Commit Graph

766 Commits

Author SHA1 Message Date
Ward Fisher
8771d0bdf4
Merge pull request #1582 from NOAA-GSD/ejh_parallel_zlib
Allow user to turn on zlib, shuffle, and/or fletcher32 filters with parallel I/O for HDF5-1.10.2+
2020-01-13 16:06:51 -07:00
Jennifer Oxelson
1b343324ea
Merge branch 'master' into jsremotetest 2020-01-10 17:35:34 -07:00
Ward Fisher
438119dd69
Merge pull request #1560 from NOAA-GSD/ejh_cache_docs
increase default cache size for netCDF-4/HDF5 files, also improve cache docs and add benchmarking program
2020-01-07 11:46:30 -07:00
Ward Fisher
20a8db5a7b
Merge pull request #1532 from NetCDF-World-Domination-Council/ejh_cmake_unit_tests
Adding rest of unit_tests to CMake build, but not running them on Windows
2020-01-07 11:44:56 -07:00
Jennifer Oxelson
feb7da82ec changed/removed references to jetstream remotetest instance. 2020-01-03 13:12:58 -07:00
Dennis Heimbigner
30b3401358 Forgot to create pingurl4.c for Cmake 2020-01-02 11:47:25 -07:00
Edward Hartnett
680e44f628 changed name of macro 2019-12-20 13:58:01 -07:00
Edward Hartnett
32a776badf getting parallel I/O with zlib working in cmake builds 2019-12-20 09:43:56 -07:00
James Sharpe
c5d1e4bdec Call find_package(MPI) to locate MPI paths and link to libdispatch if required 2019-12-18 16:48:40 +00:00
Edward Hartnett
4a5ae05dbf cleanup of RELAX_COORD_BOUND in cmake build 2019-11-26 06:59:03 -07:00
Edward Hartnett
8c648b5a2d changed cmake build to only allow relaxed coord builds 2019-11-26 05:40:03 -07:00
Edward Hartnett
a4465da974 new cache default in cmake build 2019-11-25 17:23:07 -07:00
Ward Fisher
dac41651ee Merge branch 'feature/cmake-targets' of https://github.com/kprussing/netcdf-c into v4.7.3-wellspring.wif 2019-11-19 14:12:41 -07:00
Keith F. Prussing
808803ceeb Add namespace for CMake targets
The usual convention with modern CMake is to namespace the targets.
This gives the netCDF namespace to the package.
2019-11-19 14:45:21 -05:00
Keith F. Prussing
adf2f4d098 Add include directories as netcdf property
Modern CMake tracks the properties of targets so that down stream
libraries do not have to worry about include directories.  However, the
include directories must be added to the target and not just at the
directory level.
2019-11-19 14:39:46 -05:00
Ward Fisher
e4efdd4cfb Bumped version to next development version. 2019-11-18 14:35:01 -07:00
Ward Fisher
a268e6d69f Ctest security stance. 2019-11-18 12:07:01 -07:00
Ward Fisher
7cbbc32dad Adding new security stance to cdash instance. 2019-11-18 10:58:44 -07:00
edwardhartnett
14f2b50f2f turned off unit tests for windows 2019-11-16 07:20:45 -07:00
edwardhartnett
f6ace74afb merged master 2019-11-16 07:19:40 -07:00
edwardhartnett
c1989b738e fixed setting of NC_DISPATCH_VERSION in cmake build 2019-11-15 14:57:07 -07:00
edwardhartnett
7b2ddf2537 trying unit tests on windows 2019-11-15 14:22:34 -07:00
edwardhartnett
a0f984f997 added dispatch version to netcdf_meta.h and libnetcdf.settings 2019-11-15 10:06:46 -07:00
Turing Eret
84a293351e Changes to make it possible to nest this project inside of another CMake
project.
2019-11-07 14:00:53 -07:00
Ward Fisher
f8a588843d Preparing for 4.7.3 development pushed back upstream, forking off to 4.7.2 release branch. 2019-10-18 12:09:28 -06:00
John Buonagurio
bc2a3babf9 Enable HDF5 parallel support for MSVC; add MPI dependency. 2019-09-21 21:56:39 -04:00
Greg Sjaardema
56c0d5cf8a Spelling fixes 2019-09-18 08:03:01 -06:00
Ward Fisher
7aab16254a Bumped to next development version. 2019-08-26 13:07:51 -06:00
Ward Fisher
9a92201c94 Wiring unit test directory into cmake-based builds. 2019-08-21 14:50:09 -06:00
edwardhartnett
e123957618 removed commented lines refering to run_par_test2.sh, which does not exist 2019-08-16 04:42:57 -06:00
Ward Fisher
103e5a3ff5
Merge pull request #1385 from Unidata/mmapfix.dmh
Fix cmake wrt mmap
2019-05-02 11:09:12 -06:00
Ward Fisher
44fce0904e
Merge pull request #1387 from Unidata/fixffilter.dmh
Minor config.h changes to support filters in Fortran
2019-05-01 14:44:53 -06:00
Dennis Heimbigner
62e2b472b4 Minor config.h changes to support filters in Fortran 2019-04-29 16:36:08 -06:00
Ward Fisher
c86593aca3 Corrected cmake syntax, working with a list not a string. 2019-04-26 16:28:53 -06:00
Ward Fisher
dda48ced44 Corrected a case in CMake Syntax where an empty string would cause a failure. 2019-04-26 16:00:28 -06:00
Ward Fisher
88de6f0e1c Updated versions, Release Notes. 2019-04-25 15:40:04 -06:00
Dennis Heimbigner
c9d16d82d6 Fix cmake X mmap
supercede PR: https://github.com/Unidata/netcdf-c/pull/1384

Since we have an mmap user, undeprecate it and make sure
it works. Other changes:

* fix test cases to work with make -j
* fix exposed ncgen error.
2019-04-19 20:32:26 -06:00
Ward Fisher
832c90bb56 Merge branch 'master' into cleanup.wif 2019-04-02 10:44:51 -06:00
Ward Fisher
d0a46d0eed
Merge pull request #1371 from NetCDF-World-Domination-Council/ejh_move_perf
Move performance testing from nc_test4 to new directory nc_perf
2019-04-01 11:08:13 -06:00
Ward Fisher
3823307b9e Disable run_par_test2.sh.in template processing code temporarily. 2019-03-26 15:38:22 -06:00
Ward Fisher
7addb30afd
Merge pull request #1367 from jschueller/patch-1
Fix STRNG typo in CMakeList
2019-03-26 15:33:00 -06:00
Ed Hartnett
d4ab03ea23 merged upstream/master 2019-03-26 11:29:01 -06:00
Dennis Heimbigner
4026323383 Fix minor --ansi warnings in dinfermodel.c and bzlib.c
re:

Needed to provide centralized definitions of fileno and fdopen;
also need to #include sys/types.h
2019-03-22 15:16:47 -06:00
Ward Fisher
e2b31ffae4
Merge branch 'master' into byterange.dmh 2019-03-19 12:05:44 -06:00
Ed Hartnett
5c06d40006 attempting to get cmake build working with new nc_perf directory 2019-03-18 08:15:57 -06:00
Ed Hartnett
51b8ba10b4 attempting to get cmake build working with new nc_perf directory 2019-03-18 08:09:46 -06:00
Julien Schueller
5a5981989c
Fix STRNG typo in CMakeList 2019-03-17 09:09:16 +01:00
Ward Fisher
a4d18bdd66 Bumped SO version in line with http://www.gnu.org/software/libtool/manual/libtool.html#Libtool-versioning 2019-02-28 13:25:56 -07:00
Ward Fisher
eb9f6097d5 Bringing netcdf.pc generated by cmake in line with netcdf.pc generated by configure, in support of https://github.com/Unidata/netcdf-c/issues/gh1324 2019-02-27 14:36:42 -07:00
Ward Fisher
18c403aa02 Prepping for 4.6.3 release, bumping to subsequent version in dev branch. 2019-02-26 14:00:59 -07:00
Dennis Heimbigner
0c59e13bf7 Master merge, conflict resolution, cleanup 2019-02-24 16:54:13 -07:00
Dennis Heimbigner
45a8a265b8 master merge 2019-02-23 17:14:12 -07:00
Ward Fisher
d6c845370b Added fenceposting around H5free_memory, H5allocate_memory, H5resize_memory, as these were all introduced in hdf5 1.8.15. 2019-02-21 14:02:46 -07:00
Dennis Heimbigner
c59d5ce205 Fix handling of '/' characters in names in DAP2.
re: https://github.com/Unidata/thredds/issues/1224
[note that this is an issue in thredds, but the fix is in netcdf-c]

A thredds server can encode a netcdf-4 file into DAP2
by flattening names to include the containing group path,
where the group names are separated by '/'.

But the '/' is prohibited in netcdf names even if escaped
(a decision before my time).

So, if the netcdf-c/libdap2 code encounters a DAP2 name with '/'
characters, the '/' characters are converted to the string
%2f. Unfortunately, there is a glitch, namely that converting
the leading '/' produces a name that is still illegal. This PR
modifies the code to just drop the leading '/' character.
2019-02-14 20:25:40 -07:00
Ward Fisher
1fde39c8d7
Merge branch 'master' into byterange.dmh 2019-02-07 14:28:23 -07:00
Ward Fisher
b27c7d899d Merge branch 'master' into byterange.dmh 2019-01-25 14:50:23 -07:00
Ward Fisher
766d2acfc3 Update CmakeLists.txt in support of https://github.com/Unidata/netcdf-c/issues/1295 2019-01-25 11:26:26 -07:00
Ward Fisher
591b1fd131 Merge branch 'bugfix/debian-stable-default-compilation' of https://github.com/t-b/netcdf-c into pr-aggregation.wif 2019-01-23 15:10:15 -07:00
Ward Fisher
35d0815f82 Merge remote-tracking branch 'origin/gh1245.wif' into pr-aggregation.wif 2019-01-15 15:05:51 -07:00
Ward Fisher
440a9e2ca4
Merge branch 'master' into ansifix.dmh 2019-01-10 13:36:19 -07:00
Ward Fisher
f323a5fec9 Modified cmake configuration file in support of https://github.com/Unidata/netcdf-c/issues/1253 2019-01-08 16:37:33 -07:00
Thomas Braun
531df26af0 CMakeLists.txt: Fix compilation with default settings on debian stretch
Since 209c31d3 (Bringing config.h as generagted by cmake in line with config.h as generated by autotools., 2017-01-27)
we check that we can find the hdf5.h main include file.

But this file may reside in non-standard location so we have to search
in HDF5_INCLUDE_DIR as well.
2019-01-05 14:27:45 +01:00
Dennis Heimbigner
bf2746b8ea Provide byte-range reading of remote datasets
re: issue https://github.com/Unidata/netcdf-c/issues/1251

Assume that you have the URL to a remote dataset
which is a normal netcdf-3 or netcdf-4 file.

This PR allows the netcdf-c to read that dataset's
contents as a netcdf file using HTTP byte ranges
if the remote server supports byte-range access.

Originally, this PR was set up to access Amazon S3 objects,
but it can also access other remote datasets such as those
provided by a Thredds server via the HTTPServer access protocol.
It may also work for other kinds of servers.

Note that this is not intended as a true production
capability because, as is known, this kind of access to
can be quite slow. In addition, the byte-range IO drivers
do not currently do any sort of optimization or caching.

An additional goal here is to gain some experience with
the Amazon S3 REST protocol.

This architecture and its use documented in
the file docs/byterange.dox.

There are currently two test cases:

1. nc_test/tst_s3raw.c - this does a simple open, check format, close cycle
   for a remote netcdf-3 file and a remote netcdf-4 file.
2. nc_test/test_s3raw.sh - this uses ncdump to investigate some remote
   datasets.

This PR also incorporates significantly changed model inference code
(see the superceded PR https://github.com/Unidata/netcdf-c/pull/1259).

1. It centralizes the code that infers the dispatcher.
2. It adds support for byte-range URLs

Other changes:

1. NC_HDF5_finalize was not being properly called by nc_finalize().
2. Fix minor bug in ncgen3.l
3. fix memory leak in nc4info.c
4. add code to walk the .daprc triples and to replace protocol=
   fragment tag with a more general mode= tag.

Final Note:
Th inference code is still way too complicated. We need to move
to the validfile() model used by netcdf Java, where each
dispatcher is asked if it can process the file. This decentralizes
the inference code. This will be done after all the major new
dispatchers (PIO, Zarr, etc) have been implemented.
2019-01-01 18:27:36 -07:00
Ward Fisher
264dc38bf3 Fixed plugin compilation using MSVC in support of https://github.com/Unidata/netcdf-c/issues/1245 2018-12-18 13:26:49 -07:00
Dennis Heimbigner
735ae80928 merge master and fix conflicts 2018-12-12 11:47:54 -07:00
Ward Fisher
d135fb4200 Removed confounding text from a reference file, turned on filter testing by default in Cmake-based builds. 2018-12-07 14:44:47 -07:00
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 #4 and #5 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
ce78cf2d73
Merge branch 'master' into MT-for-MSVC-release 2018-11-15 15:49:05 -07:00
Greg Sjaardema
d18457a2d0
RPATH handling is not needed for archive library
If not building shared libraries, then the RPATH handling should not be specified.  Although ignored on some compilers, the CRAY / Intel compiler will error out when installing the NetCDF executables if the RPATH settings are enabled.
2018-11-06 10:11:57 -07:00
Ward Fisher
6eec91bc5f Merge branch 'leak1.dmh' into v4.6.2-release-branch.wif 2018-11-01 12:09:53 -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
Ward Fisher
f5482d5f37 Recreating 4.6.2 release branch. 2018-10-22 16:52:07 -06:00
Ben Boeckel
005a1bf0b4 cmake: fix detection of the mmap function 2018-10-16 09:44:20 -04:00
Ben Boeckel
918cdf5155 cmake: remove duplicate check for fsync 2018-10-16 09:44:12 -04:00
Dennis Heimbigner
553de966d6 Add some visual studio bug fixes 2018-10-11 12:09:42 -06:00
Dennis Heimbigner
4636584d5b Revert/Improve nc_create + NC_DISKLESS behavior
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
2018-10-10 13:32:17 -06:00
Dennis Heimbigner
a5a34f6aba
Merge branch 'master' into nc_mpiio_nc_mpiposix 2018-10-06 13:33:55 -06:00
Dennis Heimbigner
8072d1f6bb Modify DAP2 and DAP4 to optionally allow Fillvalue/Variable mismatch
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
2018-10-01 15:51:43 -06:00
Wei-keng Liao
0ed70756cc Ignore flags NC_MPIIO and NC_MPIPOSIX. 2018-09-22 20:22:34 -05:00
Wei-keng Liao
bc63c08f41 add a check for MPI_Info_f2c 2018-09-21 17:32:36 -05:00
Wei-keng Liao
5ed6c239e1 More replacement of "parallel-netcdf" with "PnetCDF". 2018-09-20 11:45:25 -05:00
Wei-keng Liao
48da78e133 Use PnetCDF instead of parallel-netcdf to avoid confusion with
parallel netcdf4. Also, update PnetCDF web page.
2018-09-17 17:18:48 -05:00
Ward Fisher
784d777bff Merge branch 'master' into provenance.dmh 2018-09-06 15:13:09 -06:00
Ed Hartnett
efe8e3e8e6
Merge branch 'master' into ejh_loop_cleanup_2 2018-09-06 07:49:18 -06:00
Ward Fisher
746cece75d For some reason, the check for H5free() was never added to CMakeLists.txt. This becomes an issue with newer compilers, as observed in Ubuntu 18.04 and HDF5 1.10.2. The issue isn't seen in HDF 1.8.20. 2018-09-05 14:42:51 -06:00
Ward Fisher
fbe0a18b1c
Merge branch 'master' into ejh_loop_cleanup_2 2018-09-05 11:22:55 -06:00
Ward Fisher
d0bb5ddde8 Merge remote-tracking branch 'origin/inmemory10.dmh' into combined-pr.wif 2018-09-04 13:39:34 -06:00
Ward Fisher
3c3119bed2 Merge remote-tracking branch 'origin/dapcurlopt.dmh' into combined-pr.wif 2018-09-04 12:50:55 -06:00
Dennis Heimbigner
d62a9e623c Fix the NC_INMEMORY code to work in all cases with HDF5 1.10.
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.
2018-09-04 11:27:47 -06:00
Ward Fisher
ede7c5da60
Merge branch 'master' into provenance.dmh 2018-09-04 11:22:36 -06:00
Ed Hartnett
27281dfe4b
Merge branch 'master' into ejh_loop_cleanup_2 2018-08-28 17:32:40 -06:00
Ed Hartnett
5eb0d19227 merged master 2018-08-28 10:03:49 -06:00
Wei-keng Liao
ca0d2bef72 resolve a merge conflict 2018-08-27 17:57:07 -05:00
Wei-keng Liao
f88a34600e
Merge branch 'master' into default_format 2018-08-27 17:43:12 -05:00
Dennis Heimbigner
79e38de840 Add the ability to set some additional curlopt values
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.
2018-08-26 17:04:46 -06:00
Dennis Heimbigner
2ea1cf5f1b There was a request to extend the provenance information
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.
2018-08-25 21:44:41 -06:00
Ed Hartnett
33a47710b8 got par tests working in cmake build 2018-08-17 08:52:34 -06:00
Ed Hartnett
59a25093d9 added setting of mpiexec command to CMake build 2018-08-16 07:33:04 -06:00
Wei-keng Liao
4341e4f6c9 spell check 2018-07-28 16:10:07 -05:00
Wei-keng Liao
9d4fa6f542
Merge branch 'master' into configure_error_out 2018-07-26 01:40:53 -05:00
Ed Hartnett
ef7b525ce4 merged master 2018-07-23 09:45:39 -06:00
Jin-Whu
5bd160086b
Merge branch 'master' into MT-for-MSVC-release 2018-07-23 10:38:11 +08:00
Ward Fisher
b570d10e01
Merge branch 'master' into enable-cdf5 2018-07-17 11:26:02 -06:00
Wei-keng Liao
3141c1b2cc error out when conflicts with PnetCDF are detected 2018-07-16 14:42:37 -05:00
Ed Hartnett
9ac15aac46 attempting to fix ENABLE_SET_LOG_LEVEL problem with cmake build 2018-07-16 11:45:26 -06:00
Ed Hartnett
966fec740d attempting to fix ENABLE_SET_LOG_LEVEL problem with cmake build 2018-07-16 08:39:23 -06:00
Ed Hartnett
cdfa6abad8 attempting to fix ENABLE_SET_LOG_LEVEL problem with cmake build 2018-07-16 08:34:00 -06:00
Ed Hartnett
82d0302fa9 attempting to fix ENABLE_SET_LOG_LEVEL problem with cmake build 2018-07-16 06:39:15 -06:00
Ed Hartnett
987ce47f5e removed duplicate handling of logging 2018-07-16 06:24:57 -06:00
Ward Fisher
8d150a56b3 Merge remote-tracking branch 'origin/interndocs.dmh' into pr-aggregation.wif 2018-07-13 11:01:43 -06:00
Greg Sjaardema
ddabcda2c2 Test should be off by default 2018-07-11 13:40:37 -04:00
Greg Sjaardema
c3f63b6ffe Enable metadata_perf test in CMake build
Currently defaults to enabled, can change top-level
CMakeLists.txt file to change default to disabled
2018-07-11 13:40:31 -04:00
Wei-keng Liao
26f1d9137c revise #1033 and emulate CMAKE OPTION to use 3rd option AUTO 2018-07-01 19:42:03 -05:00
Dennis Heimbigner
c304b2075b
Merge branch 'master' into interndocs.dmh 2018-06-30 13:56:36 -06:00
Dennis Heimbigner
40013b72f6 The pr does some cleanup on the internal documentation
in the docs directory.
1. Add a new internal document -- testserver.dox -- to describe
   how to set up and maintain the dap test server.
2. It moves the internal documentation (internal.dox, indexing.dox,
   and testserver.dox) to later in the documentation table of contents.
3. Cleanup the formatting of the internal documents.
4. Cleanup some minor doxygen issues in other files.
2018-06-29 15:06:27 -06:00
Ward Fisher
246b56dedd
Revert "fix cdf5 configure option" 2018-06-29 14:23:40 -06:00
Wei-keng Liao
02dca6a541 add cmake -L option help string for ENABLE_CDF5 2018-06-28 13:17:08 -05:00
Wei-keng Liao
d122d53c78 fix cdf5 configure option 2018-06-28 02:26:42 -05:00
Dennis Heimbigner
1299a0fcee The Jetstream remote test server is now working.
So it now becomes the first default test server to try.
This also means that the dap4 remote testing is enabled.
The only issue to watch is to see if the jetstream-based
server can stay up for significant periods of time.
A uptimerobot (https://uptimerobot.com) has been set ups
to monitor this hourly, so we shall see.
2018-06-26 13:58:45 -06:00
Ed Hartnett
b9c0fd473d
Merge branch 'master' into ejh_logging 2018-05-17 04:26:28 -06:00
Ward Fisher
3f83cc4926 Merge branch 'master' into inmem2.dmh 2018-05-16 14:24:19 -06:00
Ed Hartnett
42d0bef7b2
Merge branch 'master' into ejh_logging 2018-05-16 01:51:42 -06:00
Ward Fisher
23abe014c0 Threads doesn't need to be required. 2018-05-15 12:19:33 -06:00
Ward Fisher
d54e133e8d Merge branch 'master' into appveyor.wif 2018-05-15 12:01:54 -06:00
Ed Hartnett
c06ec6aa48
Merge branch 'master' into ejh_logging 2018-05-14 17:17:36 -06:00
Ward Fisher
27ca221bdb Merge branch 'master' into appveyor.wif 2018-05-14 13:19:17 -06:00
Ed Hartnett
fac4bf61d6 fixed classic cmake builds without logging 2018-05-13 09:48:20 -06:00
Ed Hartnett
86fba34545 fixing cmake build 2018-05-12 13:40:38 -06:00
Ed Hartnett
82c80c8c6c fixed issue building without nc_set_log_level 2018-05-12 11:46:04 -06:00
Dennis Heimbigner
3c7ffcc6d1 Fix https://github.com/Unidata/netcdf-c/issues/963
Fix https://github.com/Unidata/netcdf-c/issues/962

1. remove the --disable-diskless option since it is no
   longer needed. Similarly for CMakeLists.txt.
2. Fixed nc4files.c where BAIL and return were mixed
   leading to situation where cleanup code was not
   being invoked. This probably occurs elsewhere,
   but I did not find any specifically.
2018-05-11 15:30:19 -06:00
Ed Hartnett
5526ca65d1 created libhdf5, moved some files 2018-05-08 11:58:01 -06:00
Ward Fisher
573cf80eb0
Merge branch 'master' into MT-for-MSVC-release 2018-05-04 14:55:18 -06:00
luz.paz
74fbacdb82 Misc. source comment typos
Some are user-facing. Found via `codespell` and through the downstream FreeCAD.
2018-04-26 23:04:01 -04:00
Ward Fisher
395841ee9b Added a cmake-based option to explicitly turn off shell script tests. 2018-04-26 16:27:20 -06:00
Ward Fisher
28ce3e4a8c Added fenceposts around bash scripts, excluding the bash.exe included with Windows 10 (for now) when searching to see if bash is available. 2018-04-26 14:38:56 -06:00
Ward Fisher
2ee4e80c2b Typo3. 2018-04-25 14:23:25 -06:00
Ward Fisher
545857ded0 Typo2. 2018-04-25 14:13:45 -06:00
Ward Fisher
569adf0981 Typo. 2018-04-25 14:10:56 -06:00
Ward Fisher
4048da1ba1 Added output from looking for m4 executable. 2018-04-25 14:02:10 -06:00
Ward Fisher
663f7706f1 Added threads package to cmake build. 2018-04-24 16:15:26 -06:00
XueyuanJin
90f463460d add CMAKE_C_FLAGS_RELEASE in specify_static_crt_flag 2018-04-24 20:14:11 +08:00
Dennis Heimbigner
3b0fb561d6 Make change work with cmake 2018-04-22 13:19:12 -06:00
Ward Fisher
1ff184d988 Enabled CDF5 support by default, in support of https://github.com/Unidata/netcdf-c/issues/931 2018-04-19 13:26:58 -06:00
Ward Fisher
308a840358
Merge branch 'master' into index.dmh 2018-03-26 17:06:19 -06:00
Ward Fisher
f460746a8b Silenced warning in CMakeLists.txt 2018-03-26 11:53:31 -06:00
Ward Fisher
36c4b7947d Merge branch 'master' into newhash1.dmh 2018-03-20 11:20:14 -06:00
Dennis Heimbigner
25f062528b This completes (for now) the refactoring of libsrc4.
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.
2018-03-16 11:46:18 -06:00
Ward Fisher
ede8f1b02e Bumping to post-4.6.1-release, for merge back into master. 2018-03-15 11:29:32 -06:00
Ed Hartnett
3e6661e1b1 fixed name 2018-03-05 04:22:15 -07:00
Ed Hartnett
17f7a76356 moved HDF4 tests 2018-03-05 03:45:18 -07:00