https://github.com/Unidata/netcdf-c/issues/1168https://github.com/Unidata/netcdf-c/issues/1163https://github.com/Unidata/netcdf-c/issues/1162
This PR partially fixes memory leaks in the netcdf-c library,
in the ncdump utility, and in some test cases.
The netcdf-c library now runs memory clean with the assumption
that the --disable-utilities option is used. The primary remaining
problem is ncgen. Once that is fixed, I believe the netcdf-c library
will run memory clean with no limitations.
Notes
-----------
1. Memory checking was performed using gcc -fsanitize=address.
Valgrind-based testing has yet to be performed.
2. The pnetcdf, hdf4, and examples code has not been tested.
Misc. Non-leak changes
1. Make tst_diskless2 only run when netcdf4 is enabled (issue 1162)
2. Fix CmakeLists.txt to turn off logging if ENABLE_NETCDF_4 is OFF
3. Isolated all my debug scripts into a single top-level directory
called debug
4. Fix some USE_NETCDF4 dependencies in nc_test and nc_test4 Makefile.am
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
In turn that caused some problems elsewhere because some files
did not include netcdf.h preceding netcdf_mem.h. Specifically,
building under visual studio fails.
So fix those cases that I can find. May need to
add more later.
re: issue https://github.com/Unidata/netcdf-c/issues/1156
Starting with HDF5 version 1.10.x, the plugin code MUST be
careful when using the standard *malloc()*, *realloc()*, and
*free()* function.
In the event that the code is allocating, reallocating, or
free'ing memory that either came from -- or will be exported to --
the calling HDF5 library, then one MUST use the corresponding
HDF5 functions *H5allocate_memory()*, *H5resize_memory()*,
*H5free_memory()* [5] to avoid memory failures.
Additionally, if your filter code leaks memory, then the HDF5 library
generates a failure something like this.
````
H5MM.c:232: H5MM_final_sanity_check: Assertion `0 == H5MM_curr_alloc_bytes_s' failed.
````
This PR modifies the code in the plugins directory to
conform to these new requirements.
This raises a question about the libhdf5 code where this
same problem may occur. We need to scan especially nc4hdf.c
to look for this problem.
re: issue https://github.com/Unidata/netcdf-c/issues/1151
Modify DAP2 and DAP4 code to handle case when _FillValue type is not
same as the parent variable type.
Specifically:
1. Define a parameter [fillmismatch] to allow this mismatch;
default is to disallow.
2. If allowed, forcibly change the type of the _FillValue to match
the parent variable.
3. If allowed Convert the values to match new type
4. Generate a log message
5. if not allowed, then fail
Implementing this required some changes to ncdap_test/dapcvt.c
Also added test cases.
Minor Unrelated Changes:
1. There were a number of warnings about e.g.
assigning a const char* to a char*. Fix these
2. In nccopy.1, replace .NP with .IP "n"
(re PR https://github.com/Unidata/netcdf-c/pull/1144)
3. fix minor error in ncdump/ocprint
