Commit Graph

583 Commits

Author SHA1 Message Date
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
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