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netcdf-c/libhdf5/hdf5debug.h

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Add support for multiple filters per variable. re: https://github.com/Unidata/netcdf-c/issues/1584 Support has been added for multiple filters per variable. This affects a number of components in netcdf. The new APIs are documented in NUG/filters.md. The primary changes are: * A set of new functions are provided (see __include/netcdf_filter.h__). - Obtain a list of the filters associated with a variable - Obtain the parameters for a specific filter. * The existing __nc_inq_var_filter__ function now returns info about the first defined filter. * The utilities (ncgen, ncdump, and nccopy) now support an extended format for specifying a sequence of filters. The general form is __<filter>|<filter>..._. * The ncdump **_Filter** attribute now dumps a list of all the filters associated with a variable using the above new format. * Filter specifications can now use a filter name instead of number for filters known to the netcdf library, which in turn is taken from the HDF5 filter registration page. * New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter is returned if an attempt is made to access an unknown filter. * Internally, the dispatch table has been extended to add a function to handle all of the filter functions. * New, filter-related, tests were added to nc_test4. * A new plugin was added to the plugins directory to help with testing. Notes: 1. The shuffle and fletcher32 filters are not part of the multifilter system. Misc. changes: 1. A debug module was added to libhdf5 to help catch error locations.
2020-02-17 03:59:33 +08:00
/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
#ifndef NCH5DEBUG_H
#define NCH5DEBUG_H
/* Warning: significant performance impact */
#undef H5CATCH
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
#undef H5BACKTRACE
Add support for multiple filters per variable. re: https://github.com/Unidata/netcdf-c/issues/1584 Support has been added for multiple filters per variable. This affects a number of components in netcdf. The new APIs are documented in NUG/filters.md. The primary changes are: * A set of new functions are provided (see __include/netcdf_filter.h__). - Obtain a list of the filters associated with a variable - Obtain the parameters for a specific filter. * The existing __nc_inq_var_filter__ function now returns info about the first defined filter. * The utilities (ncgen, ncdump, and nccopy) now support an extended format for specifying a sequence of filters. The general form is __<filter>|<filter>..._. * The ncdump **_Filter** attribute now dumps a list of all the filters associated with a variable using the above new format. * Filter specifications can now use a filter name instead of number for filters known to the netcdf library, which in turn is taken from the HDF5 filter registration page. * New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter is returned if an attempt is made to access an unknown filter. * Internally, the dispatch table has been extended to add a function to handle all of the filter functions. * New, filter-related, tests were added to nc_test4. * A new plugin was added to the plugins directory to help with testing. Notes: 1. The shuffle and fletcher32 filters are not part of the multifilter system. Misc. changes: 1. A debug module was added to libhdf5 to help catch error locations.
2020-02-17 03:59:33 +08:00
#ifdef H5CATCH
/* Place breakpoint to catch errors close to where they occur*/
Mitigate S3 test interference + Unlimited Dimensions in NCZarr This PR started as an attempt to add unlimited dimensions to NCZarr. It did that, but this exposed significant problems with test interference. So this PR is mostly about fixing -- well mitigating anyway -- test interference. The problem of test interference is now documented in the document docs/internal.md. The solutions implemented here are also describe in that document. The solution is somewhat fragile but multiple cleanup mechanisms are provided. Note that this feature requires that the AWS command line utility must be installed. ## Unlimited Dimensions. The existing NCZarr extensions to Zarr are modified to support unlimited dimensions. NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group". Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2. * Form 1: An integer representing the size of the dimension, which is used for simple named dimensions. * Form 2: A dictionary with the following keys and values" - "size" with an integer value representing the (current) size of the dimension. - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension. For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases. That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension. This is the standard semantics for unlimited dimensions. Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following. * Did a partial refactor of the slice handling code in zwalk.c to clean it up. * Added a number of tests for unlimited dimensions derived from the same test in nc_test4. * Added several NCZarr specific unlimited tests; more are needed. * Add test of endianness. ## Misc. Other Changes * Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the AWS Transfer Utility mechanism. This is controlled by the ```#define TRANSFER```` command in that file. It defaults to being disabled. * Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE). * Fixed an obscure memory leak in ncdump. * Removed some obsolete unit testing code and test cases. * Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c. * Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4. * Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects. * Modify the semantics of zodom to properly handle stride > 1. * Add a truncate operation to the libnczarr zmap code.
2023-09-27 06:56:48 +08:00
/* Warning: do not evaluate e more than once */
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
#define THROW(e) nch5throw(e,__LINE__)
Add support for multiple filters per variable. re: https://github.com/Unidata/netcdf-c/issues/1584 Support has been added for multiple filters per variable. This affects a number of components in netcdf. The new APIs are documented in NUG/filters.md. The primary changes are: * A set of new functions are provided (see __include/netcdf_filter.h__). - Obtain a list of the filters associated with a variable - Obtain the parameters for a specific filter. * The existing __nc_inq_var_filter__ function now returns info about the first defined filter. * The utilities (ncgen, ncdump, and nccopy) now support an extended format for specifying a sequence of filters. The general form is __<filter>|<filter>..._. * The ncdump **_Filter** attribute now dumps a list of all the filters associated with a variable using the above new format. * Filter specifications can now use a filter name instead of number for filters known to the netcdf library, which in turn is taken from the HDF5 filter registration page. * New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter is returned if an attempt is made to access an unknown filter. * Internally, the dispatch table has been extended to add a function to handle all of the filter functions. * New, filter-related, tests were added to nc_test4. * A new plugin was added to the plugins directory to help with testing. Notes: 1. The shuffle and fletcher32 filters are not part of the multifilter system. Misc. changes: 1. A debug module was added to libhdf5 to help catch error locations.
2020-02-17 03:59:33 +08:00
#define THROWCHK(e) (void)nch5throw(e)
extern int nch5breakpoint(int err);
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
extern int nch5throw(int err, int line);
Add support for multiple filters per variable. re: https://github.com/Unidata/netcdf-c/issues/1584 Support has been added for multiple filters per variable. This affects a number of components in netcdf. The new APIs are documented in NUG/filters.md. The primary changes are: * A set of new functions are provided (see __include/netcdf_filter.h__). - Obtain a list of the filters associated with a variable - Obtain the parameters for a specific filter. * The existing __nc_inq_var_filter__ function now returns info about the first defined filter. * The utilities (ncgen, ncdump, and nccopy) now support an extended format for specifying a sequence of filters. The general form is __<filter>|<filter>..._. * The ncdump **_Filter** attribute now dumps a list of all the filters associated with a variable using the above new format. * Filter specifications can now use a filter name instead of number for filters known to the netcdf library, which in turn is taken from the HDF5 filter registration page. * New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter is returned if an attempt is made to access an unknown filter. * Internally, the dispatch table has been extended to add a function to handle all of the filter functions. * New, filter-related, tests were added to nc_test4. * A new plugin was added to the plugins directory to help with testing. Notes: 1. The shuffle and fletcher32 filters are not part of the multifilter system. Misc. changes: 1. A debug module was added to libhdf5 to help catch error locations.
2020-02-17 03:59:33 +08:00
#else
#define THROW(e) (e)
#define THROWCHK(e)
#endif
#endif /*NCH5DEBUG_H*/
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