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
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.
The file docs/indexing.dox tries to provide design
information for the refactoring.
The primary change is to replace all walking of linked
lists with the use of the NCindex data structure.
Ncindex is a combination of a hash table (for name-based
lookup) and a vector (for walking the elements in the index).
Additionally, global vectors are added to NC_HDF5_FILE_INFO_T
to support direct mapping of an e.g. dimid to the NC_DIM_INFO_T
object. These global vectors exist for dimensions, types, and groups
because they have globally unique id numbers.
WARNING:
1. since libsrc4 and libsrchdf4 share code, there are also
changes in libsrchdf4.
2. Any outstanding pull requests that change libsrc4 or libhdf4
are likely to cause conflicts with this code.
3. The original reason for doing this was for performance improvements,
but as noted elsewhere, this may not be significant because
the meta-data read performance apparently is being dominated
by the hdf5 library because we do bulk meta-data reading rather
than lazy reading.
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.
Specific changes:
1. Add dap4 code: libdap4 and dap4_test.
Note that until the d4ts server problem is solved, dap4 is turned off.
2. Modify various files to support dap4 flags:
configure.ac, Makefile.am, CMakeLists.txt, etc.
3. Add nc_test/test_common.sh. This centralizes
the handling of the locations of various
things in the build tree: e.g. where is
ncgen.exe located. See nc_test/test_common.sh
for details.
4. Modify .sh files to use test_common.sh
5. Obsolete separate oc2 by moving it to be part of
netcdf-c. This means replacing code with netcdf-c
equivalents.
5. Add --with-testserver to configure.ac to allow
override of the servers to be used for --enable-dap-remote-tests.
6. There were multiple versions of nctypealignment code. Try to
centralize in libdispatch/doffset.c and include/ncoffsets.h
7. Add a unit test for the ncuri code because of its complexity.
8. Move the findserver code out of libdispatch and into
a separate, self contained program in ncdap_test and dap4_test.
9. Move the dispatch header files (nc{3,4}dispatch.h) to
.../include because they are now shared by modules.
10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts.
11. Make use of MREMAP if available
12. Misc. minor changes e.g.
- #include <config.h> -> #include "config.h"
- Add some no-install headers to /include
- extern -> EXTERNL and vice versa as needed
- misc header cleanup
- clean up checking for misc. unix vs microsoft functions
13. Change copyright decls in some files to point to LICENSE file.
14. Add notes to RELEASENOTES.md
Add a new function called nc_inq_format_extended that
returns more detailed format information (vis-a-vis
nc_inq_format) about an open dataset.
Note that the netcdf API will present the file as if it had
the format specified by nc_inq_format. The true file
format, however, may not even be a netcdf file; it might be
DAP, HDF4, or PNETCDF, for example. This function returns
that true file type. It also returns the effective mode for
the file.
signature: nc_inq_format_extended(int ncid, int* formatp, int* modep)
where
* ncid is the NetCDF ID from a previous call to nc_open() or
nc_create().
* formatp is a pointer to a location for returned true format.
* modep is a pointer to a location for returned mode flags.
Refer to the actual list in the file netcdf.h to see the
currently defined set.
Also added test cases (tst_formatx*).
group renaming. The primary API
is 'nc_rename_grp(int grpid, const char* name)'.
No test cases provided yet.
This also required adding a rename_grp entry
to the dispatch tables.
contain as little file-type specific info as possible. It
modifies especially libsrc so that all of the netcdf-3 data
that used to be in struct NC is now kept in a separate chunk
of data pointed to by the struct NC. This makes all of
current protocols consistent: netcdf-3, netcdf-4, and dap.
ncgen: nan bug
made semicolons optional after type decls
libncdap{3,4}: revamped the NC surrogate to better match
with libsrc
libdispatch: Added a new_nc function to the dispatch table; its purpose
is to allow hierarchical use of NC compatible data structures.
libsrc: cleaned up the NC structure by removing drno field
general: removed --with-oc options
