re: https://github.com/Unidata/netcdf-c/issues/541
re: https://github.com/Unidata/netcdf-c/issues/1208
re: https://github.com/Unidata/netcdf-c/issues/2078
re: https://github.com/Unidata/netcdf-c/issues/2041
re: https://github.com/Unidata/netcdf-c/issues/2143
For a long time, there have been known problems with the
management of complex types containing VLENs. This also
involves the string type because it is stored as a VLEN of
chars.
This PR (mostly) fixes this problem. But note that it adds new
functions to netcdf.h (see below) and this may require bumping
the .so number. These new functions can be removed, if desired,
in favor of functions in netcdf_aux.h, but netcdf.h seems the
better place for them because they are intended as alternatives
to the nc_free_vlen and nc_free_string functions already in
netcdf.h.
The term complex type refers to any type that directly or
transitively references a VLEN type. So an array of VLENS, a
compound with a VLEN field, and so on.
In order to properly handle instances of these complex types, it
is necessary to have function that can recursively walk
instances of such types to perform various actions on them. The
term "deep" is also used to mean recursive.
At the moment, the two operations needed by the netcdf library are:
* free'ing an instance of the complex type
* copying an instance of the complex type.
The current library does only shallow free and shallow copy of
complex types. This means that only the top level is properly
free'd or copied, but deep internal blocks in the instance are
not touched.
Note that the term "vector" will be used to mean a contiguous (in
memory) sequence of instances of some type. Given an array with,
say, dimensions 2 X 3 X 4, this will be stored in memory as a
vector of length 2*3*4=24 instances.
The use cases are primarily these.
## nc_get_vars
Suppose one is reading a vector of instances using nc_get_vars
(or nc_get_vara or nc_get_var, etc.). These functions will
return the vector in the top-level memory provided. All
interior blocks (form nested VLEN or strings) will have been
dynamically allocated.
After using this vector of instances, it is necessary to free
(aka reclaim) the dynamically allocated memory, otherwise a
memory leak occurs. So, the recursive reclaim function is used
to walk the returned instance vector and do a deep reclaim of
the data.
Currently functions are defined in netcdf.h that are supposed to
handle this: nc_free_vlen(), nc_free_vlens(), and
nc_free_string(). Unfortunately, these functions only do a
shallow free, so deeply nested instances are not properly
handled by them.
Note that internally, the provided data is immediately written so
there is no need to copy it. But the caller may need to reclaim the
data it passed into the function.
## nc_put_att
Suppose one is writing a vector of instances as the data of an attribute
using, say, nc_put_att.
Internally, the incoming attribute data must be copied and stored
so that changes/reclamation of the input data will not affect
the attribute.
Again, the code inside the netcdf library does only shallow copying
rather than deep copy. As a result, one sees effects such as described
in Github Issue https://github.com/Unidata/netcdf-c/issues/2143.
Also, after defining the attribute, it may be necessary for the user
to free the data that was provided as input to nc_put_att().
## nc_get_att
Suppose one is reading a vector of instances as the data of an attribute
using, say, nc_get_att.
Internally, the existing attribute data must be copied and returned
to the caller, and the caller is responsible for reclaiming
the returned data.
Again, the code inside the netcdf library does only shallow copying
rather than deep copy. So this can lead to memory leaks and errors
because the deep data is shared between the library and the user.
# Solution
The solution is to build properly recursive reclaim and copy
functions and use those as needed.
These recursive functions are defined in libdispatch/dinstance.c
and their signatures are defined in include/netcdf.h.
For back compatibility, corresponding "ncaux_XXX" functions
are defined in include/netcdf_aux.h.
````
int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count);
int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count);
int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy);
int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp);
````
There are two variants. The first two, nc_reclaim_data() and
nc_copy_data(), assume the top-level vector is managed by the
caller. For reclaim, this is so the user can use, for example, a
statically allocated vector. For copy, it assumes the user
provides the space into which the copy is stored.
The second two, nc_reclaim_data_all() and
nc_copy_data_all(), allows the functions to manage the
top-level. So for nc_reclaim_data_all, the top level is
assumed to be dynamically allocated and will be free'd by
nc_reclaim_data_all(). The nc_copy_data_all() function
will allocate the top level and return a pointer to it to the
user. The user can later pass that pointer to
nc_reclaim_data_all() to reclaim the instance(s).
# Internal Changes
The netcdf-c library internals are changed to use the proper
reclaim and copy functions. It turns out that the places where
these functions are needed is quite pervasive in the netcdf-c
library code. Using these functions also allows some
simplification of the code since the stdata and vldata fields of
NC_ATT_INFO are no longer needed. Currently this is commented
out using the SEPDATA \#define macro. When any bugs are largely
fixed, all this code will be removed.
# Known Bugs
1. There is still one known failure that has not been solved.
All the failures revolve around some variant of this .cdl file.
The proximate cause of failure is the use of a VLEN FillValue.
````
netcdf x {
types:
float(*) row_of_floats ;
dimensions:
m = 5 ;
variables:
row_of_floats ragged_array(m) ;
row_of_floats ragged_array:_FillValue = {-999} ;
data:
ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32},
{40, 41}, _ ;
}
````
When a solution is found, I will either add it to this PR or post a new PR.
# Related Changes
* Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data.
* Remove the --enable-unfixed-memory-leaks option.
* Remove the NC_VLENS_NOTEST code that suppresses some vlen tests.
* Document this change in docs/internal.md
* Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh.
* Mark types as fixed size or not (transitively) to optimize the reclaim
and copy functions.
# Misc. Changes
* Make Doxygen process libdispatch/daux.c
* Make sure the NC_ATT_INFO_T.container field is set.
re: https://github.com/Unidata/netcdf-c/issues/2117
re: https://github.com/Unidata/netcdf-c/issues/2119
* Modify libsrc to allow byte-range reading of netcdf-3 files in private S3 buckets; this required using the aws sdk. Also add a test case.
* The aws sdk can sometimes cause problems if the Awd::ShutdownAPI function is not called. So at optional atexit() support to ensure it is called. This is disabled for Windows.
* Add documentation to nczarr.md on how to build and use the aws sdk under windows. Currently it builds, but testing fails.
* Switch testing from stratus to the Unidata bucket on S3.
* Improve support for the s3: url protocol.
* Add a s3 specific utility code file: ds3util.c
* Modify NC_infermodel to attempt to read the magic number of byte-ranged files in S3.
## Misc.
* Move and rename the core S3 SDK wrapper code (libnczarr/zs3sdk.cpp) to libdispatch since it now used in libsrc as well as libnczarr.
* Add calls to nc_finalize in the utilities in case atexit is disabled.
* Add header only json parser to the distribution rather than as a built source.
## S3 Related Fixes
* Add comprehensive support for specifying AWS profiles to provide access credentials.
* Parse the files "~/.aws/config" and "~/.aws/credentials to provide credentials for the HDF5 ROS3 driver and to locate default region.
* Add a function to obtain the currently active S3 credentials. The search rules are defined in docs/nczarr.md.
* Provide documentation for the new features.
* Modify the struct NCauth (in include/ncauth.h) to replace specific S3 credentials with a profile name.
* Add a unit test to test the operation of profile and credentials management.
* Add support for URLS of the form "s3://<bucket>/<key>"; this requires obtaining a default region.
* Allows the specification of profile and/or region in a URL of the form "#mode=nczarr,...&aws.region=...&aws.profile=..."
## Misc. Fixes
* Move the ezxml code to libdispatch so that it can be used both by DAP4 and nczarr.
* Modify nclist to provide a deep clone operation.
* Modify ncuri to provide a deep clone operation.
* Modify the .rc file format to allow the specification of a path to be tested when looking for an entry in the .rc file.
* Ensure that the NC_rcload function is called.
* Modify nchttp to support setting request headers.
Filter support has three goals:
1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled
Detailed usage directions are define in docs/filters.md.
For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.
This is a big change since filters affect many parts of the code.
In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.
### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.
### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.
### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
re: https://github.com/zarr-developers/zarr-specs/issues/41
After discussions with the Zarr community, it was decided to
convert to a new representation of the NCZarr meta-data extensions: version 2.
These extensions store information necessary to mapping the Zarr data model
to the netcdf-4 data model.
The basic change is to remove the NCZarr specific objects: .nczarr, .nczgroup, .nczarray, and .nczattr.
The contents of these objects is moved into the corresponding existing Zarr objects as special keys. The mapping is as follows:
* ''.nczarr'' => ''/.zgroup/_NCZARR_SUPERBLOCK_''
* ''.nczgroup => ''.zgroup/_NCZARR_GROUP_''
* ''.nczarray => ''.zarray/_NCZARR_ARRAY_''
* ''.nczattr => ''.zattr/_NCZARR_ATTR_''
Backward compatibility is maintained by looking for the object ''/.nczarr''
and if found, then assuming that the dataset is in the older version 1 format.
This compatibility only supports reading of such version 1 datasets.
Documentation and test cases are also added.
Misc. Other Changes:
1. The json parsing code was added to the general library instead of nczarr only (ncjson.c, ncjson.h).
2. Improved support for different platform paths by allowing conversion
to a single common path representation.
3. Add some new error codes.
4. Modify nccopy usage to mention the new chunking specification.
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.
More fixes in collaboration with I.P.
- Adjusted ArcGIS and AgriMetSoft NetCDF-Extractor sections' text and spacing
*Check to see if the spacing for these sections is correct
*Did not address broken links, but should address both broken links and links that re-direct to unintended webpages
More fixes in collaboration with I.P.
* Did not fix spacing for the ArcGIS nor AgriMetSoft sections
* Did not address broken links, but should address both broken links and links that re-direct to unintended webpages
Fixed per I.P.'s work
- Need to ensure proper way to include the u umlaut in line 455
- Didn't address broken link issues
-Left MeteoExplorer's NetCDF uppercased due to library/software reference
-Didn't change Mary Haley's email in the NCL section
-Left nctoolbox's NetCDF-Java
***Stopped short off ncvtk errors (line 149)
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.
I see that there is no way to set CURLOPT_CONNECTTIMEOUT,
but there is support for CURLOPT_TIMEOUT.
So, accept the line 'HTTP.CONNECTTIMEOUT'
in .rc file to allow user to set CURLOPT_CONNECTTIMEOUT.
The CMakeLists.txt actually uses `HDF5_C_LIBRARY` and `HDF5_HL_LIBRARY`
to find non-standard HDF5 installation. This just updates the FAQ with
the correct usage.
* For URL paths, the new approach essentially centralizes all information
in the URL into the "#mode=" fragment key and uses that value
to determine the dispatcher for (most) URLs.
* The new approach has the following steps:
1. canonicalize the path if it is a URL.
2. use the mode= fragment key to determine the dispatcher
3. if dispatcher still not determined, then use the mode flags
argument to nc_open/nc_create to determine the dispatcher.
4. if the path points to something readable, attempt to read the
magic number at the front, and use that to determine the dispatcher.
this case may override all previous cases.
* Misc changes.
1. Update documentation
2. Moved some unit tests from libdispatch to unit_test directory.
3. Fixed use of wrong #ifdef macro in test_filter_reg.c
[I think this may fix an previously reported esupport query].
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.
Priority: Low
re: issue https://github.com/Unidata/netcdf-c/issues/1329
HDF5 has the ability to programmatically define new filters,
as opposed to using HDF5_PLUGIN_PATH env variable.
This PR adds support for that feature.
Not clear how useful this is, though.
See docs/filters.md for details.
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.
A user suggested that the nccopy -F option
syntax should be extended to support specification
of multiple (or all) variables in a single -F option.
The new syntax allows:
1. '*' as the name of the variable; this means apply the
filter to all variables in the data set.
2. *var1|var2|...* as the variable name to indicate that the filter
should be applied to the multiple specified variables.
re: issue https://github.com/Unidata/netcdf-c/issues/1278
re: issue https://github.com/Unidata/netcdf-c/issues/876
re: issue https://github.com/Unidata/netcdf-c/issues/806
* Major change to the handling of 8-byte parameters for nc_def_var_filter.
The old code was not well thought out.
* The new algorithm is documented in docs/filters.md.
* Added new utility file plugins/H5Zutil.c to support
* Modified plugins/H5Zmisc.c to use new algorithm
the new algorithm.
* Renamed include/ncfilter.h to include/netcdf_filter.h
and made it an installed header so clients can access the
new algorithm utility.
* Fixed nc_test4/tst_filterparser.c and nc_test4/test_filter_misc.c
to use the new algorithm
* libdap4/ fixes:
* d4swap.c has an error in the endian pre-processing such
that record counts were not being swapped correctly.
* d4data.c had an error in that checksums were being computed
after endian swapping rather than before.
* ocinitialize() was never being called, so xxdr bigendian handling
was never set correctly.
* Required adding debug statements to occompile
* Found and fixed memory leak in ncdump.c
Not tested:
* HDF4
* Pnetcdf
* parallel HDF5
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.
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.
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
