netcdf-c/ncgen/ncgen.h

242 lines
7.4 KiB
C
Raw Normal View History

2010-06-03 21:24:43 +08:00
#ifndef NC_NCGEN_H
#define NC_NCGEN_H
/*********************************************************************
2018-12-07 06:40:43 +08:00
* Copyright 2018, UCAR/Unidata
2010-06-03 21:24:43 +08:00
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncgen/ncgen.h,v 1.18 2010/06/01 15:34:53 ed Exp $
*********************************************************************/
2010-06-03 21:24:43 +08:00
#include "config.h"
2010-06-03 21:24:43 +08:00
2022-01-25 06:01:23 +08:00
#ifndef nulldup
#define nulldup(x) ((x)?strdup(x):(x))
#endif
2010-06-03 21:24:43 +08:00
#ifdef USE_NETCDF4
#define CLASSICONLY 0
#else
#define CLASSICONLY 1
#endif
#define MAX_NC_ATTSIZE 20000 /* max size of attribute (for ncgen) */
#define MAXTRST 5000 /* max size of string value (for ncgen) */
/* Define the possible classes of objects*/
/* extend the NC_XXX values*/
#define NC_GRP 100
#define NC_DIM 101
#define NC_VAR 102
#define NC_ATT 103
#define NC_TYPE 104
#define NC_ECONST 105
#define NC_FIELD 106
#define NC_ARRAY 107
#define NC_PRIM 108 /*Including NC_STRING */
#define NC_STRUCT NC_COMPOUND /* alias */
2012-01-10 02:39:37 +08:00
#define NC_LIST NC_COMPOUND /* alias */
2010-06-03 21:24:43 +08:00
/* Extend nc types with generic fill value*/
#define NC_FILLVALUE 31
/* Extend nc types with NIL value*/
#define NC_NIL 32
2010-06-03 21:24:43 +08:00
2012-09-12 04:17:24 +08:00
#define NEGNC_INFINITEF (-NC_INFINITEF)
#define NEGNC_INFINITE (-NC_INFINITEF)
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
2017-03-09 08:01:10 +08:00
2010-06-03 21:24:43 +08:00
/* nc_class is one of:
NC_GRP NC_DIM NC_VAR NC_ATT NC_TYPE
*/
typedef nc_type nc_class;
/* nc_subclass is one of:
NC_PRIM NC_OPAQUE NC_ENUM
NC_FIELD NC_VLEN NC_COMPOUND
NC_ECONST NC_ARRAY NC_FILLVALUE
*/
typedef nc_type nc_subclass;
/*
Define data structure
xto hold special attribute values
2010-06-03 21:24:43 +08:00
for a given variable.
Global values are kept as
various C global variables
*/
/* Define a bit set for indicating which*/
/* specials were explicitly specified*/
/* See also: ncgen.y.tag2name */
2010-06-03 21:24:43 +08:00
#define _STORAGE_FLAG 0x001
#define _CHUNKSIZES_FLAG 0x002
#define _FLETCHER32_FLAG 0x004
#define _DEFLATE_FLAG 0x008
#define _SHUFFLE_FLAG 0x010
#define _ENDIAN_FLAG 0x020
#define _NOFILL_FLAG 0x040
#define _FILLVALUE_FLAG 0x080
#define _NCPROPS_FLAG 0x100
#define _ISNETCDF4_FLAG 0x200
#define _SUPERBLOCK_FLAG 0x400
#define _FORMAT_FLAG 0x800
#define _FILTER_FLAG 0x1000
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
#define _CODECS_FLAG 0x2000
#define _QUANTIZEBG_FLAG 0x4000
2022-02-20 08:08:36 +08:00
#define _QUANTIZEGBR_FLAG 0x8000
#define _QUANTIZEBR_FLAG 0x10000
2016-05-12 05:31:17 +08:00
extern struct Specialtoken {
char* name;
int token;
int tag;
} specials[];
2010-06-03 21:24:43 +08:00
/* Define an enumeration of supported languages */
typedef enum Language {
L_UNDEFINED=0,
L_BINARY=1,
L_C=2,
L_F77=3,
L_JAVA=4
} Language;
2010-06-03 21:24:43 +08:00
struct Kvalues {
char* name;
int k_flag;
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
int deprecated;
2010-06-03 21:24:43 +08:00
};
extern struct Kvalues legalkinds[];
#define ZIP_ID 0xFFFFFFFF
#define SZIP_ID 0xFFFFFFFE
#define BZIP2_ID 307U
#define ZFP_ID 32013U
#define FPZIP_ID 32014U
2010-06-03 21:24:43 +08:00
/* Note: some non-var specials (i.e. _Format) are not included in this struct*/
2010-06-03 21:24:43 +08:00
typedef struct Specialdata {
int flags;
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
Datalist* _Fillvalue; /* This is a per-type ; points to the _FillValue attribute node */
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
int _Storage; /* NC_CHUNKED | NC_CONTIGUOUS | NC_COMPACT*/
2010-06-03 21:24:43 +08:00
size_t* _ChunkSizes; /* NULL => defaults*/
int nchunks; /* |_Chunksize| ; 0 => not specified*/
int _Fletcher32; /* 1=>fletcher32*/
int _DeflateLevel; /* 0-9 => level*/
int _Shuffle; /* 0 => false, 1 => true*/
int _Endianness; /* 1 =>little, 2 => big*/
int _Fill ; /* 0 => false, 1 => true WATCHOUT: this is inverse of NOFILL*/
int _Quantizer; /* algorithm */
int _NSD; /* No. of significant digits */
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.
2020-09-28 02:43:46 +08:00
NC_H5_Filterspec** _Filters;
size_t nfilters; /* |filters| */
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
char* _Codecs; /* in JSON form */
2010-06-03 21:24:43 +08:00
} Specialdata;
typedef struct GlobalSpecialdata {
int _Format ; /* kflag */
2016-05-12 05:31:17 +08:00
const char* _NCProperties ;
int _IsNetcdf4 ; /* 0 => false, 1 => true */
int _Superblock ; /* HDF5 file superblock version */
} GlobalSpecialData;
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
/*
During the generation of binary data,
we will generate a number of references
to strings and opaques that should
be reclaimed to keep the memory
checkers happy.
*/
typedef struct BinBuffer {
Bytebuffer* buf; /* top level data */
List* reclaim; /* objects that need to be free'd */
} BinBuffer;
2010-06-03 21:24:43 +08:00
/* Track a set of dimensions*/
/* (Note: the netcdf type system is deficient here)*/
typedef struct Dimset {
int ndims;
struct Symbol* dimsyms[NC_MAX_VAR_DIMS]; /* Symbol for dimension*/
} Dimset;
typedef struct Diminfo {
int isconstant; /* separate constant from named dimension*/
int isunlimited;
2010-06-03 21:24:43 +08:00
size_t declsize; /* 0 => unlimited/unspecified*/
} Diminfo;
typedef struct Attrinfo {
struct Symbol* var; /* NULL => global*/
} Attrinfo;
typedef struct Typeinfo {
struct Symbol* basetype;
int hasvlen; /* 1 => this type contains a vlen*/
nc_type typecode;
unsigned long offset; /* fields in struct*/
unsigned long alignment;/* fields in struct*/
NCConstant* econst; /* for enum values*/
2010-06-03 21:24:43 +08:00
Dimset dimset; /* for NC_VAR/NC_FIELD/NC_ATT*/
size_t size; /* for opaque, compound, etc.*/
size_t cmpdalign; /* alignment needed for total size instances */
2010-06-03 21:24:43 +08:00
size_t nelems; /* size in terms of # of datalist constants
it takes to represent it */
Datalist* _Fillvalue; /* per-type cached fillvalue
(overridden by var fillvalue) */
2010-06-03 21:24:43 +08:00
} Typeinfo;
typedef struct Varinfo {
int nattributes; /* |attributes|*/
List* attributes; /* List<Symbol*>*/
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
Specialdata special;
2010-06-03 21:24:43 +08:00
} Varinfo;
typedef struct Groupinfo {
int is_root;
} Groupinfo;
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
typedef struct Fileinfo {
char* filename;
} Fileinfo;
/* store info when the symbol
is really a reference to another
symbol
*/
typedef struct Reference {
int is_ref; /* separate name defs from refs*/
char* unescaped; /* original, unescaped name */
struct Symbol* ref; /* ptr to the symbol if is_ref is true*/
} Reference;
2010-06-03 21:24:43 +08:00
typedef struct Symbol { /* symbol table entry*/
nc_class objectclass; /* NC_DIM|NC_VLEN|NC_OPAQUE...*/
nc_class subclass; /* NC_STRUCT|...*/
char* name;
char* fqn; /* cached fully qualified C or FORTRAN name*/
2010-06-03 21:24:43 +08:00
struct Symbol* container; /* The group containing this symbol.*/
/* for fields or enumids, it is*/
/* the parent type.*/
struct Symbol* location; /* current group when symbol was created*/
List* subnodes; /* sublist for enum or struct or group*/
int is_prefixed; /* prefix was specified (vs computed).*/
List* prefix; /* List<Symbol*>*/
struct Datalist* data; /* shared by variables and attributes*/
/* Note that we cannot union these because some kinds of symbols*/
/* use more than one part*/
Typeinfo typ; /* type info for e.g. var, att, etc.*/
Varinfo var;
2016-05-12 05:31:17 +08:00
Attrinfo att;
2010-06-03 21:24:43 +08:00
Diminfo dim;
Groupinfo grp;
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
Fileinfo file;
Reference ref; /* symbol is really a reference to another symbol*/
2010-06-03 21:24:43 +08:00
/* Misc pieces of info*/
int lineno; /* at point of creation*/
int touched; /* for sorting*/
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
/* for use by -lb */
int nc_id; /* from netcdf API: varid, or dimid, or etc.*/
2010-06-03 21:24:43 +08:00
} Symbol;
#endif /*!NC_NCGEN_H*/