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730aa1f6bc
There were some irregularities in the flags for handling NCZarr S3 support. The primary change is to regularize the flags controlling this to the following. 1. Automake: --enable-nczarr-s3 and CMake: ENABLE_NCZARR_S3 2. Automake: --enable-nczarr-s3-tests and CMake: ENABLE_NCZARR_S3_TESTS Flag 1 indicates that NCZarr should be built with S3 support enabled. Flag 2 indicates that the NCZarr S3 tests should be run These two flags are separate because running the NCZarr S3 tests requires access to protected S3 resources. Currently, running these tests is restricted to Unidata personnel. However, users may want to enable S3 support even if they cannot run the tests. It is, of course, an error to specify 2 without specifying 1. Additionally, if the AWS S3 SDK library is not found, then the NCZARR S3 support and testing must be disabled. Otherwise an error is signaled during the build. Some of these NCZarr and S3 changes are propagated to nc-config. Misc. Other Changes: 1. Allow testing for CYGWIN or MSVC in shell scripts. 2. Add specific test for HDF5 library version 1.10.6. This is encoded as "HDF5_UTF8_PATHS" because that is the first version where HDF5 properly supports it under Windows. This is used in hdf5internal/nc4_ndf5_ansi_to_utf8. 3. Add a AM Conditional -- AX_IGNORE -- for use in testing when it is desirable to temporarily suppress Makefile code. 4. Add MULTIFILTER flag to CMakeLists.txt
1105 lines
32 KiB
C
1105 lines
32 KiB
C
/* Copyright 2003-2018, University Corporation for Atmospheric
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* Research. See the COPYRIGHT file for copying and redistribution
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* conditions.
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*/
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/**
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* @file @internal Internal netcdf-4 functions.
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*
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* This file contains functions internal to the netcdf4 library. None of
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* the functions in this file are exposed in the exetnal API. These
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* functions all relate to the manipulation of netcdf-4's in-memory
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* buffer of metadata information, i.e. the linked list of NC
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* structs.
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*
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* @author Ed Hartnett
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*/
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#include "config.h"
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#include "hdf5internal.h"
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#ifdef _WIN32
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#include <windows.h>
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#endif
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#undef DEBUGH5
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#ifdef DEBUGH5
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/**
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* @internal Provide a catchable error reporting function
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*
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* @param ignored Ignored.
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*
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* @return 0 for success.
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*/
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static herr_t
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h5catch(void* ignored)
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{
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H5Eprint(NULL);
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return 0;
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}
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#endif
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/* These are the default chunk cache sizes for HDF5 files created or
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* opened with netCDF-4. */
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extern size_t nc4_chunk_cache_size;
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extern size_t nc4_chunk_cache_nelems;
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extern float nc4_chunk_cache_preemption;
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#ifdef LOGGING
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/* This is the severity level of messages which will be logged. Use
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severity 0 for errors, 1 for important log messages, 2 for less
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important, etc. */
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extern int nc_log_level;
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#endif /* LOGGING */
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int nc4_hdf5_initialized = 0; /**< True if initialization has happened. */
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/**
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* @internal Provide a wrapper for H5Eset_auto
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* @param func Pointer to func.
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* @param client_data Client data.
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*
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* @return 0 for success
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*/
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static herr_t
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set_auto(void* func, void *client_data)
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{
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#ifdef DEBUGH5
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return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)h5catch,client_data);
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#else
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return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)func,client_data);
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#endif
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}
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/**
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* @internal Provide a function to do any necessary initialization of
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* the HDF5 library.
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*/
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void
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nc4_hdf5_initialize(void)
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{
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if (set_auto(NULL, NULL) < 0)
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LOG((0, "Couldn't turn off HDF5 error messages!"));
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LOG((1, "HDF5 error messages have been turned off."));
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nc4_hdf5_initialized = 1;
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}
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/**
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* @internal Provide a function to do any necessary finalization of
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* the HDF5 library.
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*/
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void
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nc4_hdf5_finalize(void)
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{
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/* Reclaim global resources */
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NC4_provenance_finalize();
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nc4_hdf5_initialized = 0;
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}
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/**
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* @internal Given a varid, return the maximum length of a dimension
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* using dimid.
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*
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* @param grp Pointer to group info struct.
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* @param varid Variable ID.
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* @param dimid Dimension ID.
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* @param maxlen Pointer that gets the max length.
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*
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* @return ::NC_NOERR No error.
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* @author Ed Hartnett
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*/
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static int
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find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid,
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size_t *maxlen)
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{
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hid_t datasetid = 0, spaceid = 0;
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NC_VAR_INFO_T *var;
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hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
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int d, dataset_ndims = 0;
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int retval = NC_NOERR;
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*maxlen = 0;
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/* Find this var. */
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var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
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if (!var) return NC_ENOTVAR;
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assert(var->hdr.id == varid);
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/* If the var hasn't been created yet, its size is 0. */
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if (!var->created)
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{
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*maxlen = 0;
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}
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else
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{
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/* Get the number of records in the dataset. */
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if ((retval = nc4_open_var_grp2(grp, var->hdr.id, &datasetid)))
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BAIL(retval);
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if ((spaceid = H5Dget_space(datasetid)) < 0)
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BAIL(NC_EHDFERR);
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/* If it's a scalar dataset, it has length one. */
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if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
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{
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*maxlen = (var->dimids && var->dimids[0] == dimid) ? 1 : 0;
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}
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else
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{
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/* Check to make sure ndims is right, then get the len of each
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dim in the space. */
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if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
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BAIL(NC_EHDFERR);
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if (dataset_ndims != var->ndims)
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BAIL(NC_EHDFERR);
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if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
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BAIL(NC_ENOMEM);
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if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
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BAIL(NC_ENOMEM);
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if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
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h5dimlen, h5dimlenmax)) < 0)
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BAIL(NC_EHDFERR);
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LOG((5, "find_var_dim_max_length: varid %d len %d max: %d",
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varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
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for (d=0; d<dataset_ndims; d++) {
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if (var->dimids[d] == dimid) {
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*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
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}
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}
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}
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}
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exit:
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if (spaceid > 0 && H5Sclose(spaceid) < 0)
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BAIL2(NC_EHDFERR);
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if (h5dimlen) free(h5dimlen);
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if (h5dimlenmax) free(h5dimlenmax);
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return retval;
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}
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/**
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* @internal Search for type with a given HDF type id.
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*
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* @param h5 File
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* @param target_hdf_typeid HDF5 type ID to find.
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*
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* @return Pointer to type info struct, or NULL if not found.
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* @author Ed Hartnett
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*/
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NC_TYPE_INFO_T *
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nc4_rec_find_hdf_type(NC_FILE_INFO_T *h5, hid_t target_hdf_typeid)
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{
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NC_TYPE_INFO_T *type;
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htri_t equal;
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int i;
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assert(h5);
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for (i = 0; i < nclistlength(h5->alltypes); i++)
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{
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NC_HDF5_TYPE_INFO_T *hdf5_type;
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hid_t hdf_typeid;
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type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes, i);
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if(type == NULL) continue;
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/* Get HDF5-specific type info. */
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hdf5_type = (NC_HDF5_TYPE_INFO_T *)type->format_type_info;
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/* Select the HDF5 typeid to use. */
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hdf_typeid = hdf5_type->native_hdf_typeid ?
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hdf5_type->native_hdf_typeid : hdf5_type->hdf_typeid;
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/* Is this the type we are searching for? */
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if ((equal = H5Tequal(hdf_typeid, target_hdf_typeid)) < 0)
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return NULL;
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if (equal)
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return type;
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}
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/* Can't find it. Fate, why do you mock me? */
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return NULL;
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}
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/**
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* @internal Find the actual length of a dim by checking the length of
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* that dim in all variables that use it, in grp or children. **len
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* must be initialized to zero before this function is called.
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*
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* @param grp Pointer to group info struct.
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* @param dimid Dimension ID.
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* @param len Pointer to pointer that gets length.
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*
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* @return ::NC_NOERR No error.
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* @author Ed Hartnett
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*/
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int
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nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len)
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{
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NC_VAR_INFO_T *var;
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int retval;
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int i;
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assert(grp && len);
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LOG((3, "%s: grp->name %s dimid %d", __func__, grp->hdr.name, dimid));
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/* If there are any groups, call this function recursively on
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* them. */
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for (i = 0; i < ncindexsize(grp->children); i++)
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if ((retval = nc4_find_dim_len((NC_GRP_INFO_T*)ncindexith(grp->children, i),
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dimid, len)))
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return retval;
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/* For all variables in this group, find the ones that use this
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* dimension, and remember the max length. */
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for (i = 0; i < ncindexsize(grp->vars); i++)
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{
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size_t mylen;
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var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
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assert(var);
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/* Find max length of dim in this variable... */
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if ((retval = find_var_dim_max_length(grp, var->hdr.id, dimid, &mylen)))
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return retval;
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**len = **len > mylen ? **len : mylen;
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}
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return NC_NOERR;
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}
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/**
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* @internal Break a coordinate variable to separate the dimension and
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* the variable.
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*
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* This is called from nc_rename_dim() and nc_rename_var(). In some
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* renames, the coord variable must stay, but it is no longer a coord
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* variable. This function changes a coord var into an ordinary
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* variable.
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*
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* @param grp Pointer to group info struct.
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* @param coord_var Pointer to variable info struct.
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* @param dim Pointer to dimension info struct.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_ENOMEM Out of memory.
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* @author Quincey Koziol, Ed Hartnett
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*/
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int
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nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var,
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NC_DIM_INFO_T *dim)
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{
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int retval;
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NC_HDF5_VAR_INFO_T* coord_h5var = (NC_HDF5_VAR_INFO_T*)coord_var->format_var_info;
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/* Sanity checks */
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assert(grp && coord_var && dim && dim->coord_var == coord_var &&
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coord_var->dim[0] == dim && coord_var->dimids[0] == dim->hdr.id &&
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!((NC_HDF5_DIM_INFO_T *)(dim->format_dim_info))->hdf_dimscaleid);
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LOG((3, "%s dim %s was associated with var %s, but now has different name",
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__func__, dim->hdr.name, coord_var->hdr.name));
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/* If we're replacing an existing dimscale dataset, go to
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* every var in the file and detach this dimension scale. */
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if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
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dim->hdr.id,
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((NC_HDF5_VAR_INFO_T *)(coord_var->format_var_info))->hdf_datasetid)))
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return retval;
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/* Allow attached dimscales to be tracked on the [former]
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* coordinate variable */
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if (coord_var->ndims)
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{
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/* Coordinate variables shouldn't have dimscales attached. */
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assert(!coord_h5var->dimscale_attached);
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/* Allocate space for tracking them */
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if (!(coord_h5var->dimscale_attached = calloc(coord_var->ndims,
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sizeof(nc_bool_t))))
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return NC_ENOMEM;
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}
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/* Detach dimension from variable */
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coord_h5var->dimscale = NC_FALSE;
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dim->coord_var = NULL;
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/* Set state transition indicators */
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coord_var->was_coord_var = NC_TRUE;
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coord_var->became_coord_var = NC_FALSE;
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return NC_NOERR;
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}
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/**
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* @internal Delete an existing dimscale-only dataset.
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*
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* A dimscale-only HDF5 dataset is created when a dim is defined
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* without an accompanying coordinate variable.
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*
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* Sometimes, during renames, or late creation of variables, an
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* existing, dimscale-only dataset must be removed. This means
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* detaching all variables that use the dataset, then closing and
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* unlinking it.
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*
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* @param grp The grp of the dimscale-only dataset to be deleted, or a
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* higher group in the hierarchy (ex. root group).
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* @param dimid id of the dimension
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* @param dim Pointer to the dim with the dimscale-only dataset to be
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* deleted.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EHDFERR HDF5 error.
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* @author Ed Hartnett
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*/
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int
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delete_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
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{
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NC_HDF5_DIM_INFO_T *hdf5_dim;
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NC_HDF5_GRP_INFO_T *hdf5_grp;
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int retval;
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assert(grp && grp->format_grp_info && dim && dim->format_dim_info);
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LOG((2, "%s: deleting dimscale dataset %s dimid %d", __func__, dim->hdr.name,
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dimid));
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/* Get HDF5 specific grp and dim info. */
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hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
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hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
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/* Detach dimscale from any variables using it */
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if ((retval = rec_detach_scales(grp, dimid, hdf5_dim->hdf_dimscaleid)) < 0)
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return retval;
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/* Close the HDF5 dataset */
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if (H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
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return NC_EHDFERR;
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hdf5_dim->hdf_dimscaleid = 0;
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/* Now delete the dataset. */
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if (H5Gunlink(hdf5_grp->hdf_grpid, dim->hdr.name) < 0)
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return NC_EHDFERR;
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return NC_NOERR;
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}
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/**
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* @internal Reform a coordinate variable from a dimension and a
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* variable.
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*
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* @param grp Pointer to group info struct.
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* @param var Pointer to variable info struct.
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* @param dim Pointer to dimension info struct.
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*
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* @return ::NC_NOERR No error.
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* @author Quincey Koziol, Ed Hartnett
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*/
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int
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nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
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{
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NC_HDF5_DIM_INFO_T *hdf5_dim;
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NC_HDF5_GRP_INFO_T *hdf5_grp;
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NC_HDF5_VAR_INFO_T *hdf5_var;
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int need_to_reattach_scales = 0;
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int retval = NC_NOERR;
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assert(grp && grp->format_grp_info && var && var->format_var_info &&
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dim && dim->format_dim_info);
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LOG((3, "%s: dim->hdr.name %s var->hdr.name %s", __func__, dim->hdr.name,
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var->hdr.name));
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/* Get HDF5-specific dim, group, and var info. */
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hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
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hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
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hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
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/* Detach dimscales from the [new] coordinate variable. */
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if (hdf5_var->dimscale_attached)
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{
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int dims_detached = 0;
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int finished = 0;
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int d;
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|
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/* Loop over all dimensions for variable. */
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for (d = 0; d < var->ndims && !finished; d++)
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{
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/* Is there a dimscale attached to this axis? */
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if (hdf5_var->dimscale_attached[d])
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{
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NC_GRP_INFO_T *g;
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int k;
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for (g = grp; g && !finished; g = g->parent)
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{
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NC_DIM_INFO_T *dim1;
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NC_HDF5_DIM_INFO_T *hdf5_dim1;
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for (k = 0; k < ncindexsize(g->dim); k++)
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{
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dim1 = (NC_DIM_INFO_T *)ncindexith(g->dim, k);
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assert(dim1 && dim1->format_dim_info);
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hdf5_dim1 = (NC_HDF5_DIM_INFO_T *)dim1->format_dim_info;
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if (var->dimids[d] == dim1->hdr.id)
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{
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hid_t dim_datasetid; /* Dataset ID for dimension */
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|
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/* Find dataset ID for dimension */
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if (dim1->coord_var)
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dim_datasetid = ((NC_HDF5_VAR_INFO_T *)
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(dim1->coord_var->format_var_info))->hdf_datasetid;
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else
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dim_datasetid = hdf5_dim1->hdf_dimscaleid;
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|
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/* dim_datasetid may be 0 in some cases when
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* renames of dims and vars are happening. In
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* this case, the scale has already been
|
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* detached. */
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if (dim_datasetid > 0)
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{
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LOG((3, "detaching scale from %s", var->hdr.name));
|
|
if (H5DSdetach_scale(hdf5_var->hdf_datasetid,
|
|
dim_datasetid, d) < 0)
|
|
BAIL(NC_EHDFERR);
|
|
}
|
|
hdf5_var->dimscale_attached[d] = NC_FALSE;
|
|
if (dims_detached++ == var->ndims)
|
|
finished++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
} /* next variable dimension */
|
|
|
|
/* Release & reset the array tracking attached dimscales. */
|
|
free(hdf5_var->dimscale_attached);
|
|
hdf5_var->dimscale_attached = NULL;
|
|
need_to_reattach_scales++;
|
|
}
|
|
|
|
/* Use variable's dataset ID for the dimscale ID. */
|
|
if (hdf5_dim->hdf_dimscaleid && grp != NULL)
|
|
{
|
|
LOG((3, "closing and unlinking dimscale dataset %s", dim->hdr.name));
|
|
if (H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
|
|
BAIL(NC_EHDFERR);
|
|
hdf5_dim->hdf_dimscaleid = 0;
|
|
|
|
/* Now delete the dimscale's dataset (it will be recreated
|
|
later, if necessary). */
|
|
if (H5Gunlink(hdf5_grp->hdf_grpid, dim->hdr.name) < 0)
|
|
return NC_EDIMMETA;
|
|
}
|
|
|
|
/* Attach variable to dimension. */
|
|
hdf5_var->dimscale = NC_TRUE;
|
|
dim->coord_var = var;
|
|
|
|
/* Check if this variable used to be a coord. var */
|
|
if (need_to_reattach_scales || (var->was_coord_var && grp != NULL))
|
|
{
|
|
/* Reattach the scale everywhere it is used. (Recall that netCDF
|
|
* dimscales are always 1-D) */
|
|
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
|
|
var->dimids[0], hdf5_var->hdf_datasetid)))
|
|
return retval;
|
|
|
|
/* Set state transition indicator (cancels earlier
|
|
* transition). */
|
|
var->was_coord_var = NC_FALSE;
|
|
}
|
|
|
|
/* Set state transition indicator */
|
|
var->became_coord_var = NC_TRUE;
|
|
|
|
exit:
|
|
return retval;
|
|
}
|
|
|
|
/**
|
|
* @internal Close HDF5 resources for global atts in a group.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
static int
|
|
close_gatts(NC_GRP_INFO_T *grp)
|
|
{
|
|
NC_ATT_INFO_T *att;
|
|
int a;
|
|
|
|
for (a = 0; a < ncindexsize(grp->att); a++)
|
|
{
|
|
att = (NC_ATT_INFO_T *)ncindexith(grp->att, a);
|
|
assert(att && att->format_att_info);
|
|
nc4_HDF5_close_att(att);
|
|
}
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Close HDF5 resources for a single attribute
|
|
*
|
|
* @param att Pointer to att info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Dennis Heimbigner, Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_HDF5_close_att(NC_ATT_INFO_T *att)
|
|
{
|
|
NC_HDF5_ATT_INFO_T *hdf5_att;
|
|
|
|
assert(att && att->format_att_info);
|
|
hdf5_att = (NC_HDF5_ATT_INFO_T *)att->format_att_info;
|
|
|
|
/* Close the HDF5 typeid. */
|
|
if (hdf5_att->native_hdf_typeid &&
|
|
H5Tclose(hdf5_att->native_hdf_typeid) < 0)
|
|
return NC_EHDFERR;
|
|
|
|
nullfree(hdf5_att);
|
|
att->format_att_info = NULL;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Close HDF5 resources for vars in a group.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
static int
|
|
close_vars(NC_GRP_INFO_T *grp)
|
|
{
|
|
NC_VAR_INFO_T *var;
|
|
NC_HDF5_VAR_INFO_T *hdf5_var;
|
|
NC_ATT_INFO_T *att;
|
|
int a, i;
|
|
|
|
for (i = 0; i < ncindexsize(grp->vars); i++)
|
|
{
|
|
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
|
|
assert(var && var->format_var_info);
|
|
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
|
|
|
|
/* Close the HDF5 dataset associated with this var. */
|
|
if (hdf5_var->hdf_datasetid)
|
|
{
|
|
LOG((3, "closing HDF5 dataset %lld", hdf5_var->hdf_datasetid));
|
|
if (H5Dclose(hdf5_var->hdf_datasetid) < 0)
|
|
return NC_EHDFERR;
|
|
|
|
if (var->fill_value)
|
|
{
|
|
if (var->type_info)
|
|
{
|
|
if (var->type_info->nc_type_class == NC_VLEN)
|
|
nc_free_vlen((nc_vlen_t *)var->fill_value);
|
|
else if (var->type_info->nc_type_class == NC_STRING && *(char **)var->fill_value)
|
|
free(*(char **)var->fill_value);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* Free the HDF5 typeids. */
|
|
if (var->type_info->rc == 1)
|
|
{
|
|
if(var->type_info->hdr.id <= NC_STRING)
|
|
/* This was a constructed atomic type; free its info */
|
|
nc4_HDF5_close_type(var->type_info);
|
|
}
|
|
|
|
for (a = 0; a < ncindexsize(var->att); a++)
|
|
{
|
|
att = (NC_ATT_INFO_T *)ncindexith(var->att, a);
|
|
assert(att && att->format_att_info);
|
|
nc4_HDF5_close_att(att);
|
|
}
|
|
|
|
/* Delete any HDF5 dimscale objid information. */
|
|
if (hdf5_var->dimscale_hdf5_objids)
|
|
free(hdf5_var->dimscale_hdf5_objids);
|
|
/* Delete information about the attachment status of dimscales. */
|
|
if (hdf5_var->dimscale_attached)
|
|
free(hdf5_var->dimscale_attached);
|
|
nullfree(hdf5_var);
|
|
|
|
/* Reclaim filters */
|
|
if(var->filters != NULL) {
|
|
(void)NC4_hdf5_filter_freelist(var);
|
|
}
|
|
var->filters = NULL;
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Close HDF5 resources for dims in a group.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
static int
|
|
close_dims(NC_GRP_INFO_T *grp)
|
|
{
|
|
NC_DIM_INFO_T *dim;
|
|
int i;
|
|
|
|
for (i = 0; i < ncindexsize(grp->dim); i++)
|
|
{
|
|
NC_HDF5_DIM_INFO_T *hdf5_dim;
|
|
|
|
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, i);
|
|
assert(dim && dim->format_dim_info);
|
|
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
|
|
|
|
/* If this is a dim without a coordinate variable, then close
|
|
* the HDF5 DIM_WITHOUT_VARIABLE dataset associated with this
|
|
* dim. */
|
|
if (hdf5_dim->hdf_dimscaleid && H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
|
|
return NC_EHDFERR;
|
|
nullfree(hdf5_dim);
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Close HDF5 resources for types in a group. Set values to
|
|
* 0 after closing types. Because of type reference counters, these
|
|
* closes can be called multiple times.
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
static int
|
|
close_types(NC_GRP_INFO_T *grp)
|
|
{
|
|
int i;
|
|
|
|
for (i = 0; i < ncindexsize(grp->type); i++)
|
|
{
|
|
NC_TYPE_INFO_T *type;
|
|
|
|
type = (NC_TYPE_INFO_T *)ncindexith(grp->type, i);
|
|
assert(type && type->format_type_info);
|
|
nc4_HDF5_close_type(type);
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Close a single type instance
|
|
*
|
|
* @param type Pointer to type info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Dennis Heimbigner, Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_HDF5_close_type(NC_TYPE_INFO_T* type)
|
|
{
|
|
NC_HDF5_TYPE_INFO_T *hdf5_type;
|
|
|
|
assert(type && type->format_type_info);
|
|
|
|
/* Get HDF5-specific type info. */
|
|
hdf5_type = (NC_HDF5_TYPE_INFO_T *)type->format_type_info;
|
|
|
|
/* Close any open user-defined HDF5 typeids. */
|
|
if (hdf5_type->hdf_typeid && H5Tclose(hdf5_type->hdf_typeid) < 0)
|
|
return NC_EHDFERR;
|
|
hdf5_type->hdf_typeid = 0;
|
|
if (hdf5_type->native_hdf_typeid &&
|
|
H5Tclose(hdf5_type->native_hdf_typeid) < 0)
|
|
return NC_EHDFERR;
|
|
hdf5_type->native_hdf_typeid = 0;
|
|
nullfree(hdf5_type);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Recursively free HDF5 objects for a group (and everything
|
|
* it contains).
|
|
*
|
|
* @param grp Pointer to group info struct.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EHDFERR HDF5 error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp)
|
|
{
|
|
NC_HDF5_GRP_INFO_T *hdf5_grp;
|
|
int i;
|
|
int retval;
|
|
|
|
assert(grp && grp->format_grp_info);
|
|
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
|
|
|
|
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
|
|
|
|
/* Recursively call this function for each child, if any, stopping
|
|
* if there is an error. */
|
|
for (i = 0; i < ncindexsize(grp->children); i++)
|
|
if ((retval = nc4_rec_grp_HDF5_del((NC_GRP_INFO_T *)ncindexith(grp->children,
|
|
i))))
|
|
return retval;
|
|
|
|
/* Close HDF5 resources associated with global attributes. */
|
|
if ((retval = close_gatts(grp)))
|
|
return retval;
|
|
|
|
/* Close HDF5 resources associated with vars. */
|
|
if ((retval = close_vars(grp)))
|
|
return retval;
|
|
|
|
/* Close HDF5 resources associated with dims. */
|
|
if ((retval = close_dims(grp)))
|
|
return retval;
|
|
|
|
/* Close HDF5 resources associated with types. */
|
|
if ((retval = close_types(grp)))
|
|
return retval;
|
|
|
|
/* Close the HDF5 group. */
|
|
LOG((4, "%s: closing group %s", __func__, grp->hdr.name));
|
|
if (hdf5_grp->hdf_grpid && H5Gclose(hdf5_grp->hdf_grpid) < 0)
|
|
return NC_EHDFERR;
|
|
|
|
nullfree(hdf5_grp);
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Given an ncid and varid, get pointers to the group and var
|
|
* metadata. Lazy var metadata reads are done as needed.
|
|
*
|
|
* @param ncid File ID.
|
|
* @param varid Variable ID.
|
|
* @param h5 Pointer that gets pointer to the NC_FILE_INFO_T struct
|
|
* for this file. Ignored if NULL.
|
|
* @param grp Pointer that gets pointer to group info. Ignored if
|
|
* NULL.
|
|
* @param var Pointer that gets pointer to var info. Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOTVAR Variable not found.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_hdf5_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5,
|
|
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var)
|
|
{
|
|
NC_VAR_INFO_T *my_var;
|
|
int retval;
|
|
/* Delegate to libsrc4 */
|
|
if((retval = nc4_find_grp_h5_var(ncid,varid,h5,grp,&my_var))) return retval;
|
|
/* Do we need to read var metadata? (hdf5 specific) */
|
|
if (!my_var->meta_read && my_var->created)
|
|
if ((retval = nc4_get_var_meta(my_var)))
|
|
return retval;
|
|
if (var) *var = my_var;
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Given an ncid, varid, and attribute name, return
|
|
* normalized name and pointers to the file, group, var, and att info
|
|
* structs. Lazy reads of attributes and variable metadata are done as
|
|
* needed.
|
|
*
|
|
* @param ncid File/group ID.
|
|
* @param varid Variable ID.
|
|
* @param name Name to of attribute.
|
|
* @param attnum Number of attribute.
|
|
* @param use_name If true, use the name to get the
|
|
* attribute. Otherwise use the attnum.
|
|
* @param norm_name Pointer to storage of size NC_MAX_NAME + 1,
|
|
* which will get the normalized name, if use_name is true. Ignored if
|
|
* NULL.
|
|
* @param h5 Pointer to pointer that gets file info struct. Ignored if
|
|
* NULL.
|
|
* @param grp Pointer to pointer that gets group info struct. Ignored
|
|
* if NULL.
|
|
* @param h5 Pointer to pointer that gets variable info
|
|
* struct. Ignored if NULL.
|
|
* @param att Pointer to pointer that gets attribute info
|
|
* struct. Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EBADID Bad ncid.
|
|
* @return ::NC_ENOTVAR Variable not found.
|
|
* @return ::NC_ENOTATT Attribute not found.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
|
|
int use_name, char *norm_name, NC_FILE_INFO_T **h5,
|
|
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var,
|
|
NC_ATT_INFO_T **att)
|
|
{
|
|
NC_FILE_INFO_T *my_h5;
|
|
NC_GRP_INFO_T *my_grp;
|
|
NC_VAR_INFO_T *my_var = NULL;
|
|
NC_ATT_INFO_T *my_att;
|
|
char my_norm_name[NC_MAX_NAME + 1] = "";
|
|
NCindex *attlist = NULL;
|
|
int retval;
|
|
|
|
LOG((4, "%s: ncid %d varid %d attnum %d use_name %d", __func__, ncid, varid,
|
|
attnum, use_name));
|
|
|
|
/* Don't need to provide name unless getting att pointer and using
|
|
* use_name. */
|
|
assert(!att || ((use_name && name) || !use_name));
|
|
|
|
/* Find info for this file, group, and h5 info. */
|
|
if ((retval = nc4_find_nc_grp_h5(ncid, NULL, &my_grp, &my_h5)))
|
|
return retval;
|
|
assert(my_grp && my_h5);
|
|
|
|
/* Get either the global or a variable attribute list. */
|
|
if (varid == NC_GLOBAL)
|
|
{
|
|
/* Do we need to read the atts? */
|
|
if (!my_grp->atts_read)
|
|
if ((retval = nc4_read_atts(my_grp, NULL)))
|
|
return retval;
|
|
|
|
attlist = my_grp->att;
|
|
}
|
|
else
|
|
{
|
|
if (!(my_var = (NC_VAR_INFO_T *)ncindexith(my_grp->vars, varid)))
|
|
return NC_ENOTVAR;
|
|
|
|
/* Do we need to read the var attributes? */
|
|
if (!my_var->atts_read)
|
|
if ((retval = nc4_read_atts(my_grp, my_var)))
|
|
return retval;
|
|
|
|
/* Do we need to read var metadata? */
|
|
if (!my_var->meta_read && my_var->created)
|
|
if ((retval = nc4_get_var_meta(my_var)))
|
|
return retval;
|
|
|
|
attlist = my_var->att;
|
|
}
|
|
assert(attlist);
|
|
|
|
/* Need a name if use_name is true. */
|
|
if (use_name && !name)
|
|
return NC_EBADNAME;
|
|
|
|
/* Normalize the name. */
|
|
if (use_name)
|
|
if ((retval = nc4_normalize_name(name, my_norm_name)))
|
|
return retval;
|
|
|
|
/* Now find the attribute by name or number. */
|
|
if (att)
|
|
{
|
|
my_att = use_name ? (NC_ATT_INFO_T *)ncindexlookup(attlist, my_norm_name) :
|
|
(NC_ATT_INFO_T *)ncindexith(attlist, attnum);
|
|
if (!my_att)
|
|
return NC_ENOTATT;
|
|
}
|
|
|
|
/* Give the people what they want. */
|
|
if (norm_name)
|
|
strncpy(norm_name, my_norm_name, NC_MAX_NAME);
|
|
if (h5)
|
|
*h5 = my_h5;
|
|
if (grp)
|
|
*grp = my_grp;
|
|
if (var)
|
|
*var = my_var;
|
|
if (att)
|
|
*att = my_att;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
* @internal Get the file chunk cache settings from HDF5.
|
|
*
|
|
* @param ncid File ID of a NetCDF/HDF5 file.
|
|
* @param sizep Pointer that gets size in bytes to set cache. Ignored
|
|
* if NULL.
|
|
* @param nelemsp Pointer that gets number of elements to hold in
|
|
* cache. Ignored if NULL.
|
|
* @param preemptionp Pointer that gets preemption stragety (between 0
|
|
* and 1). Ignored if NULL.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc4_hdf5_get_chunk_cache(int ncid, size_t *sizep, size_t *nelemsp,
|
|
float *preemptionp)
|
|
{
|
|
NC_FILE_INFO_T *h5;
|
|
NC_HDF5_FILE_INFO_T *hdf5_info;
|
|
hid_t plistid;
|
|
double dpreemption;
|
|
int retval;
|
|
|
|
/* Find info for this file, group, and h5 info. */
|
|
if ((retval = nc4_find_nc_grp_h5(ncid, NULL, NULL, &h5)))
|
|
return retval;
|
|
assert(h5 && h5->format_file_info);
|
|
hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
|
|
|
|
/* Get the file access property list. */
|
|
if ((plistid = H5Fget_access_plist(hdf5_info->hdfid)) < 0)
|
|
return NC_EHDFERR;
|
|
|
|
/* Get the chunk cache values from HDF5 for this property list. */
|
|
if (H5Pget_cache(plistid, NULL, nelemsp, sizep, &dpreemption) < 0)
|
|
return NC_EHDFERR;
|
|
if (preemptionp)
|
|
*preemptionp = dpreemption;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
#ifdef LOGGING
|
|
/* We will need to check against nc log level from nc4internal.c. */
|
|
extern int nc_log_level;
|
|
|
|
/**
|
|
* @internal This is like nc_set_log_level(), but will also turn on
|
|
* HDF5 internal logging, in addition to netCDF logging. This should
|
|
* never be called by the user. It is called in open/create when the
|
|
* nc logging level has changed.
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
hdf5_set_log_level()
|
|
{
|
|
/* If the user wants to completely turn off logging, turn off HDF5
|
|
logging too. Now I truly can't think of what to do if this
|
|
fails, so just ignore the return code. */
|
|
if (nc_log_level == NC_TURN_OFF_LOGGING)
|
|
{
|
|
set_auto(NULL, NULL);
|
|
LOG((1, "HDF5 error messages turned off!"));
|
|
}
|
|
else
|
|
{
|
|
if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0)
|
|
LOG((0, "H5Eset_auto failed!"));
|
|
LOG((1, "HDF5 error messages turned on."));
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
#endif /* LOGGING */
|
|
|
|
|
|
#ifdef _WIN32
|
|
|
|
/**
|
|
* Converts the filename from ANSI to UTF-8 if HDF5 >= 1.10.6.
|
|
* nc4_hdf5_free_pathbuf must be called to free pb.
|
|
*
|
|
* @param pb Pointer that conversion information is stored.
|
|
* @param path The filename to be converted.
|
|
*
|
|
* @return The converted filename if succeeded. NULL if failed.
|
|
*/
|
|
const char *
|
|
nc4_ndf5_ansi_to_utf8(pathbuf_t *pb, const char *path)
|
|
{
|
|
const uint UTF8_MAJNUM = 1;
|
|
const uint UTF8_MINNUM = 10;
|
|
const uint UTF8_RELNUM = 6;
|
|
static enum {UNDEF, ANSI, UTF8} hdf5_encoding = UNDEF;
|
|
wchar_t wbuf[MAX_PATH];
|
|
wchar_t *ws = NULL;
|
|
char *ns = NULL;
|
|
int n;
|
|
|
|
if (hdf5_encoding == UNDEF) {
|
|
#ifdef HDF5_UTF8_PATHS
|
|
hdf5_encoding = UTF8;
|
|
#else
|
|
hdf5_encoding = ANSI;
|
|
#endif
|
|
}
|
|
if (hdf5_encoding == ANSI) {
|
|
pb->ptr = NULL;
|
|
return path;
|
|
}
|
|
|
|
n = MultiByteToWideChar(CP_ACP, 0, path, -1, NULL, 0);
|
|
if (!n) {
|
|
errno = EILSEQ;
|
|
goto done;
|
|
}
|
|
ws = n <= _countof(wbuf) ? wbuf : malloc(sizeof *ws * n);
|
|
if (!ws)
|
|
goto done;
|
|
if (!MultiByteToWideChar(CP_ACP, 0, path, -1, ws, n)) {
|
|
errno = EILSEQ;
|
|
goto done;
|
|
}
|
|
|
|
n = WideCharToMultiByte(CP_UTF8, 0, ws, -1, NULL, 0, NULL, NULL);
|
|
if (!n) {
|
|
errno = EILSEQ;
|
|
goto done;
|
|
}
|
|
ns = n <= sizeof pb->buffer ? pb->buffer : malloc(n);
|
|
if (!ns)
|
|
goto done;
|
|
if (!WideCharToMultiByte(CP_UTF8, 0, ws, -1, ns, n, NULL, NULL)) {
|
|
if (ns != pb->buffer)
|
|
free(ns);
|
|
ns = NULL;
|
|
errno = EILSEQ;
|
|
goto done;
|
|
}
|
|
|
|
done:
|
|
if (ws != wbuf)
|
|
free (ws);
|
|
|
|
pb->ptr = ns;
|
|
return ns;
|
|
}
|
|
|
|
/**
|
|
* Free the conversion information used by nc4_ndf5_ansi_to_utf8.
|
|
*
|
|
* @param pb Pointer that hold conversion information to be freed.
|
|
*/
|
|
void
|
|
nc4_hdf5_free_pathbuf(pathbuf_t *pb)
|
|
{
|
|
if (pb->ptr && pb->ptr != pb->buffer)
|
|
free(pb->ptr);
|
|
}
|
|
|
|
#endif /* _WIN32 */
|