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df3636b959
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.
133 lines
3.7 KiB
C
133 lines
3.7 KiB
C
/* Copyright 2003-2018, University Corporation for Atmospheric
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* Research. See COPYRIGHT file for copying and redistribution
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* conditions. */
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/**
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* @file
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* @internal The netCDF-4 file functions relating to file creation.
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*
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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#include "zincludes.h"
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/** @internal These flags may not be set for create. */
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static const int ILLEGAL_CREATE_FLAGS = (NC_NOWRITE|NC_MMAP|NC_DISKLESS|NC_64BIT_OFFSET|NC_CDF5);
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/**
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* @internal Create a netCDF-4/NCZ file.
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*
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* @param path The file name of the new file.
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* @param cmode The creation mode flag.
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* @param initialsz The proposed initial file size (advisory)
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* @param nc Pointer to an instance of NC.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EINVAL Invalid input (check cmode).
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* @return ::NC_EEXIST File exists and NC_NOCLOBBER used.
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* @return ::NC_EHDFERR ZARR returned error.
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* @ingroup netcdf4
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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static int
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ncz_create_file(const char *path, int cmode, size_t initialsz, const char** controls, int ncid)
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{
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int retval = NC_NOERR;
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NC_FILE_INFO_T* h5 = NULL;
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assert(path);
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LOG((3, "%s: path %s mode 0x%x", __func__, path, cmode));
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/* Add necessary structs to hold netcdf-4 file data. */
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if ((retval = nc4_file_list_add(ncid, path, cmode, (void**)&h5)))
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BAIL(retval);
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assert(h5 && h5->root_grp);
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h5->root_grp->atts_read = 1;
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h5->mem.inmemory = ((cmode & NC_INMEMORY) == NC_INMEMORY);
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h5->mem.diskless = ((cmode & NC_DISKLESS) == NC_DISKLESS);
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h5->mem.persist = ((cmode & NC_PERSIST) == NC_PERSIST);
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/* Do format specific setup */
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if((retval = ncz_create_dataset(h5,h5->root_grp,controls)))
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BAIL(retval);
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/* Define mode gets turned on automatically on create. */
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h5->flags |= NC_INDEF;
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/* Set provenance. */
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if ((retval = NCZ_new_provenance(h5)))
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BAIL(retval);
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return NC_NOERR;
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exit: /*failure exit*/
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if(retval && h5)
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ncz_closeorabort(h5, NULL, 1); /* treat like abort */
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return retval;
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}
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/**
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* @internal Create a netCDF-4/NCZ file.
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*
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* @param path The file name of the new file.
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* @param cmode The creation mode flag.
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* @param initialsz Ignored by this function.
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* @param basepe Ignored by this function.
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* @param chunksizehintp Ignored by this function.
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* @param parameters pointer to struct holding extra data (e.g. for
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* parallel I/O) layer. Ignored if NULL.
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* @param dispatch Pointer to the dispatch table for this file.
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* @param nc_file Pointer to an instance of NC.
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*
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* @return ::NC_NOERR No error.
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* @return ::NC_EINVAL Invalid input (check cmode).
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* @ingroup netcdf4
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* @author Dennis Heimbigner, Ed Hartnett
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*/
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int
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NCZ_create(const char* path, int cmode, size_t initialsz, int basepe,
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size_t *chunksizehintp, void *parameters,
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const NC_Dispatch *dispatch, int ncid)
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{
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int stat = NC_NOERR;
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NCURI* uri = NULL;
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ZTRACE(0,"path=%s,cmode=%d,initialsz=%ld,ncid=%d)",path,cmode,initialsz,ncid);
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NC_UNUSED(parameters);
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assert(path);
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LOG((1, "%s: path %s cmode 0x%x ncid %d",
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__func__, path, cmode ,ncid));
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/* If this is our first file, initialize */
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if (!ncz_initialized) NCZ_initialize();
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#ifdef LOGGING
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/* If nc logging level has changed, see if we need to turn on
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* NCZ's error messages. */
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NCZ_set_log_level();
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#endif /* LOGGING */
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/* Check the cmode for validity. */
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if((cmode & ILLEGAL_CREATE_FLAGS) != 0)
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{stat = NC_EINVAL; goto done;}
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/* Turn on NC_WRITE */
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cmode |= NC_WRITE;
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/* Get the controls */
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ncuriparse(path,&uri);
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if(uri == NULL) goto done;
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/* Create the file */
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stat = ncz_create_file(path, cmode, initialsz, ncurifragmentparams(uri), ncid);
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done:
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ncurifree(uri);
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return ZUNTRACE(stat);
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}
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