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/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
1. When model is detected as NC_FORMATX_NC3 and is called from
nc_create_par, change the model to NC_FORMATX_PNETCDF.
2. When called from nc_create() or nc_open(), using NC_MPIIO or
NC_MPIPOSIX is considered invalid.
3. Handle the case when NETCDF4 is not enabled but cmode/omode
contains NC_NETCDF4.
4. Handle the case when PNETCDF is not enabled but cmode/omode
contains NC_PNETCDF.
5. Correct comments about PnetCDF only handles CDF-5 files.
6. Add a check for MPI_ERR_NO_SUCH_FILE error class.
Make NC_check_file_type() static, as it is used in dfile.c only.
re: github issue https://github.com/Unidata/netcdf-c/issues/1111
One of the less common use cases for the in-memory feature is
apparently failing with HDF5-1.10.x. The fix is complicated and
requires significant changes to libhdf5/nc4memcb.c. The current
setup is detailed in the file docs/inmeminternal.dox.
Additionally, it was discovered that the program
nc_test/tst_inmemory.c, which is invoked by
nc_test/run_inmemory.sh, actually was failing because of the
above problem. But the failure is not detected since the script
does not return non-zero value.
Other Changes:
1. Fix nc_test_tst_inmemory to return errors correctly.
2. Make ncdap_tests/findtestserver.c and dap4_tests/findtestserver4.c
be generated from ncdap_test/findtestserver.c.in.
3. Make LOG() print output to stderr instead of stdout to
avoid contaminating e.g. ncdump output.
4. Modify the handling of NC_INMEMORY and NC_DISKLESS flags
to properly handle that NC_DISKLESS => NC_INMEMORY. This
affects a number of code pieces, especially memio.c.
The identifier typename is apparently a reserved word in C++.
It is used as a fieldname in the ALignment struct in
include/ncoffsets.h.
Change the field name to type_name in ncoffsets.h
and also in libdispatch/doffsets.c, which uses that field.
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.
