name, nc_type *xtypep, size_t *lenp);
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EXTERNL int NCZ_inq_attid(int ncid, int varid, const char *name, int *idp);
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EXTERNL int NCZ_inq_attname(int ncid, int varid, int attnum, char *name);
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EXTERNL int NCZ_rename_att(int ncid, int varid, const char *name, const char *newname);
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EXTERNL int NCZ_del_att(int ncid, int varid, const char *name);
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/* End _att */
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/* Begin {put,get}_att */
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EXTERNL int NCZ_get_att(int ncid, int varid, const char *name, void *value, nc_type);
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EXTERNL int NCZ_put_att(int ncid, int varid, const char *name, nc_type file_type, size_t len, const void *data, nc_type mem_type);
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/* End {put,get}_att */
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/* Begin _var */
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EXTERNL int NCZ_def_var(int ncid, const char *name, nc_type xtype, int ndims, const int *dimidsp, int *varidp);
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EXTERNL int NCZ_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp, int *shufflep, int *deflatep, int *deflate_levelp, int *fletcher32p, int *contiguousp, size_t *chunksizesp, int *no_fill, void *fill_valuep, int *endiannessp, unsigned int* idp, size_t* nparamsp, unsigned int* params
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);
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EXTERNL int NCZ_inq_varid(int ncid, const char *name, int *varidp);
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EXTERNL int NCZ_rename_var(int ncid, int varid, const char *name);
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EXTERNL int NCZ_put_vara(int ncid, int varid, const size_t *start, const size_t *count, const void *value, nc_type);
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EXTERNL int NCZ_get_vara(int ncid, int varid, const size_t *start, const size_t *count, void *value, nc_type);
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extern int
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NCZ_put_vars(int ncid, int varid, const size_t *start, const size_t *count, const ptrdiff_t* stride, const void *value, nc_type);
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extern int
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NCZ_get_vars(int ncid, int varid, const size_t *start, const size_t *count, const ptrdiff_t* stride, void *value, nc_type);
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/* End _var */
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/* netCDF4 API only */
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EXTERNL int NCZ_inq_ncid(int, const char *, int *);
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EXTERNL int NCZ_inq_grps(int, int *, int *);
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EXTERNL int NCZ_inq_grpname(int, char *);
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EXTERNL int NCZ_inq_grpname_full(int, size_t *, char *);
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EXTERNL int NCZ_inq_grp_parent(int, int *);
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EXTERNL int NCZ_inq_grp_full_ncid(int, const char *, int *);
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EXTERNL int NCZ_inq_varids(int, int * nvars, int *);
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EXTERNL int NCZ_inq_dimids(int, int * ndims, int *, int);
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EXTERNL int NCZ_inq_typeids(int, int * ntypes, int *);
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EXTERNL int NCZ_inq_type_equal(int, nc_type, int, nc_type, int *);
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EXTERNL int NCZ_def_grp(int, const char *, int *);
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EXTERNL int NCZ_rename_grp(int, const char *);
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EXTERNL int NCZ_inq_user_type(int, nc_type, char *, size_t *, nc_type *, size_t *, int *);
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EXTERNL int NCZ_def_compound(int, size_t, const char *, nc_type *);
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EXTERNL int NCZ_insert_compound(int, nc_type, const char *, size_t, nc_type);
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EXTERNL int NCZ_insert_array_compound(int, nc_type, const char *, size_t, nc_type, int, const int *);
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EXTERNL int NCZ_inq_typeid(int, const char *, nc_type *);
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EXTERNL int NCZ_inq_compound_field(int, nc_type, int, char *, size_t *, nc_type *, int *, int *);
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EXTERNL int NCZ_inq_compound_fieldindex(int, nc_type, const char *, int *);
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EXTERNL int NCZ_def_vlen(int, const char *, nc_type base_typeid, nc_type *);
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EXTERNL int NCZ_put_vlen_element(int, int, void *, size_t, const void *);
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EXTERNL int NCZ_get_vlen_element(int, int, const void *, size_t *, void *);
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EXTERNL int NCZ_def_enum(int, nc_type, const char *, nc_type *);
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EXTERNL int NCZ_insert_enum(int, nc_type, const char *, const void *);
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EXTERNL int NCZ_inq_enum_member(int, nc_type, int, char *, void *);
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EXTERNL int NCZ_inq_enum_ident(int, nc_type, long long, char *);
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EXTERNL int NCZ_def_opaque(int, size_t, const char *, nc_type *);
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EXTERNL int NCZ_def_var_deflate(int, int, int, int, int);
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EXTERNL int NCZ_def_var_fletcher32(int, int, int);
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EXTERNL int NCZ_def_var_chunking(int, int, int, const size_t *);
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EXTERNL int NCZ_def_var_fill(int, int, int, const void *);
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EXTERNL int NCZ_def_var_endian(int, int, int);
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EXTERNL int NCZ_inq_unlimdims(int, int *, int *);
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2020-09-28 02:43:46 +08:00
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EXTERNL int NCZ_def_var_filter(int ncid, int varid, unsigned int filterid, size_t nparams, const unsigned int *params);
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EXTERNL int NCZ_inq_var_filter_ids(int ncid, int varid, size_t* nfiltersp, unsigned int *filterids);
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EXTERNL int NCZ_inq_var_filter_info(int ncid, int varid, unsigned int filterid, size_t* nparamsp, unsigned int *params);
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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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EXTERNL int NCZ_inq_filter_avail(int ncid, unsigned id);
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2020-09-28 02:43:46 +08:00
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2022-01-25 06:22:24 +08:00
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EXTERNL int NCZ_def_var_quantize(int ncid, int varid, int quantize_mode, int nsd);
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EXTERNL int NCZ_inq_var_quantize(int ncid, int varid, int *quantize_modep, int *nsdp);
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/**************************************************/
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/* Following functions wrap libsrc4 */
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EXTERNL int NCZ_inq_type(int ncid, nc_type xtype, char *name, size_t *size);
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EXTERNL int NCZ_inq_dimid(int ncid, const char *name, int *idp);
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EXTERNL int NCZ_inq_unlimdim(int ncid, int *unlimdimidp);
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EXTERNL int NCZ_inq_attname(int ncid, int varid, int attnum, char *name);
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EXTERNL int NCZ_inq_varid(int ncid, const char* name, int *varidp);
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EXTERNL int NCZ_inq_ncid(int ncid, const char* name, int* grpidp);
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EXTERNL int NCZ_inq_grps(int ncid, int* n, int* ncids);
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EXTERNL int NCZ_inq_grpname(int ncid, char* name);
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EXTERNL int NCZ_inq_grpname_full(int ncid, size_t* lenp, char* fullname);
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EXTERNL int NCZ_inq_grp_parent(int ncid, int* parentidp);
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EXTERNL int NCZ_inq_grp_full_ncid(int ncid, const char* fullname, int* grpidp);
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EXTERNL int NCZ_inq_varids(int ncid, int* nvars, int* varids);
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EXTERNL int NCZ_inq_dimids(int ncid, int* ndims, int* dimids, int inclparents);
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EXTERNL int NCZ_inq_typeids(int ncid, int* ntypes, int* typeids);
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EXTERNL int NCZ_inq_user_type(int ncid, nc_type xtype, char* name, size_t* size, nc_type* basetid, size_t* nfields, int* classp);
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/**************************************************/
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2021-09-03 07:04:26 +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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#if defined(__cplusplus)
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}
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#endif
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#endif /* ZDISPATCH_H */
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