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.
(I hope) metadata mechanism. This mostly just adds new pieces of
code (e.g. nclistmap) and does some minor fixes.
It should be transparent to everything else.
The next set of changes will be the big step.
2. Fixed plugin building (nc_test4/hdf5plugins)
to be done properly by cmake and automake.
4. Duplicated part of the nc_test4 filter test code
in examples/C
An incomplete and untested set of hooks exist
for OS-X in nc_test4/findplugins.in. They need testing.
re pull request https://github.com/Unidata/netcdf-c/pull/405
re pull request https://github.com/Unidata/netcdf-c/pull/446
Notes:
1. This branch is a cleanup of the magic.dmh branch.
2. magic.dmh was originally merged, but caused problems with parallel IO.
It was re-issued as pull request https://github.com/Unidata/netcdf-c/pull/446.
3. This branch + pull request replace any previous pull requests and magic.dmh branch.
Given an otherwise valid netCDF file that has a corrupted header,
the netcdf library currently crashes. Instead, it should return
NC_ENOTNC.
Additionally, the NC_check_file_type code does not do the
forward search required by hdf5 files. It currently only looks
at file position 0 instead of 512, 1024, 2048,... Also, it turns
out that the HDF4 magic number is assumed to always be at the
beginning of the file (unlike HDF5).
The change is localized to libdispatch/dfile.c See
https://support.hdfgroup.org/release4/doc/DSpec_html/DS.pdf
Also, it turns out that the code in NC_check_file_type is duplicated
(mostly) in the function libsrc4/nc4file.c#nc_check_for_hdf.
This branch does the following.
1. Make NC_check_file_type return NC_ENOTNC instead of crashing.
2. Remove nc_check_for_hdf and centralize all file format checking
NC_check_file_type.
3. Add proper forward search for HDF5 files (but not HDF4 files)
to look for the magic number at offsets of 0, 512, 1024...
4. Add test tst_hdf5_offset.sh. This tests that hdf5 files with
an offset are properly recognized. It does so by prefixing
a legal file with some number of zero bytes: 512, 1024, etc.
5. Off-topic: Added -N flag to ncdump to force a specific output dataset name.
2. Factored out the parameter string parsing for ncgen and nccopy
int libdispatch/dfilter.c + include/ncfilter.h
3. Allow a parameter string to use constant types other than
unsigned int. See docs/filters.md for details.
4. Moved the old content of include/netcdf_filter.h into include/netcdf.h
and removed include/netcdf_filter.h as no longer needed.
5. Force the test filter (bzip2) in nc_test4/filter_test to
be built using BUILT_SOURCES.
it tries to infer the file kind based on
the constructs and types used in the .cdl
file. Previously, it included cdf5 as an
inferrable kind, but this is almost never
what is wanted. So limit inferable kinds
to netcdf classic vs netcdf enhanced.
Also fix tst_inttags4.sh test.
This is a follow-on in that the old utf8 code was still being
used in ncgen to convert utf8->utf16 when converting cdl to Java
(see genj.c).
The new code apparently has no utf16 support, but it does have
utf32 support. Converting utf32 -> utf16 can be approximated by
truncating the 32bits to 16 bits, unless the top 16 bits are
not zero. This latter condition is unlikely to be common because
it implies use of some rather obscure characters.
So solution is to convert to utf32 and truncate to 16 bits to
get utf16. An error is reported if the high-order truncated 16
bits are not zero. If we get complaints, then I will figure out
how to convert full utf32 to a utf16 pair.
Also removed the old code from ncgen.
1. Allow nccopy to apply filters, especially on the output file.
This provides a third way to do this other than using ncgen or
programatically
2. Make sure that even if the filter code is not available, it is
possible to see the filter id and parameters for variables using
e.g ncdump -hs.
3. Fix bug in nccopy so that the input file does
not necessarily have to be netcdf-4.
4. At last minute decided to change to using a
single "_Filter" attribute for ncgen
5. Added a test to tst_filter.sh to generate C code using ncgen.
This relies on the HDF5 capability to
dynamically load compression filters.
Note that a compression filter is just
a subcase of filters.
The primary user-visible changes are as follows:
1. Add a standard header "netcdf_filter.h" that defines
the necessary API extensions
2. Modify ncgen to support two new special attributes
"_Filter_ID" and "_Filter_Parameters" so that compression
can be turned on when creating a file using ncgen.
4. Add a detailed description of filtering support
to the user's guide; see the file filters.md
5. Add a test case directory for this: nc_test4/filter_test.
It is fragile and a ./configure flags (-enable-filter-test)
is defined (default disabled) to shut this off this test
to avoid spurious 'make check' failures.
Note that the HDF5 documentation is not up-to-date, so
much of what is encoded here comes from examining the
actual code in the file H5PL.c in the HDF5 source code.
