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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
..
cdl Fix pull request https://github.com/Unidata/netcdf-c/pull/374 (dap4.dmh) 2017-04-03 21:39:44 -06:00
expected NetCDF-c Github issue #178 2015-12-26 18:19:04 -07:00
bom.c make -j working for classic only in ncdump 2017-11-17 08:22:49 -07:00
cdl.h Add new capabilities to filter code: 2017-05-14 18:10:02 -06:00
chunkspec.c Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
chunkspec.h This PR primarily addresses Issue https://github.com/Unidata/netcdf-c/issues/725. 2018-07-26 20:16:02 -06:00
CMakeLists.txt Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
ctests.sh Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
depend moving to trunk subdir 2010-06-03 13:24:43 +00:00
dimmap.c Fix nccopy chunking and rechunking functionality when copying classic files with custom chunking specified for netCDF-4 output. 2011-01-09 21:41:07 +00:00
dimmap.h Fix nccopy chunking and rechunking functionality when copying classic files with custom chunking specified for netCDF-4 output. 2011-01-09 21:41:07 +00:00
dumplib.c Revert/Improve nc_create + NC_DISKLESS behavior 2018-10-10 13:32:17 -06:00
dumplib.h Begin changing over to use strlcat instead of strncat because 2017-11-23 10:55:24 -07:00
env re: NCF-317 2014-10-07 12:37:41 -06:00
indent.c Fixed bug NCF-144 (ncdump of variables with multiple unlimited 2012-11-16 21:37:43 +00:00
indent.h added guards for header files that needed them 2018-01-17 09:20:20 -07:00
inttags4.cdl re: gihub issue https://github.com/Unidata/netcdf-c/issues/380 2017-03-24 18:56:14 -06:00
inttags.cdl ckp 2015-11-19 13:44:55 -07:00
isnan.h added guards for header files that needed them 2018-01-17 09:20:20 -07:00
L512.bin re e-support UBS-599337 2017-10-24 16:25:09 -06:00
list.c This PR primarily addresses Issue https://github.com/Unidata/netcdf-c/issues/725. 2018-07-26 20:16:02 -06:00
list.h This PR primarily addresses Issue https://github.com/Unidata/netcdf-c/issues/725. 2018-07-26 20:16:02 -06:00
Makefile.am Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
nc4print.c Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
nccomps.h Fixed bug NCF-144 (ncdump of variables with multiple unlimited 2012-11-16 21:37:43 +00:00
nccopy.1 Fix failure in the nccopy -c option 2018-11-12 12:59:56 -07:00
nccopy.c Merge branch 'master' into provenance.dmh 2018-09-04 11:22:36 -06:00
ncdump.1 hyphens used as minus signs 2015-01-16 13:12:11 +01:00
ncdump.c Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
ncdump.h Add provenance info for netcdf-4 files. 2016-05-07 14:32:07 -06:00
nciter.c corrected an undefined value error identified by clang. 2014-10-02 12:43:27 -06:00
nciter.h re: github issues 2018-10-30 20:48:12 -06:00
nctime0.c changed macro STREQ to NCSTREQ to avoid name collusion with HDF4 library 2018-05-12 08:55:51 -06:00
nctime0.h added guards for header files that needed them 2018-01-17 09:20:20 -07:00
nctrunc.c make -j working for classic only in ncdump 2017-11-17 08:22:49 -07:00
ocprint.c Modify DAP2 and DAP4 to optionally allow Fillvalue/Variable mismatch 2018-10-01 15:51:43 -06:00
ref1.ncml Fix github issue: https://github.com/Unidata/netcdf-c/issues/236 2016-03-17 22:05:46 -06:00
ref_ctest1_nc4.cdl Wiring in more validation 2016-11-18 11:53:53 -07:00
ref_ctest1_nc4c.cdl Fix ncdump clang warnings. Fix invalid encodings for some non-ascii strings in tests. 2015-08-02 16:09:47 -06:00
ref_ctest64.c different attempt to deal with ncdump dependencies 2017-11-11 17:33:51 -07:00
ref_ctest.c another attempt at reducing ncdump dependencies 2017-11-11 16:45:03 -07:00
ref_inttags4.cdl Working on getting cdf5 tests running. 2017-09-15 18:00:28 -06:00
ref_inttags.cdl ckp 2015-11-19 13:44:55 -07:00
ref_nc_test_netcdf4_4_0.nc Support Dave Allured's ncdump mods for time-valued attributes. Refactor all ncdump time code into nctime.c. Add '-i' option for strict ISO-8601 time notation. Fix backward compatibility test to not use DBL_MAX, which is the same as IEEE infinity when using only 15 significant digits of precision. Document ncdump time functionality in man page. 2011-09-12 21:31:08 +00:00
ref_nc_test_netcdf4.cdl Support Dave Allured's ncdump mods for time-valued attributes. Refactor all ncdump time code into nctime.c. Add '-i' option for strict ISO-8601 time notation. Fix backward compatibility test to not use DBL_MAX, which is the same as IEEE infinity when using only 15 significant digits of precision. Document ncdump time functionality in man page. 2011-09-12 21:31:08 +00:00
ref_nccopy3_subset.nc Wiring new test into autotools. 2017-09-01 11:57:28 -06:00
ref_null_byte_padding_test.nc Wiring in a quick test. 2017-11-20 13:52:06 -07:00
ref_provenance_v1.nc There was a request to extend the provenance information 2018-08-25 21:44:41 -06:00
ref_test_360_day_1900.cdl Solve issue https://github.com/Unidata/netcdf-c/issues/359 2017-07-25 11:58:34 -06:00
ref_test_360_day_1900.nc Makefile.am cleanup 2017-11-18 14:20:04 -07:00
ref_test_365_day_1900.cdl Solve issue https://github.com/Unidata/netcdf-c/issues/359 2017-07-25 11:58:34 -06:00
ref_test_365_day_1900.nc Makefile.am cleanup 2017-11-18 14:20:04 -07:00
ref_test_366_day_1900.cdl Solve issue https://github.com/Unidata/netcdf-c/issues/359 2017-07-25 11:58:34 -06:00
ref_test_366_day_1900.nc Makefile.am cleanup 2017-11-18 14:20:04 -07:00
ref_test_corrupt_magic.nc re e-support UBS-599337 2017-10-24 16:25:09 -06:00
ref_times.cdl Fixed bug NCF-175: ncdump -t incorrectly interpreting units attribute 2012-06-07 18:14:02 +00:00
ref_tst_charfill.cdl add test for fix for Jira NCF-131 2011-12-13 03:08:56 +00:00
ref_tst_comp2.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_comp.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_compounds2.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_compounds2.nc moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_compounds3.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_compounds3.nc moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_compounds4.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_compounds4.nc moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_enum_data.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_fillbug.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_format_att_64.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_format_att.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_group_data_v23.cdl Clarified documentation for nc_inq_grp_ncid(), differentiating it from nc_inq_ncid(). Fixed problem returning values from functions declared void in some libsrc4/ test programs. Added test for bug in ncdump for dimensions with same name in nested groups, and fix for bug. Fixed nccopy bug involving dimensions with smae name in nested groups. Added code for specifying chunking by dimension to nccopy (but not implemented yet). 2010-12-30 18:17:04 +00:00
ref_tst_group_data.cdl Clarified documentation for nc_inq_grp_ncid(), differentiating it from nc_inq_ncid(). Fixed problem returning values from functions declared void in some libsrc4/ test programs. Added test for bug in ncdump for dimensions with same name in nested groups, and fix for bug. Fixed nccopy bug involving dimensions with smae name in nested groups. Added code for specifying chunking by dimension to nccopy (but not implemented yet). 2010-12-30 18:17:04 +00:00
ref_tst_grp_spec0.cdl Add -g option to ncdump and test it 2011-09-21 23:10:03 +00:00
ref_tst_grp_spec.cdl Add -g option to ncdump and test it 2011-09-21 23:10:03 +00:00
ref_tst_irish_rover.nc tests for ncdump issue with irish rover 2018-05-15 08:09:52 -06:00
ref_tst_mud4_chars.cdl Fixed bug NCF-310 (ncdump char vars with multiple unlimited dims). 2014-08-07 14:35:29 -06:00
ref_tst_mud4-bc.cdl Add reference file for ncdump -bc test 2013-11-13 13:45:20 -07:00
ref_tst_mud4.cdl Fixed bug NCF-144 (ncdump of variables with multiple unlimited 2012-11-16 21:37:43 +00:00
ref_tst_nans.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_nc4_utf8_4.cdl Work towards parallel testing via cmake. 2017-11-22 12:10:58 -07:00
ref_tst_ncf213.cdl There was a request to extend the provenance information 2018-08-25 21:44:41 -06:00
ref_tst_noncoord.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_opaque_data.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_small.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_solar_1.cdl ckp 2015-11-19 13:44:55 -07:00
ref_tst_solar_2.cdl Fix ncdump bug displaying NC_USHORT attribute values as NC_SHORT in netCDF-4 files. Add test for fix. 2011-06-24 04:51:11 +00:00
ref_tst_special_atts3.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_special_atts.cdl There was a request to extend the provenance information 2018-08-25 21:44:41 -06:00
ref_tst_string_data.cdl Fix NCF-186, ncdump bug not escaping quotes and newlines in string data 2012-08-03 04:40:06 +00:00
ref_tst_unicode.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_utf8_4.cdl re: Jira NCF-320 2015-08-20 15:53:48 -06:00
ref_tst_utf8.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
ref_tst_vlen_data2.cdl premerge 2012-01-29 18:50:02 +00:00
ref_tst_vlen_data.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
rewrite-scalar.c Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
run_back_comp_tests.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
run_ncgen_nc4_tests.sh Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
run_ncgen_tests.sh replace USE_CDF5 with ENABLE_CDF5 2018-06-29 21:17:07 -05:00
run_tests.sh moved irish rover ncdump test to netcdf-4 test script 2018-05-15 08:13:25 -06:00
run_utf8_nc4_tests.sh eliminated dependencies 2017-11-25 05:18:04 -07:00
run_utf8_tests.sh eliminated dependencies 2017-11-25 05:18:04 -07:00
small2.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
small.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
test0.cdl [NCF-267]/SAI-630695 2013-09-23 17:11:59 -06:00
test_corrupt_magic.cdl re e-support UBS-599337 2017-10-24 16:25:09 -06:00
tst_64bit.sh replace USE_CDF5 with ENABLE_CDF5 2018-06-29 21:17:07 -05:00
tst_bom.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_brecs.cdl Allow double NaNs and Infinities in double to double conversions. Add tests for nccopy deflation, shuffling, and dimension-fixing options. Add man-page documentation for new nccopy topions, with examples. Run tst_nccopy3.sh test even for netCDF-4 builds. 2010-08-31 22:41:00 +00:00
tst_bug321.cdl Add test CDL file and tst_nccopy4.sh test for fix of NCF-321 2015-01-03 17:18:14 -07:00
tst_calendars.cdl Fixed bug NCF-175: ncdump -t incorrectly interpreting units attribute 2012-06-07 18:14:02 +00:00
tst_calendars.sh Makefile.am cleanup 2017-11-18 14:20:04 -07:00
tst_charfill.cdl add test for fix for Jira NCF-131 2011-12-13 03:08:56 +00:00
tst_charfill.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_chunking.c This PR primarily addresses Issue https://github.com/Unidata/netcdf-c/issues/725. 2018-07-26 20:16:02 -06:00
tst_comp2.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_comp.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_compress.c move C program invokations to scripts to clean up dependencies in build 2017-11-16 13:03:35 -07:00
tst_create_files.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_dimsizes.c merged master 2018-07-23 09:45:39 -06:00
tst_dimsizes.sh make -j working for classic only in ncdump 2017-11-17 08:22:49 -07:00
tst_enum_data.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_fileinfo.c There was a request to extend the provenance information 2018-08-25 21:44:41 -06:00
tst_fileinfo.sh There was a request to extend the provenance information 2018-08-25 21:44:41 -06:00
tst_fillbug.c re: github issues 2018-10-30 20:48:12 -06:00
tst_fillbug.sh move C program invokations to scripts to clean up dependencies in build 2017-11-16 13:03:35 -07:00
tst_formatx3.sh replace USE_CDF5 with ENABLE_CDF5 2018-06-29 21:17:07 -05:00
tst_formatx4.sh make -j working for classic only in ncdump 2017-11-17 08:22:49 -07:00
tst_group_data.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_grp_spec.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_h_rdc0.c removing dependencies between tests 2017-11-25 05:19:11 -07:00
tst_h_scalar.c move C program invokations to scripts to clean up dependencies in build 2017-11-16 13:03:35 -07:00
tst_h_scalar.sh move C program invokations to scripts to clean up dependencies in build 2017-11-16 13:03:35 -07:00
tst_hdf5_offset.sh Swapped /bin/bash for /bin/sh to test on osx. 2018-08-12 23:01:08 -06:00
tst_inmemory_nc3.sh make -j working for classic only in ncdump 2017-11-17 08:22:49 -07:00
tst_inmemory_nc4.sh make -j working for classic only in ncdump 2017-11-17 08:22:49 -07:00
tst_inttags4.sh Working on getting cdf5 tests running. 2017-09-15 18:00:28 -06:00
tst_inttags.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_iter.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_lengths.sh replace USE_CDF5 with ENABLE_CDF5 2018-06-29 21:17:07 -05:00
tst_mslp.cdl moving to trunk subdir 2010-06-03 13:24:43 +00:00
tst_mud.sh Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_nans.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_nccopy3_subset.sh Swapped /bin/bash for /bin/sh to test on osx. 2018-08-12 23:01:08 -06:00
tst_nccopy3.sh There was a request to extend the provenance information 2018-08-25 21:44:41 -06:00
tst_nccopy4.sh Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
tst_nccopy5.sh Fix failure in the nccopy -c option 2018-11-12 12:59:56 -07:00
tst_ncgen4_classic.sh The ncdap_tests were a mess, so I decided to clean them up 2018-03-20 21:31:31 -06:00
tst_ncgen4_cycle.sh removed many dependencies in ncdump testing 2017-11-25 07:28:07 -07:00
tst_ncgen4_diff.sh removed many dependencies in ncdump testing 2017-11-25 07:28:07 -07:00
tst_ncgen4.sh Swapped /bin/bash for /bin/sh to test on osx. 2018-08-12 23:01:08 -06:00
tst_ncgen_shared.sh Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
tst_ncml.cdl Fix github issue: https://github.com/Unidata/netcdf-c/issues/236 2016-03-17 22:05:46 -06:00
tst_netcdf4_4.sh Updated and removed a check for _NCProperties during file comparison, as this test fails if the environment is different from the environment the reference file was built on. 2018-09-06 15:53:25 -06:00
tst_netcdf4.sh Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
tst_null_byte_padding.sh Corrected pathing oversight. 2017-11-21 12:17:32 -07:00
tst_opaque_data.c Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_output.sh 1. Keep up to date by merging master 2018-01-16 11:00:09 -07:00
tst_special_atts.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_string_data.c move C program invokations to scripts to clean up dependencies in build 2017-11-16 13:03:35 -07:00
tst_unicode.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_utf8.c Primary change: add dap4 support 2017-03-08 17:01:10 -07:00
tst_vlen_data.c Refactoring tests to separate out error macros from tests, in support of fixing http://github.com/Unidata/netcdf-c/issues/321 2016-10-21 17:17:39 +00:00
tst_vlen_demo.c Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
utils.c re: github issues 2018-10-30 20:48:12 -06:00
utils.h re: github issues 2018-10-30 20:48:12 -06:00
vardata.c Fix more memory leaks in netcdf-c library 2018-11-15 10:00:38 -07:00
vardata.h added guards for header files that needed them 2018-01-17 09:20:20 -07:00
XGetopt.c Merge from latest netcdf-cmake branch. 2012-12-05 18:35:42 +00:00