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Commit Graph

563 Commits

Author SHA1 Message Date
Dennis Heimbigner
1a7531392f Make the netcdf-c library compile with gcc -ansi.
Primary fixes to get -ansi to work.
1. Convert all '//' C++ style comments to /*...*/ or to use #if 0...#endif
2. It turns out that when -ansi is specified, then a number of
   functions no longer are defined in the header -- but they are still
   in the .so file.<br>
   The big example is strdup(). So, added code to include/ncconfig.h to define
   externs for those missing functions that occur in more than one place.
   These are enabled if !_WIN32 && __STDC__ == 1 (__STDC__ is supposed to
   be the equivalent compile time flag to -ansi). Note that this requires
   config.h (which references ncconfig.h) to be included in files where it is
   currently not included. Single uses will be only in the file that uses them.
3. Added mmap test for the MAP_ANONYMOUS flag to configure.ac. Apparently
   this is not always defined with -ansi.
4. fix some large integer constants in nc_test4/tst_atts3.c and nc_test4/tst_filterparser.c
   to avoid compiler complaints.
5. fix a double constant in nc_test4/tst_filterparser.c to avoid compiler complaints.

[Note I suspect  and  will be a problem on big-endian machines, but we have no way to test]

Misc. Changes:
1. convert more instances of _MSC_VER to _WIN32.
2. added some debugging code to include/nctestserver.h
3. added comment about libdispatch/drc.c always being compiled.
4. modify parser generation in ncgen to remove unneeded files.
2018-12-05 19:20:43 -07:00
Ward Fisher
0f72f42d3a Merge branch 'ejh_next_17' of https://github.com/NetCDF-World-Domination-Council/netcdf-c into pr-aggregation.wif 2018-11-28 13:28:26 -07:00
Ward Fisher
a8673c3dfe Moving provenance info out so that it doesn't depend on netCDF4 support to display. 2018-11-27 16:09:17 -07:00
Ed Hartnett
c638c8de92 cleanup 2018-11-26 11:22:32 -07:00
Ed Hartnett
016f675fad more separation of lazy att reads from libsrc4 2018-11-26 10:44:48 -07:00
Ed Hartnett
c710b42707 moving lazy att code to libhdf5 2018-11-26 10:14:03 -07:00
Ed Hartnett
cc18944fa7 moved lazy atts handling for nc_inq_attid() 2018-11-26 09:58:31 -07:00
Ed Hartnett
d97824d3e6 moved lazy atts handling for nc_inq_att() 2018-11-26 09:51:28 -07:00
Ed Hartnett
ff0d526404 adding hdf5dispatch.h to git 2018-11-26 08:26:28 -07:00
Ed Hartnett
1df4bb1762 moving lazy atts code to libhdf5 2018-11-26 08:21:32 -07:00
Ed Hartnett
1f64c66cdf rename HDF5 dispatch functions to start with NC4_HDF5 2018-11-26 08:13:57 -07:00
Ed Hartnett
aade08ee22 moving checking for lazy att reads to libhdf5 2018-11-26 07:49:58 -07:00
Ed Hartnett
0e9784a867 more changes to separate HDF5 from libsrc4 initialization 2018-11-26 05:44:59 -07:00
Ed Hartnett
e8ab6286e3 header file cleanup 2018-11-26 05:20:35 -07:00
Ed Hartnett
6dbcc42eb6 changes in support of separating HDF5 and libsrc4 2018-11-26 04:31:23 -07:00
Ed Hartnett
8dc1ffea38 removing HDF5 type info from libsrc4 2018-11-20 14:26:11 -07:00
Ed Hartnett
ab963e3d41 removing HDF5 type info from libsrc4 2018-11-20 14:24:40 -07:00
Ed Hartnett
9aedbd0c41 changing over native_hdf_typeid 2018-11-20 10:55:45 -07:00
Ed Hartnett
5104262f6b changing types 2018-11-20 08:00:48 -07:00
Ed Hartnett
7d01ffb030 merged master 2018-11-20 06:38:47 -07:00
Ed Hartnett
6bebb703a6 trying types again 2018-11-20 06:37:53 -07:00
Ed Hartnett
1d5307b600 merged in ejh_next_10 2018-11-19 09:25:04 -07:00
Ed Hartnett
3ec8b34bfb removed unneeded HDF5 fields 2018-11-19 09:23:43 -07:00
Ward Fisher
128b649190 Fixed a whitespace issue that occurs on OSX. 2018-11-16 15:08:17 -07:00
Ed Hartnett
4c1b3a225b clean up 2018-11-16 10:07:54 -07:00
Ed Hartnett
8ae5ebf6bc remove unneeded params from function 2018-11-16 08:26:09 -07:00
Ed Hartnett
60a33b9e8b removed hdf5 stuff from NC_FIELD_INFO_T 2018-11-15 16:46:22 -07:00
Ed Hartnett
8aa4577bef merged ejh_next_7 2018-11-15 16:40:14 -07:00
Dennis Heimbigner
751300ec59 Fix more memory leaks in netcdf-c library
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.
2018-11-15 10:00:38 -07:00
Ed Hartnett
fda69e6b23 moving rest of var stuff 2018-11-13 17:05:50 -07:00
Ed Hartnett
6a66ecd3d0 moving rest of var stuff 2018-11-13 17:03:11 -07:00
Ed Hartnett
d7fe095066 moving rest of var stuff 2018-11-13 16:59:07 -07:00
Ed Hartnett
d7aac4501b removing hid_t from NC_VAR_INFO_T 2018-11-13 16:10:49 -07:00
Ed Hartnett
4045588516 removing hid_t from NC_VAR_INFO_T 2018-11-13 16:10:34 -07:00
Ed Hartnett
f7cb5ead1c moving var hdf5-specific info into libhdf5 2018-11-13 05:44:39 -07:00
Ed Hartnett
578ddb2a28 cleaning up nc4internal.h 2018-11-13 05:27:46 -07:00
Ed Hartnett
286e276390 cleaning up nc4internal.h 2018-11-13 05:18:00 -07:00
Ed Hartnett
825047b8f6 rest of moving HDF5 specific group info to libhdf5 2018-11-12 14:04:17 -07:00
Ed Hartnett
c35aa3ccb9 changed header files to separate HDF5-specific grp info 2018-11-12 07:40:15 -07:00
Ed Hartnett
7534cb24fe cleanup 2018-11-08 11:12:38 -07:00
Ed Hartnett
856e4ead03 moved hdf_dimscaleid to hdf5-specific dim info 2018-11-08 10:55:21 -07:00
Ed Hartnett
8aabd2020c moving HDF5 dim fields to hdf5internal.h from nc4internal.h 2018-11-08 07:09:11 -07:00
Ed Hartnett
8d31f5b806 clean up 2018-11-07 14:23:55 -07:00
Ed Hartnett
6f4b4ac80d moving attribute HDF5 stuff to libhdf5 2018-11-07 14:21:57 -07:00
Ed Hartnett
11d725facc allocating and freeing memory for hdf5-specific attribute info 2018-11-07 13:45:51 -07:00
Ed Hartnett
9929e7acf9 moving att HDF5 stuff to libhdf5 2018-11-07 11:33:02 -07:00
Ed Hartnett
5f36a3b425 merged master 2018-11-02 10:00:53 -06:00
Dennis Heimbigner
245961de00 re: github issues
https://github.com/Unidata/netcdf-c/issues/1168
    https://github.com/Unidata/netcdf-c/issues/1163
    https://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
2018-10-30 20:48:12 -06:00
Ed Hartnett
35cfaefc0c closing HDF5 objects separately 2018-10-23 05:39:00 -06:00
Ed Hartnett
c90ab24b48 moving towards separating HDF5 file close from netcdf4 file close 2018-10-18 03:17:38 -06:00