Without this define parallel netCDF-Fortran did not work
correctly with Open MPI, for example
examples/F90/simple_xy_par_wr.f90
reported
*** An error occurred in MPI_Info_dup
*** reported by process [2543714305,2]
*** on communicator MPI_COMM_WORLD
*** MPI_ERR_INFO: invalid info object
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
FixesUnidata/netcdf-fortran#109
The primary change is to support the use of a zip file as a
storage format. Simultaneously the .nz4 support is made obsolete
Use of zip requires the libzip support library, so a number of
changes to the build files (Makefile.am, CMakeLists.txt) are
necessary to locate and incorporate libzip. The nczarr_tests
tests are also changed to add zip testing.
Other changes:
* Make sure distcheck leaves no files around.
* Add some functions to netcdf_aux to export some functions of libnetcdf.
* Add a new error NC_EFOUND as the complement of NC_EEMPTY.
* Add tracing support to nclog and use it in libnczarr.
* Modify the zmap interface to support the writeonce semantics of zip.
* Create a new s3util.c to support a variety of S3 auxilliary functions.
* EXTERNL'ize a number of functions so they can be used in s3util.
* Add support for the S3 ListObjects CommonPrefixes mechanism
to improve search.
* Add experimental support for running nczarr X s3 tests against
the actual Amazon S3 cloud.
Re: GH Issue https://github.com/Unidata/netcdf-c/issues/1900
Apparently the clock_gettime() function is not always available.
It is used in unit_test/tst_exhash.c and unit_test/tst_xcache.c.
To solve this, a number of things were changed:
* Move the timing code to a new file unit_tests/timer_utils.[ch]
* Modify the timing code to choose one of several timing methods
depending on availability. The prioritized order is as follows:
1. If Windows, use the QueryPerformanceCounter mechanism else
2. Use clock_gettime if available else
3. Use gettimeofday if available else
4. Use getrusage if available
Note that the resolution of 3 and 4 is less than 1 or 2.
Misc. Other Changes:
* Move the test in CMakeLists.txt that disables unit tests for WIN32 to unit_test/CMakeLists.txt since some unit tests actually work under Visual Studio.
* Fix some of the unit tests to work under visual studio
* Fix problem with using remove() in zmap_nzf.c
* Remove some warning about use of EXTERNL
Primary changes:
* Add an improved cache system to speed up performance.
* Fix NCZarr to properly handle scalar variables.
Misc. Related Changes:
* Added unit tests for extendible hash and for the generic cache.
* Add config parameter to set size of the NCZarr cache.
* Add initial performance tests but leave them unused.
* Add CRC64 support.
* Move location of ncdumpchunks utility from /ncgen to /ncdump.
* Refactor auth support.
Misc. Unrelated Changes:
* More cleanup of the S3 support
* Add support for S3 authentication in .rc files: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY.
* Remove the hashkey from the struct OBJHDR since it is never used.
There were some irregularities in the flags for handling NCZarr S3 support.
The primary change is to regularize the flags controlling this to the following.
1. Automake: --enable-nczarr-s3 and CMake: ENABLE_NCZARR_S3
2. Automake: --enable-nczarr-s3-tests and CMake: ENABLE_NCZARR_S3_TESTS
Flag 1 indicates that NCZarr should be built with S3 support enabled.
Flag 2 indicates that the NCZarr S3 tests should be run
These two flags are separate because running the NCZarr S3 tests
requires access to protected S3 resources. Currently, running
these tests is restricted to Unidata personnel. However, users
may want to enable S3 support even if they cannot run the tests.
It is, of course, an error to specify 2 without specifying 1.
Additionally, if the AWS S3 SDK library is not found, then the NCZARR S3
support and testing must be disabled. Otherwise an error is signaled
during the build.
Some of these NCZarr and S3 changes are propagated to nc-config.
Misc. Other Changes:
1. Allow testing for CYGWIN or MSVC in shell scripts.
2. Add specific test for HDF5 library version 1.10.6.
This is encoded as "HDF5_UTF8_PATHS" because that is the first
version where HDF5 properly supports it under Windows. This is used
in hdf5internal/nc4_ndf5_ansi_to_utf8.
3. Add a AM Conditional -- AX_IGNORE -- for use in testing
when it is desirable to temporarily suppress Makefile code.
4. Add MULTIFILTER flag to CMakeLists.txt
re: https://github.com/Unidata/netcdf-c/issues/1836
Revert the internal filter code to simplify it. From the user's
point of view, the only visible changes should be:
1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h
2. Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter.
Internally,the dispatch table has been modified to get rid of the filter_actions
entry and associated complex structures. It has been replaced with
inq_var_filter_ids and inq_var_filter_info entries and the dispatch table
version has been bumped to 3. Corresponding NOOP and NOTNC4 functions
were added to libdispatch/dnotnc4.c. Also, the filter_action entries
in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2,
etc). This should only impact UDF users.
In the process, it became clear that the form of the filters
field in NC_VAR_INFO_T was format dependent, so I converted it to
be of type void* and pushed its management into the various dispatch
code bases. Specifically libhdf5 and libnczarr now manage the filters
field in their own way.
The auxilliary functions for parsing textual filter specifications
were moved to netcdf_aux.h and were renamed to the following:
* ncaux_h5filterspec_parse
* ncaux_h5filterspec_parselist
* ncaux_h5filterspec_free
* ncaux_h5filter_fix8
Misc. Other Changes:
1. Document NUG/filters.md updated to reflect the changes above.
2. All the old data types (structs and enums)
used by filter_actions actions were deleted.
The exception is the NC_H5_Filterspec because it is needed
by ncaux_h5filterspec_parselist.
3. Clientside filters were removed -- another enhancement
for which no-one ever asked.
4. The ability to remove filters was itself removed.
5. Some functionality needed by nczarr was moved from libhdf5
to libsrc4 e.g. nc4_find_default_chunksizes
6. All the filterx code was removed
7. ncfilter.h and nc4filter.c no longer used
Misc. Unrelated Changes:
1. The nczarr_test makefile clean was leaving some directories; so
add clean-local to take care of them.
re: Issue https://github.com/Unidata/netcdf-c/issues/1848
The existing Virtual File Driver built to support byte-range
read-only file access is quite old. It turns out to be extremely
slow (reason unknown at the moment).
Starting with HDF5 1.10.6, the HDF5 library has its own version
of such a file driver. The HDF5 developers have better knowledge
about building such a driver and what incantations are needed to
get good performance.
This PR modifies the byte-range code in hdf5open.c so
that if the HDF5 file driver is available, then it is used
in preference to the one written by the Netcdf group.
Misc. Other Changes:
1. Moved all of nc4print code to ncdump to keep appveyor quiet.
As it was, nccopy -c dim/x was sometimes being ignored. So
modify nccopy to properly take into account. This also required
a change to the nczarr code because it was not applying default
chunking in the same way as libhdf5.
Modify ncdump/tst_nccopy4.sh to test this feature properly.
Also add a similar test to nczarr_test.
Additionally, fix some other things that were causing Visual
Studio builds with testing to not work.
* fix curl testing under CMake to properly handle case
where DAP is disabled, but byterange support is enabled.
* properly test and/or define uintptr_t
* Convert _O_XXX to O_XXX flags used by open();
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
re: https://github.com/Unidata/netcdf-c/issues/1684
re: e-support VZL-904142
Two issues:
1. As of libcurl 7.66, the semantics of CURLOPT_SSL_VERIFYHOST
changed so that the non-zero values affects certificate processing.
2. The current library was forcing the values of VERIFYPEER
and VERIFYHOST to zero instead of leaving them to the default values.
Solution was first to leave the defaults in place for VERIFYPEER and VERIFYHOST
as long as they are not set in .ocrc/.dodsrc file.
Second, the value of HTTP.SSL.VERIFYPEER or HTTP.SSL.VERIFYHOST
as set in .ocrc/.dodrc is used to set the corresponding CURLOPT flags.
So for example, adding
> HTTP.SSL.VERIFYHOST=2
will set the value of CURLOPT_SSL_VERIFYHOST to 2, the default.
Using
> HTTP.SSL.VERIFYHOST=0
will set the value of CURLOPT_SSL_VERIFYHOST to 0, which disables it.
Similarly for VERIFYPEER.
Finally the semantics of HTTP.SSL.VALIDATE is now equivalent to
> HTTP.SSL.VERIFYPEER=1
> HTTP.SSL.VERIFYHOST=2
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.
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.
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.
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.
In C, `char`, `signed char`, and `unsigned char` are three separate,
distinct types, so just because `char` happens to be signed does not
mean it is interchangeable with `signed char`.
(I hope) metadata mechanism. This mostly just adds new pieces of
code (e.g. nclistmap) and does some minor fixes.
It should be transparent to everything else.
The next set of changes will be the big step.
strlcat provides better protection against buffer overflows.
Code is taken from the FreeBSD project source code. Specifically:
https://github.com/freebsd/freebsd/blob/master/lib/libc/string/strlcat.c
License appears to be acceptable, but needs to be checked by e.g. Debian.
Step 1:
1. Add to netcdf-c/include/ncconfigure.h to use our version
if not already available as determined by HAVE_STRLCAT in config.h.
2. Add the strlcat code to libdispatch/dstring.c
3. Turns out that strlcat was already defined in several places.
So remove it from:
ncgen3/genlib.c
ncdump/dumplib.c
3. Define strlcat extern definition in ncconfigure.h.
4. Modify following directories to use strlcat:
libdap2 libdap4 ncdap_test dap4_test
Will do others in subsequent steps.
