* Replaced last sprintf with snprintf
To have the size of the buffer, it was required to change a function signature, and change all users of it.
In most cases, determining the buffer size wasn't trivial and so SIZE_MAX is passed. But at least this improves the infrastructure. Someone can later figure out the correct sizes.
* Fix for github issue #2414: segfault when copying dataset with attributes.
This also fixes github issue #3241: segfault when copying dataset.
Need to set the location via H5T_set_loc() of the src datatype
when copying dense attributes.
Otherwise the vlen callbacks are not set up therefore causing seg fault
when doing H5T_convert() -> H5T__conv_vlen().
* Switch warnings as errors to default OFF
* Enable mac docs
* Add doxygen action uses step
* Use html div around snippet
* Allow preset name to be an argument to cmake-ctest.yml
Remove cached datatype conversion path table entries on file close
When performing datatype conversions during I/O, the library
checks to see whether it can re-use a cached datatype conversion
pathway by performing comparisons between the source and destination
datatypes of the current operation and the source and destination
datatypes associated with each cached datatype conversion pathway.
For variable-length and reference datatypes, a comparison is made
between the VOL object for the file associated with these datatypes,
which may change as a file is closed and reopened. In workflows
involving a loop that opens a file, performs I/O on an object with a
variable-length or reference datatype and then closes the file, this
can lead to constant memory usage growth as the library compares the
file VOL objects between the datatypes as different and adds a new
cached conversion pathway entry on each iteration during I/O. This is
now fixed by clearing out any cached conversion pathway entries for
variable-length or reference datatypes associated with a particular
file when that file is closed.
off_t is a 32-bit signed value on Windows, so we should use HDoff_t
(which is __int64 on Windows) internally instead.
Also defines HDftell on Windows to be _ftelli64().
* Add 'warning density' computation to the warnhist script, along with several
cleanups to it. Add "--enable-show-all-warnings" configure (and CMake)
option to disable compiler diagnostic suppression (and therefore show all the
otherwise suppressed compiler diagnostics), disabled by default. Clean up
a buncn of misc. warnings.
Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.
* Fixed some calculations and add test cases for issues spotted from review
* Removed a variable that was compensating for previous miscalculations
* Added missing \since tags to H5D.
* Committing clang-format changes
* Fixed H5T version info.
* Committing clang-format changes
* Added missing version info to H5E.
* Committing clang-format changes
* Added version info to H5F public APIs.
* Committing clang-format changes
* Added missing H5Z public API version info.
* Added missing version info to H5G public APIs
* Added missing version info to H5I public API.
* Added missing version info to H5 public APIs
* Committing clang-format changes
* Added missing version info to H5P public APIs
* Added missing version info to H5R public APIs
* Fix comment error.
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Changes for ECP-344: Implement selection vector I/O with collective chunk filling.
Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization
when computing max address.
* Fixes based on PR review comments:
For H5Dchunk.c: fix H5MM_xfree()
For H5FDmpio.c:
1) Revert the fix to H5FD__mpio_write_vector()
2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types()
* Put back the logic of dividing up the work among all the mpi ranks similar to the
original H5D__chunk_collective_fill() routine.
* Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector().
* Make filter callbacks use top-level API functions
When using VOL connectors, H5I_iterate may not provide
valid object pointers to its callback. This change keeps
existing functionality in H5Zunregister() without using
potentially unsafe pointers.
* Filter callbacks use internal API
* Skip MPI work on non-native VOL
The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization.
Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore.
Fixes#3831
The parallel compression test code tests for the case where all MPI ranks have no selection in a dataset when writing to it. Add an early exit to the code to avoid attempting to use a NULL pointer due to there being no work to do.
When opening a file with the core VFD and a file image, if the file
already exists, the file check would leak the POSIX file handle.
Fixes GitHub issue #635
Allow H5Pset_evict_on_close to be called regardless of whether a parallel build of HDF5 is being used
Fail during file opens if H5Pset_evict_on_close has been set to true on the given File Access Property List and the size of the MPI communicator being used is greater than 1
Add functions/callbacks for explicit control over chunk index open/close
Add functions/callbacks to check if chunk index is open or not so
that it can be opened if necessary before temporarily disabling
collective metadata reads in the library
Add functions/callbacks for requesting loading of additional chunk
index metadata beyond the chunk index itself
Adds a small cache of the first N bytes of a file opened with the
read-only S3 (ros3) VFD, where N is 4kiB or the size of the file,
whichever is smaller. This avoids a lot of small I/O operations
on file open.
Addresses GitHub issue #3381
This function allows the user to determine if the library performed selection I/O, vector I/O, or scalar (legacy) I/O during the last HDF5 operation performed with the provided DXPL. Expanded existing tests to check this functionality.
