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308 Commits

Author SHA1 Message Date
Ward Fisher
f43bf8f1da Addressed a handful of issues identified by 
Coverity static analysis.
 2013-08-05 20:36:33 +00:00
Ward Fisher
909f569de0 Changed argument list of nc_rename_grp to match definition of nc_rename_grp, 
changed invocation of nc_rename_grp in renamegroup.c.
 2013-07-22 17:27:43 +00:00
Ward Fisher
0401fafb3b Changed argument list of nc_rename_grp to match definition of nc_rename_grp, 
changed invocation of nc_rename_grp in renamegroup.c.
 2013-07-22 17:04:54 +00:00
Dennis Heimbigner
b85d3568ec Added the necessary code to support 
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.
 2013-07-19 21:48:37 +00:00
Russ Rew
6cd8fca60d Quincey's fixes for NCF-250, netCDF-4 parallel independent access with 
unlimited dimension hanging.  Extending the size of an unlimited
dimension in HDF5 must be a collective operation, so now an error is
returned if trying to extend in independent access mode.

Quincey's bug fixes for parallel build portability, particularly
OpenMPI on MacOS-X.
 2013-07-08 21:31:13 +00:00
Russ Rew
58a63708cc Fix contributed by Nath Gopalaswamy to large file problem reading 
netCDF classic or 64-bit offset files that have a UINT32_MAX flag for
large last record size of a variable that has values larger than 1
byte.  This problem had previously been fixed for *writing* such data,
but was only tested with an ncbyte variable.  Fixed test to
demonstrate problem and the fix.

More updates to chunking documentation, cosmetic fixes for some
"--option=" documentation that doxygen turns into mdash.
 2013-06-25 17:04:10 +00:00
Ward Fisher
33d3d06971 Added initial 'make dist', 'make distcheck' support to 
CMake-based builds.
 2013-06-03 16:42:04 +00:00
Ward Fisher
1df00fa579 Re-added fix for very small files. 2013-05-22 18:56:52 +00:00
Dennis Heimbigner
228e8439d2 1. The code to parse a constraint 
was losing the initial double quote
for a quoted string.
2. The code in ncuri.c was not properly
   handling occurrences of e.g. %xx
 2013-05-16 21:37:58 +00:00
Dennis Heimbigner
253a26cb82 change format of url parameters in fragment part 2013-05-13 19:12:37 +00:00
Dennis Heimbigner
5be772b6c0 1. Moved all the PNETCDF code 
(primarily from libsrc4)
   into its own dispatch library
   called libsrc5.

2. Fixed part of Jira NCF-253
   by removing the need for the
   pnetcdf_ndims field.
   For some reason, the original
   code tried to cache the variable
   ranks rather than computing them
   as needed. Fixed by doing
   an ...inq_varndims call as needed.

3. found some places where NC_MAX_DIMS
   was being stack allocated and changed
   to heap allocation.
   Still some cases in nc_test4.
 2013-05-11 20:04:33 +00:00
Dennis Heimbigner
de34ed2d5b merge from netcdf/trunk prior to merge back to trunk 2013-05-11 19:37:38 +00:00
Dennis Heimbigner
cc7cd9a142 Fix part of JIRA NCF-253. 
libdispatch/dv2i.c
now heap allocates rs[NC_MAX_VARS]
instead of stack allocation.
 2013-05-10 18:15:11 +00:00
Dennis Heimbigner
c583f91992 merge with trunk and fix conflicts 2013-05-10 17:04:28 +00:00
Ward Fisher
2d0dbcfa1d Merged latest from CMake branche. 
Fixed an error on very small files (< 4 bytes) that was only occuring on sol. Updated CMake configuration file.
 2013-05-01 23:55:24 +00:00
Dennis Heimbigner
19c1c11f1d It turns out that my dap code 
is not properly checking the incoming
count argument for nc_get_vars.
It is treating the count as pre-stride
rather than post-stride.
 2013-05-01 22:31:01 +00:00
Ward Fisher
67f96188ff Merged latest from netCDF-cmake branch in preparation for 4.3.0 release. 2013-04-23 21:50:07 +00:00
Ward Fisher
b113f6f8b6 Merged a handful of changes from netcdf-cmake branch. 
Addressed the following coverity issues:

711762
711763
711766
711788
711933
711934
711935
 2013-04-16 23:02:54 +00:00
Dennis Heimbigner
c659633d2e merge from trunk 2013-03-26 16:45:02 +00:00
Dennis Heimbigner
ab17dded89 Caron says to use thredds-test 
as the default test server.
 2013-03-25 18:01:32 +00:00
Dennis Heimbigner
b15a7b1191 Make some initial changes to support move to thredds.ucar.edu 2013-03-25 17:44:08 +00:00
Dennis Heimbigner
9b4db7a039 Make some things static that do not need to be externally visible 2013-03-24 17:33:17 +00:00
Dennis Heimbigner
11c2083b1c Add note about nc_put/get_varm to discourage their use 2013-03-17 21:23:28 +00:00
Dennis Heimbigner
dea3c726c8 merge trunk into this branch 2013-03-15 20:31:07 +00:00
Dennis Heimbigner
1abb2ecb56 Fix jira NCF-243 
Problem was that the NC_create
code was not checking for the NC_CLASSIC_MODEL
mode flag in deciding what dispatch table to use.
This meant that it was then defaulting to use
the default format, and if that was changed
to e.g. NC_FORMAT_NETCDF4, then it would try
to create a netcdf-4 format file, even is
NC_CLASSIC_MODEL mode flag was set.
 2013-03-15 20:03:59 +00:00
Dennis Heimbigner
9eaac2a595 Apply Wei-Keng's fix 
for JIRA issue NCF-241.
This is only temporary
until I can make pnetcdf
operate as a separate dispatch table.

Also, fix nc_test4/tst_pnetcdf
to open with nc_open_par;
this is necessary because a pnetcdf
created file cannot be opened
as a netcdf classic file.
 2013-03-13 17:34:47 +00:00
Ward Fisher
0444a6c711 Fixed a couple of tests on Windows, 
Fixed some compile errors on Windows.
 2013-02-21 23:56:15 +00:00
Ward Fisher
ddf3c31bb0 Corrected a handful of syntax issues in CMake config files, 
probably introduced more.  

Added CMake-related files to Makefile.am files for inclusion
when creating a distribution package.
 2013-02-20 23:28:28 +00:00
Dennis Heimbigner
b0b6c77a3e 1. corrected the nc_get_varm/put_varm documentation 
to indicate that they only work for atomic types,
   not user defined types.

2. modified NCDEFAULT_{get/put}_vars to no longer use
   nc_get/put_varm. They now directly use nc_get/put_vara
   directly. This means that nc_get/put_vars now work
   properly for user defined types as well as atomic types.

3. Added test cases for get_vars/put_vars with a
   user defined type. Tests placed into
   nc_test/tst_compounds.c
 2013-02-17 23:42:15 +00:00
Russ Rew
ba1a494579 Fix bug NCF-226 2013-02-11 18:04:03 +00:00
Dennis Heimbigner
4109174d00 Add quick check for Error {...} at start of the datadds data part 2013-02-07 22:14:57 +00:00
Ward Fisher
ff062bb588 Fixed a windows-specific issue in nc_open. When attempting to 
read 4 bytes from a 3 byte file, Windows would fail with an
error 22, "Invalid Operation". This would happen when trying to
read the 4-byte magic number from a very small file.

This problem was uncovered by nc_test/tst_misc.c.  

When fread returns 0 and errno is 22, NC_ENOTNC is returned.
 2013-01-24 20:23:18 +00:00
Russ Rew
2e29d2876e Distinguish between NC_MAX_DIMS and NC_MAX_VAR_DIMS 2013-01-23 23:31:34 +00:00
Russ Rew
c7e69906a5 Finish fix of Jira ticket NCF-216, modifying nc_copy_var() limitation so that dimension IDs in output don't have to match dimension IDs in input. 2013-01-23 21:46:22 +00:00
Dennis Heimbigner
0d8c0b9276 more pnetcdf fixes 2013-01-18 02:25:12 +00:00
Ward Fisher
91188cea7a Merging CMake branch into trunk. Changes include: 
CMake related changes in CMakeLists.txt files,
cmake_config.h.in. Other changes relate to 
Windows-specific issues, and changes made
when regenerating generated source files.
 2013-01-15 22:43:09 +00:00
Ward Fisher
7b91248723 Merged changes from netcdf-branch. 
o Changed variable names 'typeid' to 'typeid1' to avoid a namespace conflict
in visual studio.
o Cleaned up a handful of warnings in Visual Studio.
o Addressed a few Coverity-discovered issuesl
o Made changes to CMake-based builds.
 2012-12-13 22:09:41 +00:00
Russ Rew
068b35cb4d Updated doxygen and texinfo documentation for nc_var_copy function. 2012-12-13 18:00:03 +00:00
Dennis Heimbigner
fc91587e26 Fix weird code in nc.c/free_NC; wonder how it got that way? 2012-12-11 23:51:05 +00:00
Dennis Heimbigner
6bed1e932e fix previous change to ensure proper return code 2012-12-07 02:25:57 +00:00
Dennis Heimbigner
c114861e68 fix dfile.c error reporting 2012-12-06 21:17:36 +00:00
Ward Fisher
81280c7878 Merge from latest netcdf-cmake branch. 
- Fixes for Windows.
- CMake-based changes (functionality, tests).
- Smattering of coverity-informed bug-fixes.
 2012-12-05 18:35:42 +00:00
Ward Fisher
027e503c3e Fixed a dangling pointer post-free. Marcos uncovered this issue 
when using netcdf on linux via JNI.
 2012-11-27 23:56:36 +00:00
Russ Rew
592a120a55 Fixed bug NCF-206 (Fix strided access for NC_STRING type). Verified 
fix with new test for strided access for NC_STRING type.
 2012-11-19 17:20:53 +00:00
Ward Fisher
7a226dd3f1 Merging the win_netcdf branch into the trunk. 2012-09-27 22:50:41 +00:00
Ward Fisher
f2d2ddf435 2012-09-26 20:30:19 +00:00
Ward Fisher
98675a8047 Merged with latest trunk. 2012-09-26 17:08:23 +00:00
Russ Rew
a92c7c98a0 Fixed DOS line endings in source file. 
Fixed minor memory leak found by Coverity.
Fixed misleading error message in configure.
 2012-09-25 21:48:14 +00:00
Ward Fisher
f820e5e5ee 2012-09-10 21:19:57 +00:00
Ward Fisher
54a3c8290a 2012-09-07 16:34:23 +00:00
Ward Fisher
776e179f23 Corrected CMakeList files. 2012-09-06 21:50:00 +00:00
Ward Fisher
e55d002dbc Merged Dennis' changes from trunk. 2012-09-06 21:15:37 +00:00
Dennis Heimbigner
5ca78309cc The effect of this change is to make the struct NC structure 
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.
 2012-09-06 19:44:03 +00:00
Ward Fisher
2fdea864a2 Changes to includes to supress a few specific MSVC warnings. 2012-09-04 22:39:10 +00:00
Ward Fisher
419c6a3b0a 2012-09-04 22:10:32 +00:00
Ward Fisher
5f92acd032 2012-09-04 21:06:23 +00:00
Ward Fisher
7736efcc62 2012-09-04 20:46:45 +00:00
Dennis Heimbigner
880b5c3f7e fix perf bug in bytebuffer code where setlength was always realloc'ing even when enough space was available 2012-08-30 16:43:34 +00:00
Ward Fisher
04e61d5894 Added MSVC-compatibility items. 2012-08-27 21:19:25 +00:00
Ward Fisher
7ef113df5f 2012-08-24 18:24:58 +00:00
Ward Fisher
58035ff8f2 Added new tests, CMake functionality. 2012-08-21 20:08:53 +00:00
Ward Fisher
e8453be1e5 Merged from trunk into branch 2012-08-20 18:30:04 +00:00
Dennis Heimbigner
5380aa5b67 update utilities: list,byte,hash,uri,log 2012-08-19 21:54:30 +00:00
Dennis Heimbigner
2a0d68c530 update nchashmap; move some old stuff in libdap2; fix new debug code 2012-08-19 21:12:35 +00:00
Ward Fisher
fa681b231b 2012-08-17 22:26:55 +00:00
Russ Rew
8d53da4826 Fixed bug "adding a bad _FillValue" bug (NCF-190). Fixed minor bugs 
reported by static analysis, including memory leak in ncdump, missing
size_t cast for chunk cache.  Fixed various doc problems, including
byte vs. char issues, missing NC_UBYTE in type list, needed link to
"Building with Windows" page.
 2012-08-16 18:31:48 +00:00
Ward Fisher
3ccf4c78c3 2012-08-13 20:41:11 +00:00
Ward Fisher
747cd16106 2012-08-13 20:27:48 +00:00
Ward Fisher
ffb7dc6f0d Merged latest trunk into branch 2012-08-13 19:57:51 +00:00
Dennis Heimbigner
23e66f5adb update list utilities 2012-08-09 19:42:02 +00:00
Ward Fisher
14619ec4c4 2012-08-09 18:40:41 +00:00
Ward Fisher
0607b62375 Added coverage test flags to CMakeLists.txt files. 2012-08-09 17:07:41 +00:00
Dennis Heimbigner
499f8d3a1c complete update of utilities: ncbyte, nclist, ncuri, nclog 2012-08-08 23:15:18 +00:00
Ward Fisher
02a1448dd1 2012-08-08 21:34:53 +00:00
Ward Fisher
402c4277e1 2012-08-08 21:29:57 +00:00
Ward Fisher
c8e9772237 2012-08-08 21:04:44 +00:00
Ward Fisher
c9fae163fb 2012-08-08 20:51:41 +00:00
Ward Fisher
a6c95c65b1 2012-08-08 19:45:38 +00:00
Ward Fisher
0d90326575 Integrated latest changes to trunk, added preliminary CPack support. 2012-08-02 22:56:57 +00:00
Dennis Heimbigner
bc3a732e25 fix e-support YOP-841363 plus a number of coverity found bugs 2012-08-02 18:43:21 +00:00
Dennis Heimbigner
faa1c81671 fix a cosmetic issue with config.h 2012-08-01 17:18:58 +00:00
Ward Fisher
1af2b768b0 Merged changes from trunk (mainly Dennis' oc2 inclusion). 2012-07-31 22:04:25 +00:00
Dennis Heimbigner
42999f4c7c move from oc1.0 to oc2.0; create new dir oc2 2012-07-31 20:34:13 +00:00
Ward Fisher
86b9a01f2d Merged changes from trunk. 2012-07-19 21:38:43 +00:00
Ward Fisher
b9a8bd4bc3 2012-07-19 17:25:24 +00:00
Ward Fisher
71075cee2e Additional changes in support of CMake. 2012-07-18 21:12:58 +00:00
Ward Fisher
d66293beca More changes in support of CMake support 2012-07-17 21:44:41 +00:00
Ward Fisher
b1faefede0 More changes related to CMake support. 2012-07-17 20:50:43 +00:00
Dennis Heimbigner
5ecd5854a9 fix server ping in test_varm3 2012-07-16 20:34:31 +00:00
Dennis Heimbigner
d61af2ab31 fix typo 2012-06-25 17:03:18 +00:00
Dennis Heimbigner
7ddd90c577 Added some more documentation about NC_MMAP 2012-06-25 16:48:39 +00:00
Dennis Heimbigner
a6b932826b add NC_MMAP flag and tests 2012-06-23 19:25:49 +00:00
Dennis Heimbigner
1041a4c25b add procedure and program to locate a working dts test server 2012-06-22 21:54:52 +00:00
Ward Fisher
1de595508f Merged changes from trunk 2012-06-12 19:51:17 +00:00
Ward Fisher
43b5dcccb9 Updated nvdims to return -1 in appropriate instances, on appropriate platforms. (see notes for previous commit.) 2012-06-12 18:52:50 +00:00
Ward Fisher
aa33c3c85c o Under right circumstances, nvdims would return an uninitialized value 
(on windows platforms), resulting in a downstream SIGSEGV upon memory
  allocation of 0 bytes.  Gave nvdims a default value of 1. This may not
  be the best possible fix, but in the short term it has fixed the issue.
  The problem would occur when NetCDF was compiled with NetCDF-4 support,
  on Windows, in 64-bit mode, and when nctest/nctest.exe would run.
 2012-06-11 23:17:20 +00:00
Russ Rew
024f318431 Fixed bug NCF-175: ncdump -t incorrectly interpreting units attribute 
(such as "days") without a base time (such as "since 2007-01-01") as a
time unit.
 2012-06-07 18:14:02 +00:00
Ward Fisher
6b8107b25a Merged trunk changes 2160-2239 into my branch 2012-06-05 17:09:51 +00:00
Dennis Heimbigner
7a9c9347a8 fix NCF-173 2012-05-24 00:58:48 +00:00
Ward Fisher
f2516809c5 Corrected a typo in dv21.c, added a stanza for zlib.dll into configure.ac 2012-05-21 21:08:49 +00:00
Ward Fisher
16336f9e87 Integrated latest changes from trunk 2012-05-18 15:23:27 +00:00
Dennis Heimbigner
4f68d6c5f8 win32/mingw fixes 2012-05-15 03:13:08 +00:00
Ward Fisher
9ec37b647f Balanced ifdef, endif statements in dfile.c 2012-05-08 19:25:43 +00:00
Dennis Heimbigner
cb25985208 another scan-build bug fix 2012-04-30 15:58:40 +00:00
Russ Rew
b569613737 Fixed // style comments, for IBM XL C/C++ for AIX V10.1 compiler. 2012-04-25 16:29:59 +00:00
Russ Rew
c6f399c731 Fix non-portable test that depends on nonstandardized floating-point format using e+08, not e+008. Fixes for some problems reported in scan-build static analysis. 2012-04-23 23:59:24 +00:00
Dennis Heimbigner
00e50f5a44 1. changed from using port 8080 to 8081 for motherlode 
2. Fixed Ward's IGNORE problem with oc
3. Mmap support now works.
4. Fix an uninitialized variable pointed out by Russ in dnclog.c
 2012-04-22 20:34:21 +00:00
Dennis Heimbigner
279f910774 change comments associated with nc_create. 2012-04-16 00:49:47 +00:00
Dennis Heimbigner
5536bccee1 allow NC_DISKLESS with nc_open() to operate as a in-memory cache 2012-04-08 22:47:38 +00:00
Dennis Heimbigner
60e48cf51d Fixed documentation as suggested in e-support ticket KJK-861023 (H/T Charlie Zender) 2012-04-04 04:44:51 +00:00
Dennis Heimbigner
f5bd3bf525 cleanup and remove unused code 2012-04-01 20:15:06 +00:00
Dennis Heimbigner
7dcf52719a add a documentation note about NC_DISKLESS 2012-03-28 02:44:29 +00:00
Dennis Heimbigner
5570117513 fix NC_DISKLESS documentation in nc_create 2012-03-27 03:20:05 +00:00
Dennis Heimbigner
7e27052f87 - Implemented diskless files for both netcdf classic and extended. 
The in-memory files can be made persistent if nc_create is called with
  NC_DISKLESS|NC_WRITE flags set. Initial test case also included.
- Modified ncio mechanism to support
  multiple ncio packages; this is so we
  can have posixio and memio operating
  at the same time.
- cleanup up a bunch of lint issues (unused variables, etc).
 2012-03-26 01:34:32 +00:00
Dennis Heimbigner
25c3167841 ckp 2012-03-26 01:30:22 +00:00
Dennis Heimbigner
88f7950d6f fix a bunch of uninitialized variables 2012-03-16 22:29:09 +00:00
Dennis Heimbigner
99eef24bc2 - Fix NCF-158 to modify ncgen flag defaults. 
- Fix NCF-157 to modify DAP code to support
  partial variable retrieval.
- Fix of NCF-154 to solve problem of ncgen
  improperly processing data lists for variables
  of size greater than 2**18 bytes.
- Fix ncgen processing of char variables that have
  multiple unlimited dimensions.
- Partly fix Jira issue: NCF-145 (vlen issues).
- Benchmark program nc_test4/tst_ar4_*) requires arguments
  and should only be invoked inside a shell
  script; fixed so that they terminate cleanly
  if invoked with no arguments.
- Fix the Doxygen processing so it will work
  with make distcheck.
- Begin switchover to using an alternative to ncio.
- Begin support for in-memory (diskless) files.
 2012-03-14 23:26:48 +00:00
Dennis Heimbigner
787d32fffd changed form of some static data to work with cxx4 2012-03-08 22:21:12 +00:00
Dennis Heimbigner
aebd11348a 1)Integrate the oc with improved performance 2012-01-29 18:56:29 +00:00
Russ Rew
e39dc1ed39 Revert libtool version to 7.1.1. Disable libdiskless. 2012-01-12 23:27:30 +00:00
Russ Rew
0a8c4dba22 Merge my branch back into trunk! 2011-12-21 21:16:29 +00:00
Russ Rew
0e48e0a671 Jira NCF-137: Fix documentation of ncid parameter to include group ids 2011-12-15 21:21:38 +00:00
Dennis Heimbigner
efd9808b0a completely rewritten constraint system 2011-11-14 04:20:19 +00:00
Ed Hartnett
9e30d5d3be some windows changes 2011-10-26 19:18:09 +00:00
Dennis Heimbigner
d10a2605ce moved librpc/ from major branch to trunk 2011-10-23 20:17:56 +00:00
Ed Hartnett
2be90120b6 fixed strdup vs. nulldap problem 2011-09-30 16:48:55 +00:00
Dennis Heimbigner
1578ddac0c 2011-09-20 20:39:04 +00:00
Dennis Heimbigner
b995d52b73 2011-09-20 18:47:49 +00:00
Dennis Heimbigner
732fbff7ce 2011-09-20 17:30:02 +00:00
Dennis Heimbigner
12d4f46668 2011-09-18 20:57:51 +00:00
Dennis Heimbigner
d7790e7e7e 2011-09-16 18:36:08 +00:00
Dennis Heimbigner
16dee702b7 fix NCF-120 2011-09-15 16:57:16 +00:00
Dennis Heimbigner
616aadc321 fix ncaux when --disable-netcdf4 2011-09-04 23:27:34 +00:00
Dennis Heimbigner
dcca0b78a3 final missing file: ncaux.c (I hope) 2011-09-02 22:43:02 +00:00
Dennis Heimbigner
7eccec950f Merge librpc 2011-09-01 22:32:28 +00:00
Ed Hartnett
d58c18c623 added diskless files API, subsetting not working, classic model only 2011-08-16 21:04:33 +00:00
Ed Hartnett
f81628eeb1 fixed def_var_chunking call bug 2011-08-12 14:24:03 +00:00
Ed Hartnett
2b2bcded42 removed cxx and cxx4, bumped version to 4.2, and fixed up documentation some 2011-08-10 18:00:32 +00:00
Dennis Heimbigner
2245d70844 Fixed Jira buf NCF-103 2011-07-27 21:46:00 +00:00
Ed Hartnett
b6aaedaea1 more doxygen changes 2011-07-20 21:39:14 +00:00
Dennis Heimbigner
091ee67be0 Makefile.am: nc4.c->dgroup.c 2011-07-15 00:47:31 +00:00
Dennis Heimbigner
a7fdbb176d Fixed nulldup issues: Jira # NCF-94 2011-07-14 22:43:43 +00:00
Dennis Heimbigner
05ee522676 cleanup misc. issues 2011-07-14 22:23:38 +00:00
Dennis Heimbigner
5c002466e3 cleanup misc. items 2011-07-14 22:21:46 +00:00
Ed Hartnett
b600df57c8 fixed file name problems 2011-07-14 21:39:44 +00:00
Ed Hartnett
8afc4a27bf added forgotten file 2011-07-14 21:35:00 +00:00
Ed Hartnett
e044b404bb renamed file 2011-07-14 18:31:27 +00:00
Ed Hartnett
07ec18ee81 doxygen work on netcdf4 functions 2011-07-14 12:21:03 +00:00
Ed Hartnett
fd4a63c4d2 changed file names to allow visual studio to cope 2011-07-14 09:50:37 +00:00
Ed Hartnett
0bbe605ca2 fix for v2i.c compile on visual studio builds 2011-07-13 21:31:03 +00:00