Commit Graph

4 Commits

Author SHA1 Message Date
Dennis Heimbigner
df3636b959 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.
2023-09-26 16:56:48 -06:00
Dennis Heimbigner
56c549af0f Make sure mode flags are properly defined in netcdf.h
In a number of places in the netcdf-c library, some of the
high order mode flags (the mode argument to nc_open or nc_close)
are being used to save state information. This means that the
description of the defined and open mode flags in netcdf.h
were not accurate.

This PR moves all those hack flags so that the list of mode flags
in netcdf.h is correct.
2022-01-11 19:05:46 -07:00
Dennis Heimbigner
9380790ea8 Support MSYS2/Mingw platform
re:

The current netcdf-c release has some problems with the mingw platform
on windows. Mostly they are path issues.

Changes to support mingw+msys2:
-------------------------------
* Enable option of looking into the windows registry to find
  the mingw root path. In aid of proper path handling.
* Add mingw+msys as a specific platform in configure.ac and move testing
  of the platform to the front so it is available early.
* Handle mingw X libncpoco (dynamic loader) properly even though
  mingw does not yet support it.
* Handle mingw X plugins properly even though mingw does not yet support it.
* Alias pwd='pwd -W' to better handle paths in shell scripts.
* Plus a number of other minor compile irritations.
* Disallow the use of multiple nc_open's on the same file for windows
  (and mingw) because windows does not seem to handle these properly.
  Not sure why we did not catch this earlier.
* Add mountpoint info to dpathmgr.c to help support mingw.
* Cleanup dpathmgr conversions.

Known problems:
---------------
* I have not been able to get shared libraries to work, so
  plugins/filters must be disabled.
* There is some kind of problem with libcurl that I have not solved,
  so all uses of libcurl (currently DAP+Byterange) must be disabled.

Misc. other fixes:
------------------
* Cleanup the relationship between ENABLE_PLUGINS and various other flags
  in CMakeLists.txt and configure.ac.
* Re-arrange the TESTDIRS order in Makefile.am.
* Add pseudo-breakpoint to nclog.[ch] for debugging.
* Improve the documentation of the path manager code in ncpathmgr.h
* Add better support for relative paths in dpathmgr.c
* Default the mode args to NCfopen to include "b" (binary) for windows.
* Add optional debugging output in various places.
* Make sure that everything builds with plugins disabled.
* Fix numerous (s)printf inconsistencies betweenb the format spec
  and the arguments.
2021-12-23 22:18:56 -07:00
Dennis Heimbigner
f6e25b695e Fix additional S3 support issues
re: https://github.com/Unidata/netcdf-c/issues/2117
re: https://github.com/Unidata/netcdf-c/issues/2119

* Modify libsrc to allow byte-range reading of netcdf-3 files in private S3 buckets; this required using the aws sdk. Also add a test case.
* The aws sdk can sometimes cause problems if the Awd::ShutdownAPI function is not called. So at optional atexit() support to ensure it is called. This is disabled for Windows.
* Add documentation to nczarr.md on how to build and use the aws sdk under windows. Currently it builds, but testing fails.
* Switch testing from stratus to the Unidata bucket on S3.
* Improve support for the s3: url protocol.
* Add a s3 specific utility code file: ds3util.c
* Modify NC_infermodel to attempt to read the magic number of byte-ranged files in S3.

## Misc.

* Move and rename the core S3 SDK wrapper code (libnczarr/zs3sdk.cpp) to libdispatch since it now used in libsrc as well as libnczarr.
* Add calls to nc_finalize in the utilities in case atexit is disabled.
* Add header only json parser to the distribution rather than as a built source.
2021-10-29 20:06:37 -06:00