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https://github.com/Unidata/netcdf-c.git
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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.
204 lines
3.3 KiB
C
204 lines
3.3 KiB
C
/*
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* Copyright 2018 University Corporation for Atmospheric
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* Research/Unidata. See COPYRIGHT file for more info.
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*
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* This header file is for the parallel I/O functions of netCDF.
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*
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*/
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/* "$Id: netcdf_par.h,v 1.1 2010/06/01 15:46:49 ed Exp $" */
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#ifndef NCCONFIGURE_H
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#define NCCONFIGURE_H 1
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#ifdef HAVE_STDLIB_H
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#include <stdlib.h>
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#endif
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#ifdef HAVE_STDIO_H
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#include <stdio.h>
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#endif
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#ifdef HAVE_STDINT_H
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#include <stdint.h>
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#endif
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/*
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This is included in bottom
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of config.h. It is where,
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typically, alternatives to
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missing functions should be
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defined and missing types defined.
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*/
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#ifdef _WIN32
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#ifndef HAVE_SSIZE_T
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#include <basetsd.h>
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typedef SSIZE_T ssize_t;
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#define HAVE_SSIZE_T 1
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#endif
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#ifndef HAVE_MODE_T
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typedef int mode_t;
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#define HAVE_MODE_T 1
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#endif
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#ifndef F_OK
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#define F_OK 00
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#endif
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#endif
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/*Warning: Cygwin with -ansi does not define these functions
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in its headers.*/
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#ifndef _WIN32
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#if __STDC__ == 1 /*supposed to be same as -ansi flag */
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#if defined(__cplusplus)
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extern "C" {
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#endif
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/* WARNING: in some systems, these functions may be defined as macros, so check */
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#ifndef HAVE_STRDUP
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#ifndef strdup
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char* strdup(const char*);
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#endif
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#endif
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#ifndef HAVE_STRLCAT
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#ifndef strlcat
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size_t strlcat(char*,const char*,size_t);
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#endif
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#endif
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#ifndef HAVE_SNPRINTF
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#ifndef snprintf
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int snprintf(char*, size_t, const char*, ...);
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#endif
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#endif
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#ifndef HAVE_STRCASECMP
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#ifndef strcasecmp
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int strcasecmp(const char*, const char*);
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#endif
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#endif
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#ifndef HAVE_STRTOLL
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#ifndef strtoll
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long long int strtoll(const char*, char**, int);
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#endif
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#endif
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#ifndef HAVE_STRTOULL
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#ifndef strtoull
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unsigned long long int strtoull(const char*, char**, int);
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#endif
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#endif
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#if defined(__cplusplus)
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}
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#endif
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#endif /*STDC*/
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#else /*_WIN32*/
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#ifndef HAVE_STRLCAT
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#define strlcat(d,s,n) strcat_s((d),(n),(s))
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#endif
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#ifndef HAVE_STRLCPY
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#define strlcpy(d,s,n) strcpy_s((d),(n),(s))
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#endif
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#ifndef __MINGW32__
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#ifndef strcasecmp
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#define strcasecmp _stricmp
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#endif
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#ifndef strncasecmp
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#define strncasecmp _strnicmp
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#endif
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#ifndef snprintf
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#if _MSC_VER<1900
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#define snprintf _snprintf
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#endif
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#endif
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#ifndef fileno
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#define fileno(f) _fileno(f)
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#endif
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#endif /*__MINGW32__*/
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#endif /*_WIN32*/
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#ifndef nulldup
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#define nulldup(s) ((s)==NULL?NULL:strdup(s))
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#endif
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#ifndef nulllen
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#define nulllen(s) ((s)==NULL?0:strlen(s))
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#endif
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#ifndef nullfree
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#define nullfree(s) {if((s)!=NULL) {free(s);} else {}}
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#endif
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#ifndef HAVE_UCHAR
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typedef unsigned char uchar;
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#endif
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#ifndef HAVE_LONGLONG
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typedef long long longlong;
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typedef unsigned long long ulonglong;
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#endif
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#ifndef HAVE_USHORT
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typedef unsigned short ushort;
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#endif
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#ifndef HAVE_UINT
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typedef unsigned int uint;
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#endif
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#ifndef HAVE_UINT64
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typedef unsigned long long uint64;
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#endif
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#ifndef HAVE_UINT64_T
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typedef unsigned long long uint64_t;
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#endif
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#ifndef _WIN32
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#ifndef HAVE_UINTPTR_T
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#ifndef uintptr_t
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#if SIZEOF_VOIDP == 8
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#define uintptr_t unsigned long
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#else
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#define uintptr_t unsigned int
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#endif
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#endif
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#endif
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#endif
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#ifndef HAVE_SIZE64_T
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typedef unsigned long long size64_t;
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#endif
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#ifndef HAVE_SSIZE64_T
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typedef long long ssize64_t;
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#endif
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#ifndef HAVE_PTRDIFF_T
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typedef long ptrdiff_t;
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#endif
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/* Provide a fixed size alternative to off_t or off64_t */
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typedef long long fileoffset_t;
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#ifndef NC_UNUSED
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#define NC_UNUSED(var) (void)var
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#endif
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#endif /* NCCONFIGURE_H */
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