1) We have to use H5Tequal() to compare HDF5 type IDs.
2) When checking if we can re-use an NC_CHAR attribute it is enough to
compare data types (H5Tequal() takes care of the size comparison).
3) This commit adds missing code (reuse_att was set but not used).
Now an attribute in a NetCDF-4 file can be modified as many times as
necessary, as long its type and length remain the same.
Modifications changing either type or length of an attribute require
deleting and re-creating an attribute which increments the attribute
order creation index. Once this index reaches 65535 all attribute
modifications (for a particular group or variable) will fail.
For reference:
Issue 350 title: NetCDF-4 limits the number of times an attribute can
be modified
Pull request 1119 title: Fix checking for HDF5 max dims, no longer
re-create atts if not needed, confirm behavior for HDF5 cyclical
files, allow user to set mpiexec
Priority: Low
re: issue https://github.com/Unidata/netcdf-c/issues/1329
HDF5 has the ability to programmatically define new filters,
as opposed to using HDF5_PLUGIN_PATH env variable.
This PR adds support for that feature.
Not clear how useful this is, though.
See docs/filters.md for details.
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173
Sorry that it is so big, but leak suppression can be complex.
This PR fixes all remaining memory leaks -- as determined by
-fsanitize=address, and with the exceptions noted below.
Unfortunately. there remains a significant leak that I cannot
solve. It involves vlens, and it is unclear if the leak is
occurring in the netcdf-c library or the HDF5 library.
I have added a check_PROGRAM to the ncdump directory to show the
problem. The program is called tst_vlen_demo.c To exercise it,
build the netcdf library with -fsanitize=address enabled. Then
go into ncdump and do a "make clean check". This should build
tst_vlen_demo without actually executing it. Then do the
command "./tst_vlen_demo" to see the output of the memory
checker. Note the the lost malloc is deep in the HDF5 library
(in H5Tvlen.c).
I am temporarily working around this error in the following way.
1. I modified several test scripts to not execute known vlen tests
that fail as described above.
2. Added an environment variable called NC_VLEN_NOTEST.
If set, then those specific tests are suppressed.
This should mean that the --disable-utilities option to
./configure should not need to be set to get a memory leak clean
build. This should allow for detection of any new leaks.
Note: I used an environment variable rather than a ./configure
option to control the vlen tests. This is because it is
temporary (I hope) and because it is a bit tricky for shell
scripts to access ./configure options.
Finally, as before, this only been tested with netcdf-4 and hdf5 support.
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.
