2011-07-15 06:24:02 +08:00
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/*
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2018-12-07 05:13:56 +08:00
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* Copyright 2018 University Corporation for Atmospheric
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2011-07-15 06:24:02 +08:00
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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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2014-08-26 05:14:10 +08:00
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*
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2011-07-15 06:24:02 +08:00
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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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2022-02-01 08:16:23 +08:00
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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2017-11-24 01:55:24 +08:00
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#ifdef HAVE_STDLIB_H
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#include <stdlib.h>
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#endif
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2019-03-23 05:16:47 +08:00
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#ifdef HAVE_STDIO_H
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#include <stdio.h>
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#endif
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2021-03-07 05:09:37 +08:00
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#ifdef HAVE_STDINT_H
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#include <stdint.h>
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#endif
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2017-11-24 01:55:24 +08:00
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2011-07-15 06:24:02 +08:00
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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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2018-02-25 11:36:24 +08:00
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defined and missing types defined.
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2011-07-15 06:24:02 +08:00
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*/
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2019-05-30 04:35:29 +08:00
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#ifdef _WIN32
|
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
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2018-03-27 05:35:48 +08:00
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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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2018-05-15 04:37:07 +08:00
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#define HAVE_SSIZE_T 1
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2018-03-27 05:35:48 +08:00
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#endif
|
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
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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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2018-03-27 05:35:48 +08:00
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#endif
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2018-12-06 10:20:43 +08:00
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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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2019-02-20 05:42:34 +08:00
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2022-02-01 08:16:23 +08:00
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#if defined(__cplusplus)
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extern "C" {
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#endif
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2019-05-30 04:35:29 +08:00
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/* WARNING: in some systems, these functions may be defined as macros, so check */
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2023-10-13 06:22:47 +08:00
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#if ! defined(HAVE_STRDUP) || defined(__CYGWIN__)
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2023-04-26 07:15:06 +08:00
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#ifndef strdup
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2022-02-01 08:16:23 +08:00
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char* strdup(const char*);
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#endif
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2019-02-20 05:42:34 +08:00
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#endif
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2022-02-01 08:16:23 +08:00
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#ifndef HAVE_STRLCAT
|
2019-01-16 05:36:07 +08:00
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#ifndef strlcat
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2024-04-08 19:13:08 +08:00
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#define strlcat nc_strlcat
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size_t nc_strlcat(char*,const char*,size_t);
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2022-02-01 08:16:23 +08:00
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#endif
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2017-11-24 01:55:24 +08:00
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#endif
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2022-02-01 08:16:23 +08:00
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#ifndef HAVE_SNPRINTF
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2019-01-16 05:36:07 +08:00
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#ifndef snprintf
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2022-02-01 08:16:23 +08:00
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int snprintf(char*, size_t, const char*, ...);
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#endif
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2017-11-24 01:55:24 +08:00
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#endif
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2022-02-01 08:16:23 +08:00
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#ifndef HAVE_STRCASECMP
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2019-05-30 04:35:29 +08:00
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#ifndef strcasecmp
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2023-04-26 07:15:06 +08:00
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int strcasecmp(const char*, const char*);
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2019-05-30 04:35:29 +08:00
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#endif
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#endif
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2022-02-01 08:16:23 +08:00
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#ifndef HAVE_STRTOLL
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2019-05-30 04:35:29 +08:00
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#ifndef strtoll
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2022-02-01 08:16:23 +08:00
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long long int strtoll(const char*, char**, int);
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2019-05-30 04:35:29 +08:00
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#endif
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2022-02-01 08:16:23 +08:00
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#endif
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#ifndef HAVE_STRTOULL
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2019-05-30 04:35:29 +08:00
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#ifndef strtoull
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2022-02-01 08:16:23 +08:00
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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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2019-05-30 04:35:29 +08:00
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#endif
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2019-03-23 05:16:47 +08:00
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#endif /*STDC*/
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2011-09-30 23:56:02 +08:00
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2021-09-05 15:13:23 +08:00
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#else /*_WIN32*/
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2019-05-30 04:35:29 +08:00
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#ifndef HAVE_STRLCAT
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2018-12-06 10:20:43 +08:00
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#define strlcat(d,s,n) strcat_s((d),(n),(s))
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#endif
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2021-09-05 15:13:23 +08:00
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2023-04-26 07:15:06 +08:00
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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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2021-10-02 06:07:37 +08:00
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2021-09-05 15:13:23 +08:00
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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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2019-02-20 05:42:34 +08:00
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#endif
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2021-09-05 15:13:23 +08:00
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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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2021-09-29 04:03:19 +08:00
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#ifndef fileno
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#define fileno(f) _fileno(f)
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#endif
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2021-09-05 15:13:23 +08:00
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#endif /*__MINGW32__*/
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#endif /*_WIN32*/
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2018-12-06 10:20:43 +08:00
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2011-07-15 06:24:02 +08:00
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#ifndef nulldup
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#define nulldup(s) ((s)==NULL?NULL:strdup(s))
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2023-04-26 07:15:06 +08:00
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#endif
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2019-05-30 04:35:29 +08:00
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2011-07-15 06:24:02 +08:00
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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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2019-05-30 04:35:29 +08:00
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2011-07-15 06:43:43 +08:00
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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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2011-07-15 06:24:02 +08:00
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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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2015-08-16 06:26:35 +08:00
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#ifndef HAVE_USHORT
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typedef unsigned short ushort;
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#endif
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2011-07-15 06:24:02 +08:00
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#ifndef HAVE_UINT
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typedef unsigned int uint;
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#endif
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2020-11-20 08:01:04 +08:00
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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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2020-05-12 00:35:56 +08:00
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#ifndef _WIN32
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2020-05-11 23:42:31 +08:00
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#ifndef HAVE_UINTPTR_T
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2023-04-26 07:15:06 +08:00
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#ifndef uintptr_t
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2020-05-11 23:42:31 +08:00
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#if SIZEOF_VOIDP == 8
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2020-09-02 03:44:24 +08:00
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#define uintptr_t unsigned long
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2020-05-11 23:42:31 +08:00
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#else
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2020-09-02 03:44:24 +08:00
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#define uintptr_t unsigned int
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2020-05-11 23:42:31 +08:00
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#endif
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#endif
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2020-05-12 00:35:56 +08:00
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#endif
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2023-04-26 07:15:06 +08:00
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#endif
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2019-02-08 05:28:23 +08:00
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This PR adds EXPERIMENTAL support for accessing data in the
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-29 08:02:47 +08:00
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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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|
2023-04-26 07:15:06 +08:00
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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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2022-02-01 08:16:23 +08:00
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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 byte-range reading of remote datasets
re: issue https://github.com/Unidata/netcdf-c/issues/1251
Assume that you have the URL to a remote dataset
which is a normal netcdf-3 or netcdf-4 file.
This PR allows the netcdf-c to read that dataset's
contents as a netcdf file using HTTP byte ranges
if the remote server supports byte-range access.
Originally, this PR was set up to access Amazon S3 objects,
but it can also access other remote datasets such as those
provided by a Thredds server via the HTTPServer access protocol.
It may also work for other kinds of servers.
Note that this is not intended as a true production
capability because, as is known, this kind of access to
can be quite slow. In addition, the byte-range IO drivers
do not currently do any sort of optimization or caching.
An additional goal here is to gain some experience with
the Amazon S3 REST protocol.
This architecture and its use documented in
the file docs/byterange.dox.
There are currently two test cases:
1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle
for a remote netcdf-3 file and a remote netcdf-4 file.
2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote
datasets.
This PR also incorporates significantly changed model inference code
(see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259).
1. It centralizes the code that infers the dispatcher.
2. It adds support for byte-range URLs
Other changes:
1. NC_HDF5_finalize was not being properly called by nc_finalize().
2. Fix minor bug in ncgen3.l
3. fix memory leak in nc4info.c
4. add code to walk the .daprc triples and to replace protocol=
fragment tag with a more general mode= tag.
Final Note:
Th inference code is still way too complicated. We need to move
to the validfile() model used by netcdf Java, where each
dispatcher is asked if it can process the file. This decentralizes
the inference code. This will be done after all the major new
dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-02 09:27:36 +08:00
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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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2019-01-17 04:51:22 +08:00
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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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2011-07-15 06:24:02 +08:00
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#endif /* NCCONFIGURE_H */
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