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. |
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| fuzz | ||
| h5_test | ||
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| include | ||
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| libdispatch | ||
| libhdf4 | ||
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| liblib | ||
| libncpoco | ||
| libncxml | ||
| libnczarr | ||
| libsrc | ||
| libsrc4 | ||
| libsrcp | ||
| nc_perf | ||
| nc_test | ||
| nc_test4 | ||
| ncdap_test | ||
| ncdump | ||
| ncgen | ||
| ncgen3 | ||
| nctest | ||
| nczarr_test | ||
| NUG | ||
| oc2 | ||
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| cmake_uninstall.cmake.in | ||
| CMakeInstallation.cmake | ||
| CMakeLists.txt | ||
| COMPILE.cmake.txt | ||
| config.h.cmake.in | ||
| config.h.cmake.in.old-works | ||
| configure.ac | ||
| COPYRIGHT | ||
| CTestConfig.cmake.in | ||
| CTestCustom.cmake.in | ||
| dods.m4 | ||
| FixBundle.cmake.in | ||
| INSTALL.md | ||
| lib_flags.am | ||
| libnetcdf.settings.in | ||
| Makefile.am | ||
| mclean | ||
| nc-config.cmake.in | ||
| nc-config.in | ||
| netcdf.pc.in | ||
| netCDFConfig.cmake.in | ||
| PostInstall.cmake | ||
| README.md | ||
| RELEASE_NOTES.md | ||
| s3cleanup.in | ||
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| test_common.in | ||
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Unidata NetCDF
About
The Unidata network Common Data Form (netCDF) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data. The current netCDF software provides C interfaces for applications and data. Separate software distributions available from Unidata provide Java, Fortran, Python, and C++ interfaces. They have been tested on various common platforms.
Properties
NetCDF files are self-describing, network-transparent, directly
accessible, and extendible. Self-describing means that a netCDF file
includes information about the data it contains. Network-transparent
means that a netCDF file is represented in a form that can be accessed
by computers with different ways of storing integers, characters, and
floating-point numbers. Direct-access means that a small subset of a
large dataset may be accessed efficiently, without first reading through
all the preceding data. Extendible means that data can be appended to
a netCDF dataset without copying it or redefining its structure.
Use
NetCDF is useful for supporting access to diverse kinds of scientific data in heterogeneous networking environments and for writing application software that does not depend on application-specific formats. For information about a variety of analysis and display packages that have been developed to analyze and display data in netCDF form, see
More information
For more information about netCDF, see
Latest releases
You can obtain a copy of the latest released version of netCDF software for various languages:
Copyright
Copyright and licensing information can be found here, as well as in the COPYRIGHT file accompanying the software
Installation
To install the netCDF-C software, please see the file INSTALL in the netCDF-C distribution, or the (usually more up-to-date) document:
Documentation
A language-independent User's Guide for netCDF, and some other language-specific user-level documents are available from:
- Language-independent User's Guide
- NetCDF-C Tutorial
- Fortran-90 User's Guide
- Fortran-77 User's Guide
- netCDF-Java/Common Data Model library
- netCDF4-python
A mailing list, netcdfgroup@unidata.ucar.edu, exists for discussion of the netCDF interface and announcements about netCDF bugs, fixes, and enhancements. For information about how to subscribe, see the URL
Feedback
We appreciate feedback from users of this package. Please send comments, suggestions, and bug reports to support-netcdf@unidata.ucar.edu.