re: https://github.com/Unidata/netcdf-c/issues/1642
Modify ncdump, nccopy, and ncgen to support the NC_COMPACT storage option.
Added test cases and added description to the man pages for the utilities.
1. ncdump: For compact storage variable, print special attribute __Storage_ as
````
<var>: _Storage = "compact";
````
2. ncgen: parse and implement
````
<var>: _Storage = "compact";
````
in a .cdl file
3. nccopy: Extend the chunk specification (-c flag) to support
compact using the forms
````
nccopy ... -c <var>:compact
and
nccopy ... -c <var>:contiguous
````
Misc. other changes
1. cleanup the copy_chunking function in ncdump/nccopy.c
re: https://github.com/Unidata/netcdf-c/issues/1584
Support has been added for multiple filters per variable. This
affects a number of components in netcdf. The new APIs are
documented in NUG/filters.md.
The primary changes are:
* A set of new functions are provided (see __include/netcdf_filter.h__).
- Obtain a list of the filters associated with a variable
- Obtain the parameters for a specific filter.
* The existing __nc_inq_var_filter__ function now returns info
about the first defined filter.
* The utilities (ncgen, ncdump, and nccopy) now support
an extended format for specifying a sequence of filters.
The general form is __<filter>|<filter>..._.
* The ncdump **_Filter** attribute now dumps a list of all the
filters associated with a variable using the above new format.
* Filter specifications can now use a filter name instead of number
for filters known to the netcdf library, which in turn is taken
from the HDF5 filter registration page.
* New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter
is returned if an attempt is made to access an unknown filter.
* Internally, the dispatch table has been extended to add a function
to handle all of the filter functions.
* New, filter-related, tests were added to nc_test4.
* A new plugin was added to the plugins directory to help with testing.
Notes:
1. The shuffle and fletcher32 filters are not part of the multifilter system.
Misc. changes:
1. A debug module was added to libhdf5 to help catch error locations.
This fixes an issue hit by GDAL, and that is found in netcdf 4.6.3
and 4.7.0
git bisect pointed the problem to have started with
```
77ab979c5f is the first bad commit
commit 77ab979c5f
Author: Ed Hartnett <edwardjameshartnett@gmail.com>
Date: Sat Jun 16 09:58:48 2018 -0600
using get_vars but not put_vars
:040000 040000 8611e77aaefc9ffd1d13 M libsrc4
```
where nc_get_vara_double() started using nc4_get_vars() underneath.
It turns out that nc4_get_vars() was buggy in the situation exercised by GDAL.
This can be reproduced with the following simple test case:
```
int main()
{
int status;
int cdfid = -1;
int first_dim;
int varid;
int other_var;
size_t anStart[NC_MAX_DIMS];
size_t anCount[NC_MAX_DIMS];
double* val = (double*)calloc(3, sizeof(double));
status = nc_create("foo.nc", NC_NETCDF4, &cdfid);
assert( status == NC_NOERR );
status = nc_def_dim(cdfid, "unlimited_dim", NC_UNLIMITED, &first_dim);
assert( status == NC_NOERR );
status = nc_def_var(cdfid, "my_var", NC_DOUBLE, 1, &first_dim, &varid);
assert( status == NC_NOERR );
status = nc_def_var(cdfid, "other_var", NC_DOUBLE, 1, &first_dim, &other_var);
assert( status == NC_NOERR );
status = nc_enddef(cdfid);
assert( status == NC_NOERR );
/* Write 3 elements to set the size of the unlimited dim to 3 */
anStart[0] = 0;
anCount[0] = 3;
status = nc_put_vara_double(cdfid, other_var, anStart, anCount, val);
assert( status == NC_NOERR );
/* Read 2 elements starting with index=1 */
anStart[0] = 1;
anCount[0] = 2;
status = nc_get_vara_double(cdfid, varid, anStart, anCount, val);
assert( status == NC_NOERR );
status = nc_close(cdfid);
assert( status == NC_NOERR );
free(val);
return 0;
}
```
Running it under Valgrind without this patch leads to
```
==19637==
==19637== Invalid write of size 8
==19637== at 0x4C326CB: memcpy@@GLIBC_2.14 (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==19637== by 0x4EDBE3D: NC4_get_vars (hdf5var.c:2131)
==19637== by 0x4EDA24C: NC4_get_vara (hdf5var.c:1342)
==19637== by 0x4E68878: NC_get_vara (dvarget.c:104)
==19637== by 0x4E69FDB: nc_get_vara_double (dvarget.c:815)
==19637== by 0x400C08: main (in /home/even/netcdf-c/build/test)
==19637== Address 0xb70e3e8 is 8 bytes before a block of size 24 alloc'd
==19637== at 0x4C2FB55: calloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==19637== by 0x4009E8: main (in /home/even/netcdf-c/build/test)
==19637==
```
re: issue https://github.com/Unidata/netcdf-c/issues/1398
re: esupport NDY-294972
The new chunking code added to nccopy missed one case.
In the event that there are no chunking specifications
of any kind, and the input is not netcdf-4, and the output
is netcdf-4 and must be chunked, then use the default chunking
that the library computes as part of the nc_def_var() function.
Misc. changes:
1. add some chunking debug code to hdf5var.c
