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.
disengagement of enable-netcdf4 from enable-hdf5.
That is, with the advent of nczarr, it is possible
to turn off hdf5 but still need netcdf-4 enabled
because nczarr uses libsrc4, but not libhdf5.
This change involves a bunch of things:
1. Modify configure.ac and CMakelist to make enable_hdf5
control if hdf5 support is provided. For back compatibility,
disable-netcdf4 is treated as disable-hdf5. But internally,
netcdf4 support is controlled only by the enabling of formats
that require it.
2. In support of #1, modify .travis.yml to use enable/disable-hdf5
instead of enable/disable-netcdf4.
3. test_common.in is modified to track selected features,
including enable-hdf5 and enable-s3-tests. This is used in
selected tests that mix netcdf-3 and netcdf4 tests.
4. The conflation of USE_HDF5 and USE_NETCDF4 is common in
code, tests, and build files, so all of those had to be weeded out.
5. It turns out that some of the NC4_dim functions really are HDF5 specific,
but are not treated as such. So they are moved from nc4dim.c to
hdf5dim.c or hdf5dispatch.c
6. Some generic functions in libhdf5 can be (and were) moved to libsrc4.
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.
Fix Issue https://github.com/Unidata/netcdf-c/issues/1725.
Replace PR https://github.com/Unidata/netcdf-c/pull/1726
Also replace PR https://github.com/Unidata/netcdf-c/pull/1694
The general problem is that under Visual Studio, we are seeing
a number of undefined reference and other scoping errors.
The reason is that the code is not properly using Visual Studio
_declspec() declarations.
The basic solution is to ensure that when compiling the code itself
one needs to ensure that _declspec(dllexport) is used. There
are several sets of macros to handle this, but they all rely
on the flag DLL_EXPORT being define when the code is compiled,
but not being defined when the code is used via a .h file.
As a test, I modified XGetOpt.c to build properly. I also
fixed the oc2 library to properly _declspec things like ocdebug.
I also made some misc. changes to get all the tests to run
if cygwin is installed (to get bash, sed, etc).
Misc. Changes:
* Put XGetOpt.c into libsrc and copy at build time
to the other directories where it is needed.
Add Wei-King Liao's ncvalidator program (with his permission) as
an uninstalled (for now) tool in the ncdump directory. It has in
the past been useful for debugging netcdf-3 files.
re: Issue https://github.com/Unidata/netcdf-c/issues/1365
At some point (4.6.1) we changed the diskless handling of flags
and added a new NC_PERSIST flag. Looks like we did not fix all
occurrences of the old flag set, specifically for 'nccopy -w' command.
Also added some tests (tst_nccopy_w{3,4}.sh) for this situation.
re: https://github.com/Unidata/netcdf-c/issues/1330
The ncgen utility is documented to accept octal integer constants
if the leading digit is zero. This was not implemented. Fix ncgen.l
to properly handle such constants. Also add a test to c0.cdl.
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.
After a long discussion, I implemented the rules at the end of that issue.
They are documented in nccopy.1.
Additionally, I added a new, per-variable, -c flag that allows
for the direct setting of the chunking parameters for a variable.
The form is
-c var:c1,c2,...ck
where var is the name of the variable (possibly a fully qualified name)
and the ci are the chunksizes for that variable. It must be the case
that the rank of the variable is k. If the new form is used as well
as the old form, then the new form overrides the old form for the
specified variable. Note that multiple occurrences of the new form
-c flag may be specified.
Misc. Other fixes
1. Added -M <size> option to nccopy to specify the minimum
allowable chunksize.
2. Removed the unused variables from bigmeta.c
(Issue https://github.com/Unidata/netcdf-c/issues/1079)
3. Fixed failure of nc_test4/tst_filter.sh by using the new -M
flag (#1) to allow filter test on a small chunk size.
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.
add_sh_test only creates the test if HAVE_BASH is TRUE.
Therefore we can only call SET_TESTS_PROPERTIES on the created test if
HAVE_BASH is equally true.
tst_h_rdc0 depends on ncdump_tst_netcdf4, which isn't build if HAVE_BASH
isn't true. But CMake errors out with:
-- Bash shell not found; disabling shell script tests.
CMake Error at CMakeLists.txt:1521 (SET_PROPERTY):
SET_PROPERTY given TEST names that do not exist:
tst_h_rdc0
There are also some tests which cdl_do_maps depends on, but it is
also not defined if HAVE_BASH isn't true. CMake errors out with:
CMake Error at examples/CDL/CMakeLists.txt:10 (SET_TESTS_PROPERTIES):
SET_TESTS_PROPERTIES Can not find test to add properties to:
cdl_do_comps
This patch makes these tests conditional, making CMake happy.
