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(see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259).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.
re: https://github.com/Unidata/netcdf-c/issues/1154
Inadvertently, the behavior of NC_DISKLESS with nc_create() was
changed in release 4.6.1. Previously, the NC_WRITE flag needed
to be explicitly used with NC_DISKLESS in order to cause the
created file to be persisted to disk.
Additional analyis indicated that the current NC_DISKLESS
implementation was seriously flawed.
This PR attempts to clean up and regularize the situation with
respect to NC_DISKLESS control. One important aspect of diskless
operation is that there are two different notions of write.
1. The file is read-write vs read-only when using the netcdf API.
2. The file is persisted or not to disk at nc_close().
Previously, these two were conflated. The rules now are
as follows.
1. NC_DISKLESS + NC_WRITE means that the file is read/write using the netcdf API
2. NC_DISKLESS + NC_PERSIST means that the file is persisted to a disk file at nc_close.
3. NC_DISKLESS + NC_PERSIST + NC_WRITE means both 1 and 2.
The NC_PERSIST flag is new and takes over the obsolete NC_MPIPOSIX flag.
NC_MPIPOSIX is still defined, but is now an alias for the NC_MPIIO flag.
It is also now the case that for netcdf-4, NC_DISKLESS is independent
of NC_INMEMORY and in fact it is an error to specify both flags
simultaneously.
Finally, the MMAP code was fixed to use NC_PERSIST as well.
Also marked MMAP as deprecated.
Also added a test case to test various combinations of NC_DISKLESS,
NC_PERSIST, and NC_WRITE.
This PR affects a number of files and especially test cases
that used NC_DISKLESS.
Misc. Unrelated fixes
1. fixed some warnings in ncdump/dumplib.c
Add the ability to set some additional curlopt values via .daprc (aka .dodsrc).
This effects both DAP2 and DAP4 protocols.
Related issues:
[1] re: esupport: KOZ-821332
[2] re: github issue https://github.com/Unidata/netcdf4-python/issues/836
[3] re: github issue https://github.com/Unidata/netcdf-c/issues/1074
1. CURLOPT_BUFFERSIZE: Relevant to [1]. Allow user to set the read/write
buffersizes used by curl.
This is done by adding the following to .daprc (aka .dodsrc):
HTTP.READ.BUFFERSIZE=n
where n is the buffersize in bytes. There is a built-in (to curl)
limit of 512k for this value.
2. CURLOPT_TCP_KEEPALIVE (and CURLOPT_TCP_KEEPIDLE and CURLOPT_TCP_KEEPINTVL):
Relevant (maybe) to [2] and [3]. Allow the user to turn on KEEPALIVE
This is done by adding the following to .daprc (aka .dodsrc):
HTTP.KEEPALIVE=on|n/m
If the value is "on", then simply enable default KEEPALIVE. If the value
is n/m, then enable KEEPALIVE and set KEEPIDLE to n and KEEPINTVL to m.
stored in the _NCProperties attribute to allow two things:
1. capture of additional library dependencies (over and above
hdf5)
2. Recognition of non-netcdf libraries that create netcdf-4 format
files.
To this end, the _NCProperties format has been extended to be
and arbitrary set of key=value pairs separated by commas.
This new format has version = 2, and uses commas as the pair separator.
Thus the general form is:
_NCProperties = "version=2,key1=value,key2=value2..." ;
This new version is accompanied by a new ./configure option of the form
--with-ncproperties="key1=value1,key2=value2..."
that specifies pairs to add to the _NCProperties attribute for all
files created with that netcdf library.
At this point, what is missing is some programmatic way to
specify either all the pairs or additional pairs
to the _NCProperties attribute. Not sure of the best way
to do this.
Builders using non-netcdf libraries can specify
whatever they want in the key value pairs (as long
as the version=2 is specified first).
By convention, the primary library is expected to be the
the first pair after the leading version=2 pair, but this
is convention only and is neither required nor enforced.
Related changes:
1. Fixed the tests that check _NCProperties to properly operate with version=2.
2. When reading a version 1 _NCProperties attribute, convert it to look
like a version 2 attribute.
2. Added some version 2 tests to ncdump/tst_fileinfo.c and
ncdump/tst_fileinfo.sh
Misc Changes:
1. Fix minor problem in ncdap_test/testurl.sh where a parameter to
buildurl needed to be quoted.
2. Minor fix to ncgen to swap switches -H and -h to be consistent
with other utilities.
3. Document the -M flag in nccopy usage() and the nccopy man page.
4. Modify a test case to use the nccopy -M flag.
So it now becomes the first default test server to try.
This also means that the dap4 remote testing is enabled.
The only issue to watch is to see if the jetstream-based
server can stay up for significant periods of time.
A uptimerobot (https://uptimerobot.com) has been set ups
to monitor this hourly, so we shall see.
corresponding HDF5 operations.
re: github issue https://github.com/Unidata/netcdf-c/issues/908
also in reference to https://github.com/pydata/xarray/issues/2004
The netcdf-c library has implemented the nc_get_vars and nc_put_vars
operations as element at a time. This has resulted in very slow
operation.
This pr attempts to improve the situation for netcdf-4/hdf5 files
by using the slab operations provided by the hdf5 library. The new
implementation passes the get/put vars stride information down to
the hdf5 slab operations.
The result appears to improve performance significantly. Some simple
tests on large 2-D arrays shows speedups in excess of 150.
Misc. other changes:
1. fix bug in ncgen/semantics.c; using a list's allocated length
instead of actual length.
2. Added a temporary hook in the netcdf library plus a performance
test case (tst_varsperf.c) to estimate the speedup. After users
have had some experience with this, I will remove it, probably
after the 4.7 release.
