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112 Commits

Author SHA1 Message Date
Larry Knox
95fa8f15e8
Sync develop changes June 6 - July 2 to hdf5_1_14 () 
* Fix typos in context/property documentation ()

* Fix CI markdown link check http 500 errors ()

Sites like GitLab can have internal problems that return http 500
errors while they fix their problems. Some sites also return http
200 OK, which is fine.

This PR adds a config file to the markdown link check so those
are considered "passing" and don't break the CI.

* Simplify property copying between lists internally ()

* Add Python examples ()

These examples are referred to from the replacement page of https://portal.hdfgroup.org/display/HDF5/Other+Examples.

* Correct property cb signatures in docs ()

* Correct property cb signatures in docs
* Correct delete callback type name in docs
* add missing word to H5P__free_prop doc

* Move C++ and Fortran and examples to HDF5Examples folder ()

* Document 'return-and-read' field in API context ()

* Add compression includes to tests needing zlib support ()

* Allow usage of page buffering for serial file access from parallel HDF5 builds ()

* Remove old version of libaec ()

* Add property names to context field docs ()

* Document property shared name behavior ()

* Clarify H5CX macro documentation ()

* Document H5Punregister modifying default properties ()

* Update NVHPC to 24.5 ()

We don't test parallel in other GitHub actions, so this also converts the
NVHPC check to configure and build only while we discuss how we'll
test parallel HDF5 in GitHub.

There is a blocking GitHub issue to address the test failures for
HDF5 1.14.5 ().

* Clean up comments in H5FDros3.c ()

* Rename INSTALL_Auto.txt to INSTALL_Autotools.txt ()

* Clean up ros3 VFD stats code ()

* Removes printf debugging
* Simplifies and centralizes stats code
* Use #ifdef ROS3_STATS instead of #if
* Other misc tidying

* Turn off ros3 VFD stat collection by default ()

Not a new change - an artifact from a previous check-in.

* Pause recording errors instead of clearing the error stack ()

An internal capability that's similar to the H5E_BEGIN_TRY / H5E_END_TRY
macros in H5Epublic.h, but more efficient since we can avoid pushing errors on
the stack entirely (and those macros use public API routines).

This capability (and other techniques) can be used to remove use of
H5E_clear_stack() and H5E_BEGIN_TRY / H5E_END_TRY within library routines.

We want to remove H5E_clear_stack() because it can trigger calls to the H5I
interface from within the H5E code, which creates a great deal of complexity
for threadsafe code.  And we want to remove H5E_BEGIN_TRY / H5E_END_TRY's
because they make public API calls from within the library code.

Also some other minor tidying in routines related to removing the use of
H5E_clear_stack() and H5E_BEGIN_TRY / H5E_END_TRY from H5Fint.c

* Add page buffer cache command line option to tools ()


Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Clarify documentation for H5CX_get_data_transform ()

* Correct comment for H5CX_get_data_transform

* Document why data transform ctx field doesnt use macro

* Remove public API call from ros3 VFD ()

* Remove printf debugging from H5FDs3comms.c ()

* Cleanup of ros3 test ()

* Removed JS* macro scheme (replaced w/ h5test.h macros)
* Moved curl setup/teardown to main()
* A lot of cleanup and simplification

* Removed unused code from H5FDs3comms.c ()

* H5FD_s3comms_nlowercase()
* H5FD_s3comms_trim()
* H5FD_s3comms_uriencode()

* Remove magic fields from s3comms structs ()

* Remove dead H5FD_s3comms_percent_encode_char() ()

* Rework the TestExpress usage and refactor dead code ()

* Skip examples if running sanitizers ()

* Clean up s3comms test code ()

* Remove JS* macros
* Remove dead code
* Bring in line with other test code

* Add publish to bucket workflow ()

* Update abi report CI workflow for last release ()

* Update abi report workflow to handle 1.14.4.3 release

* Update name of java report

* Document that ctx VOL property isn't drawn from the FAPL ()

* Update macos workflow to 14 (keep 13 as alternate) ()

* Removed unnecessary call to H5E_clear_stack ()

H5FO_opened and H5SL_search don't push errors on the stack

* Bring subfiling VFD code closer to typical library code ()

Remove API calls, use FUNC_ENTER/LEAVE macros, use the library's error macros,
rename functions to have more standardized names, etc.

* Correct documentation for return-and-read fields ()

* These two generators create strings without NUL for testing ()

* Fix Fortran pkconfig to indicate full path of modules ()

* Updated release schedule ()

1.16 and 2.0 information

* Document VOL object wrapping context ()

* Earray.c and farray.c in hdf5_1_14 still need time_t curr_time for HDsrandom.

* Remove line to use future 116_API from CMakeListat.txt files in HDF5
examples directories
 2024-07-03 10:50:52 -05:00
Larry Knox
b69c6fcbf6
1 14 dev sync lrk () 
* Added new H5E with tests. ()

Added Fortran H5E APIs:
h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f
h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f,
h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f,
h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature)

Addresses Issue 

* Don't load toolchain file in CMake workflows ()

* Add support for the new MSVC preprocessor ()

Microsoft has added a new, standards-conformant preprocessor
to MSVC, which can be enabled with /Zc:preprocessor. This
preprocessor trips over our HDopen() function-like variadic
macro since it uses a hack that only works with the legacy
MSVC preprocessor.

This fix adds ifdefs to use the correct HDopen() macro
depending on the MSVC preprocessor selected.

Fixes 

* Increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096 to accommodate long AWS secret tokens ()

ros3: increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096; stratified the debugging statements so there is more control over the output

* Close and reopen file during dset vlen IO API tests ()

- Close/reopen file and file objects to prevent cache from being used instead of actual I/O.
- Moved vlen io test datasets under the dset container group instead of the root group
- Moved the PASSED() invocation to after individual test cleanup in case an error occurs during H5Treclaim

* New option for building with static CRT in Windows ()

* addressed compilation errors with gfortran 4.8 ()

* Fix bin/trace script w/ out params ()

The bin/trace script adds TRACE macros to public API calls in the main
C library. This script had a parsing bug that caused functions that
were annotated with /*out*/, etc. to be labeled as void pointers
instead of typed pointers.

This is mainly a developer feature and not visible to consumers
of the public API.

The bin/trace script now annotates public API calls properly.

Fixes GH 

* Use H5T_STD_I32LE to create datatype in vds examples ()

Fixes issues when VDS examples are tested on BE systems

* Remove printf debugging in H5HL code ()

* Fixed asserts due to H5Pset_est_link_info() values ()

* Fixed asserts due to H5Pset_est_link_info() values

If large values for est_num_entries and/or est_name_len were passed
to H5Pset_est_link_info(), the library would attempt to create an
object header NIL message to reserve enough space to hold the links in
compact form (i.e., concatenated), which could exceed allowable object
header message size limits and trip asserts in the library.

This bug only occurred when using the HDF5 1.8 file format or later and
required the product of the two values to be ~64k more than the size
of any links written to the group, which would cause the library to
write out a too-large NIL spacer message to reserve the space for the
unwritten links.

The library now inspects the phase change values to see if the dataset
is likely to be compact and checks the size to ensure any NIL spacer
messages won't be larger than the library allows.

Fixes GitHub 

* Fix copy-paste comments

* update macOS support statement ()

* fixes compilation failures due to H5E additions ()

* Remove extra whitespaces from nvhpc-cmake action. ()

* Remove printf debugging in H5I package ()

* Add subfiling for h5dump filedriver option help message ()

* Merge HDF4 release workflow changes to hdf5 ()

* Update long double test with correct values ()

Update long double test with correct values

* virtual creates must use the same datatype as the main file ()

* Fixed -Wdeprecated-copy-dtor warnings by implementing a copy assignment operator ()

Example warning was:

warning: definition of implicit copy assignment operator for 'Group' is deprecated because it has a user-declared destructor [-Wdeprecated-copy-dtor]

* Expand check for variable-length or reference types when clearing datatype conversion paths ()

When clearing out datatype conversion paths involving variable-length or reference datatypes
on file close, also check for these datatypes inside compound or array datatypes

* Remove H5B debug checks ()

The H5B (version 1 B-tree) package would add some computationally
expensive integrity checks when H5B_DEBUG was defined. Due to their
negative effects on performance, this option was rarely turned on,
making the H5B__assert() check function stale, if not dead, code.

This change:

* Builds H5B__assert() when NDEBUG is not defined (the function
  relies on assert()) so it gets compiled more often.
* Removes some printf debugging statements in the B-tree code
* Removes all H5B "extra debug" checks that are leftover from
  past debugging sessions. Maintainers can add H5B__assert()
  selectively to perform integrity checks when debugging.
* Removes the HDF5_ENABLE_DEBUG_H5B CMake option

H5B_DEBUG now has no effect

* Fix the last C++ stack size warning ()

* Clean up off_t usage ()

* Add comments to C++ and Fortran API calls that use off_t
* Remove noise casts for small integers

* Correct missing change of source path for S3 build ()

* Remove leading / from relative path. ()

* msvc: don't declare `HAVE_TIMEZONE` for older MSVC ()

It was introduced in MSVC 15 (Visual Studio 2017).

* Remove a few H5O printf debugging statements ()

These were in H5Oint.c, were protected by H5O_DEBUG, and only dumped
to stdout if the HDF5_DEBUG environment variable were set to do so.

* Remove H5DEBUG() calls from H5Dmpio.c ()

Just use stdout when a stream is needed.

* Remove printf debugging from H5Smpio.c ()

* Change how stats are printed in H5Z ()

H5Z used the soon-to-be-removed HDEBUG macro to decide if stats
would be dumped and to what stream. This is now handled by a
DUMP_DEBUG_STATS_g variable and the output is always sent to
stdout.

This is an internal change, not normally visible to users.

* Refactor datatype conversion code to use pointers rather than IDs ()

The datatype conversion code previously used IDs for the source and
destination datatypes rather than pointers to the internal structures
for those datatypes. This was mostly due to the need for an ID for these
datatypes that can be passed to an application-registered datatype
conversion function or datatype conversion exception function. However,
using IDs internally caused a lot of unnecessary ID lookups and hurt
performance of datatype conversions in general. This was especially
problematic for compound datatype conversions, where the ID lookups were
occuring on every member of every compound element of a dataset. The
code has now been refactored to use pointers internally and only create
IDs for datatypes when necessary.

Fixed a test issue in dt_arith where a library datatype conversion
function was being cast to an application conversion function. Since the
two have different prototypes, this started failing after the parameters
for a library conversion function changed from hid_t to H5T_t * and an
extra parameter was added. This appears to have worked coincidentally in
the past since the only different between a library conversion function
and application conversion function was an extra DXPL parameter at the
end of an application conversion function

Fixed an issue where memory wasn't being freed in the h5fc_chk_idx test
program. Even though the program exits quickly after allocating the
memory, it still causes failures when testing with -fsanitize=address

* Minimize use of abort() ()

The abort() call is used at several places where it probably shouldn't.

* Clean up a few things in H5T.c ()

* remove (size_t) noise casts
* replace (hid_t)FAIL with H5I_INVALID_HID

* Convert H5B__assert to use error checks ()

Switches assert() calls to HGOTO_ERROR in H5B__assert() so it can be
used in production mode. Also renames it to H5B__verify_structure()
to better reflect what it checks.

* Move common variables out of cache test blocks ()

Fixes a stack size warning w/ XCode

* Remove lint comments ()

* Change compression tests reference files to use masking for compression ratios ()

Rework TEST_FILTER tests to handle slightly different compression ratios

* Add Doxygen for HDFS VFD ()

* Add Doxygen for HDFS VFD

* Fix Doxygen warning

* Update H5FDhdfs.h

* long double tests has problems setting precision with offset ()

* long double tests has problems setting precision with offset

* Disable long double until more development fixes issues

* Fix up dsets test for some platforms with different long double format ()

* Adjust aocc workflow to fit the autotools/cmake pattern of other callable workflows. ()

* Implement ID creation optimization for container datatype conversions ()

Makes the datatype conversion context object available during both the
initialization and conversion processes for a datatype conversion
function, allowing the compound, variable-length and array datatype
conversion functions to avoid creating IDs for the datatypes when they
aren't necessary

Adds internal H5CX_pushed routine to determine if an API context is
available to retrieve values from

Also adds error checking to several places in H5T.c and H5Tconv.c where
the code had previously assumed object close operations would succeed

* Handle IBM long double issues in dsets.c test_floattypes test ()

* Handle IBM long double issues in dsets.c test_floattypes test

* Remove old cmake check ()

* Use AC_SYS_LARGEFILE on Autotools ()

We previously used a hack introduced in 1.8.5 to paper over differences
in off_t and off64_t when determining the type sizes. We no longer explicitly
support off64_t in the library and AC_SYS_LARGEFILE works fine.

* Initialize selection type in chunk struct ()

* Overhaul CMake LFS support ()

Externally visible:
* The HDF_ENABLE_LARGE_FILE option (advanced) has been removed
* We no longer run a test program to determine if LFS works, which
  will help with cross-compiling
* On Linux we now unilaterally set -D_LARGEFILE_SOURCE and
  -D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake
  doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since
  those options do nothing on 64-bit systems, this seems safe and
  covers all our bases. We don't set -D_LARGEFILE64_SOURCE since
  we don't use any of the POSIX 64-bit specific API calls like
  ftello64, as noted above.
* We didn't test for LFS support on non-Linux platforms. We've added
  comments for how LFS should probably be supported on AIX and Solaris,
  which seem to be alive, though uncommon. PRs would be appreciated if
  anyone wishes to test this.

Internal:
* Drops off64_t size checks since this is unused (as in Autotools)
* Remove HDF_EXTRA_FLAGS, which is now unused
* Remove hack around deprecated LINUX_LFS

Fixes 

* Update CMake comment about _POSIX_C_SOURCE ()

Was missng the 2008 pread/write info

* Deprecate bin/cmakehdf5 ()

* Deprecate bin/cmakehdf5

* Add reference text

* Don't set the rpath when linking statically ()

* Remove invalid compile flag ()

* Fix segfault in vlen io API test ()

* Update URLs in RELEASE.txt ()

* Add cygwin CI and update yaml files for consistency and accuracy ()

* Add cygwin CI

* add cygwin packages

* Correct option names

* Cleanup yaml file and synch look and feel

* Synch CI look and feel and correct path issues

* Upgrade oneapi version

* pwsh needs env: for vars

* No continuation char for pwsh

* restore correct pwsh step

* Run subset of tests for cygwin workflow

* Remove space chars in regex

* restore full tests

* Remove ros3 and hdfs VFDs from Autotools VFD list ()

These will never pass `make check` and would require a custom test
suite for more comprehensive testing.

* Skip part of dsets.c test for IBM long double type ()

* Capitalize option message for consistency. ()

* Fixed misc. H5E fortran failures due to previous PR ()

* fixed promotion of integers and reals tests and check-passthrough-vol failure

* fixed cygwin issue

* Fix Autotools -Werror cleanup ()

The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
  so configure checks don't trip over warnings generated by configure
  check programs. The sed line originally only scrubbed -Werror but not
  -Werror=something, which would cause errors when the '=something' was
  left behind in CFLAGS.

  The sed line has been updated to handle -Werror=something lines.

  Fixes one issue raised in 

* Fix doxygen link to example function usage ()

* Remove useless headers ()

Removes unnecessary headers from C library source files.

* Clean up some hbool_t/TRUE/FALSE stragglers ()

It looks like most of these snuck in via selection I/O work

* Fix error when overwriting an indirectly nested vlen with a shorter sequence ()

* defined CMAKE_H5_HAVE_DARWIN ()

* Make the newsletter scheme work like HDF4 ()

* Remove  at the end of list item. ()

* Fix buffer size calculation in the deflate filter ()

* Remove H5O header and friend status from H5A.c ()

* Remove HDF from Fortran 2003 configuration check message. ()

* Suppress H5Dmpio debugging output unless HDF5_DEBUG=d is set ()

* Header cleanup in C library ()

* Ensure H5FL header is included everywhere

* Ensure H5SL header is included everywhere

* Ensure H5MM header is included everywhere

* Add Doxygen to H5FDmirror.h ()

* Remove lseek64 and stat64 symbols from CMake ()

We don't use these in the library.

* Remove HAVE_IOEO checks from CMake ()

This was intended to check for thread-safety functionality on Windows.
The required functionality has been standard since Windows Vista, so
these checks can be removed.

* Fix some minor warnings ()

* Bump the size of the mirror VFD IP field ()

The IP address string isn't big enought to hold an IPv4-mapped IPv6
address.

* Fix mirror VFD script ()

This had directory problems when running locally.

* Fix an issue where the Subfiling VFD's context cache grows too large ()

* Address code page issues w/ Windows file paths ()

On Windows, HDF5 attempted to convert file paths passed to open() and
remove() to UTF-16 in order to handle Unicode file paths. This scheme
does not work when the system uses code pages to handle non-ASCII
file names.

As suggested in the forum post below, we now also try to see if we
can open the file with open(), which should handle systems where
non-ASCII code pages are in use.

https://forum.hdfgroup.org/t/open-create-hdf5-files-with-non-utf8-chars-such-as-shift-jis/11785

* Add Doxygen to API calls in H5VLnative.h ()

* Allow H5Soffset_simple to accept NULL offsets ()

The reference manual states that the offset parameter of H5Soffset_simple()
  can be set to NULL to reset the offset of a simple dataspace to 0. This
  has never been true, and passing NULL was regarded as an error.

  The library will now accept NULL for the offset parameter and will
  correctly set the offset to zero.

  Fixes HDFFV-9299

* Add filter plugin user guide text. Fix registered URL in docs ()

* Add support for _Float16 16-bit floating point type ()

Fixed some conversion issues with Clang due to problematic undefined
behavior when casting a negative floating-point value to an integer

Fixed a bug in the library's software integer to floating-point
conversion function where a user's conversion exception function
returning H5T_CONV_UNHANDLED in the case of overflows would result in
incorrect data after conversion

Added configure checks for functions and macros related to _Float16
usage since some compilers expose the datatype but not the functions or
macros

Fixed a dt_arith test failure when H5_WANT_DCONV_EXCEPTION isn't defined

Fixed a few warnings from not explicitly casting some _Float16 variables
upwards

* Remove some H5T_copy calls that are now unnecessary ()

Removes some datatype copying calls that are now unnecessary after
refactoring the datatype conversion code to use pointers internally
rather than IDs

Rewrites the enum conversion function so that it uses cached copies
of the source and destination datatypes in order to avoid modifying
the datatypes passed in

Adds a 'recursive' field to the datatype conversion context which
allows the conversion functions for members of a container datatype
to skip unnecessary repetitive conversion setup code

Changes internal datatype conversion callback functions so that the
source and destination datatype structure pointers are const

Removes some unused and unnecessary internal IDs registered with
H5I_register

* Add RELEASE.txt note for cmpd segfault fix ()

RELEASE notice for the fix in 

* Clean up CMake direct VFD handling ()

There's no need to build and run programs, or even check the operating
system. We just need to check for O_DIRECT and posix_memalign().

* Capitalize linux for consistency ()

* Reworked H5Epush_f ()

* Add const to new _Float16 conversion routine parameters ()

* Update Release Specific Information link. ()

* Filter plugins updates for registration URL ()

* Update filter plugin URL to new location

* Adjust test array size

* Add daily VFD CI workflow ()

Adds testing of Subfiling VFD

* Exclude shell tests from sanitizers ()

* Add a missing period at the end of sentence. ()

* last-file.txt should not be created for release workflow ()

* Skip part of dtypes.c _Float16 file size check for certain VFDs ()

* Fixes several MinGW + Autotools issues ()

* Fixes detection of various Windows libraries, etc.
* Corrects alarm(2) configure checks
* Uses Win32 threads by default w/ Pthreads override, if desired
* Set _WIN32_WINNT correctly for MinGW
* Fix setenv(3) wrapper for MinGW, which does not have getenv_s()

MinGW Autotools support is still not Amazing, but this at least
allows the library and tools build and is better about thread-safety

* Add semicolons to the end of HSYS_GOTO_ERROR ()

Looks like we forgot these when we did the other macros.

* Remove broken links ()

* Skip vlen IO API test for cache VOL ()

* Fix cache VOL segfault in vlen io test
* Skip vlen IO API test

* Handle certain empty subfiling environment variables  ()

* h5diff compares attribute data like dataset data ()

Updates tools docs to indicate that dataset and attribute data are compared in the same way

* A path component may include a dot with other characters ()

* Add RELEASE.txt note for recent datatype conversion improvements ()

* Add NEWSLETTER item about _Float16 support ()

* Correct download link for develop doxygen ()

* Update version in new .yml files.
 2024-03-21 09:17:22 -05:00
jhendersonHDF
ea3f926057
1.14 sync with develop () 
* Rework tools.cmake and add C flags ()

* Fix gh pages so that the doxygen files are uploaded ()

* Add workspace path
* add debug
* Make one job so workspace files are available
* Put doxygen docs under docs folder in gh-pages

* Fix a misc warning in test/vol.c ()

The compiler complains about using integers instead of size_t
for some sizes.

* Remove H5detect and H5make_libsettings ()

Removes H5detect and H5make_libsettings from the build and replaces
their functionality with things that don't affect cross-compiling.

H5detect --> floating-point types are now detected on library load
H5make_libsettings --> Moved functionality to a new H5build_settings.c template file

* clang-tidy clang-analyzer-core issues addressed ()

src/H5system.c:1293:13: warning: Dereference of null pointer
[clang-analyzer-core.NullDereference]
src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains
uninitialized data (e.g., via the field chain: 'initial.user')
[clang-analyzer-core.CallAndMessage]

* Add note for issue 3056 ()

* Use 1.14 toolchain ()

* Remove the checkposix script ()

This script was used to ensure that all non-HDF5 calls were prefixed
with 'HD'. We are removing this scheme so this script is no longer
needed.

* Remove unused HD macros ()

* Remove unused HD macros
The library prefixes most C and POSIX API calls with 'HD'. We are
going to start removing these so the code looks like normal C.

This PR removes most of the unused HD markup macros.

* Replace ntohl/ntohs

* Adds an optional version arg to bin/format_source ()

* Clean up mirror VFD code in utils dir ()

* Remove dead code
* Replace mybzero with memset
* Replace hbool_t/TRUE/FALSE with bool/true/false

* Fix spelling issues flagged by codespell ()

* Make autogen.sh output message consistent ()

* Add Python for HDF-EOS zoo description ()

* Fix function name in comment in ros3 VFD ()

* Revert long double checks ()

* Revert "Remove long double conversion work-arounds ()"

This reverts commit 1e1dac1dac.

* Update comments to reflect newer systems

* Add java options to build scripts ()

* Add java options to build scripts

Previously, cmakehdf5 turned on compiling of the java interface
by default due to a value set in cacheinit.cmake.

Now, consistent with how Fortran and CPP interfaces are handled,
the script overwrites this default value to disable the libraries,
fixing .

I also implemented the --enable-java/--disable java options for
cmakehdf5, and -java for buildhdf5.

Allen said these scripts should mention that
compilers are to be specified in environment variables, but missing
compilers causes errors at the CMake level, and
CMake's error messages are already pretty informative (See the one
in  about JAVA_COMPILER).

* Removed .lnt linter files ()

These were last usefully modified in 2004

* Fix path to libhdf5.settings in cmakehdf5 ()

* Many clang -Wextra-semi-stmt fixes ()

* Adds semicolons to function-like macros
* Adds a do..while(0) loop to some macros
* Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END

* Remove HD prefix from network calls ()

HDsocket(), etc. Only affects the mirror VFD and its test code.

* Remove hbool_t/TRUE/FALSE from java ()

Replaces with bool/true/false

* CMake: (feature) ROS3 and cmake config file. ()

- Added a cmake variable to the hdf5-config.cmake file which
  indicate if the library has been build with or without the
  read-only S3 functionality.

* Define minimal permissions for new GitHub workflows ()

* Track s3 i/o when S3COMMS_DEBUG enabled ()

* Track s3 i/o when S3COMMS_DEBUG enabled

* Fix the snapshots workflow ()

* Add upload url as artifact
* Change doxygen path and comment log-url upload
* zip doxygen files for upload
* add workspace var

* chore: fix grammar ()

* chore: fix grammar

* Removes the HD prefix from java C99 calls ()

POSIX calls (HDstrndup, etc.) are unchanged

* Correct the zip usage ()

* Many fixes to various compiler warnings ()

* Fixed various -Wmissing-variable-declarations by adding static keyword
* In a few cases, renamed the variable suffix from _g to _s.
* Fixed some -Wmissing-variable-declarations by using different declaration macros
* Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero
* Fixed various -Wcomma warnings
* Fixed clang -Wstrict-prototypes warnings
* Fixed various -Wunused-variable warnings
* Updated some casts to fix the only 3 -Wcast-qual warnings
* Fixed the only -Wsometimes-uninitialized warning

* Create Security Policy ()

* Fix  h5vers usage message. ()

Update Platforms Tested in RELEASE.txt.

* speed-up building HDF5 ()

Disables building the tests when building the netCDF, etc.

* Remove dead code behind #ifdef OLD_WAY ()

* Remove H5F_evict_tagged_metadata() ()

The rest of the library just calls H5AC_evict_tagged_metadata()
directly.

* Add missing space in zip command ()

* Fixed check for a VOL's async compatibility  ()

* cap flag fix in test

* added async comp. output

* Update Linux workflows ()

* Consolidate environment setup
* Turn on ros3 VFD in CMake (Linux only)

* Add gh-pages doxygen link ()

* Fix the doxygen to gh pages and artifact creation ()

* Tidy the list of options in main.yml ()

* Remove HD/hbool_t from fortran ()

* Remove HD/hbool_t from high-level lib ()

* Remove HDva_(arg|copy|end|start) ()

* Drop HD prefix & hbool_t from H5TS ()

* Remove HD from fork/exec*/wait* ()

These are not C99 but are hidden behind ifdefs and are highly
unlikely to ever have non-POSIX equivalents.

* Fix assertion failure when attempting to use IOC VFD directly ()

* Rename HDqsort() to qsort() ()

* Rename HDqsort() to qsort()

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Rename HDpipe() to pipe() ()

Pipe is POSIX but implemented in Microsoft's CRT

* Rename HDassert() to assert() ()

* Change HDassert to assert

* Fix bin/make_err

* Rename HD(f)printf() to (f)printf() ()

* Add note about HDF5_VOL_CONNECTOR to tools usage ()

* Rename HDsystem() to system() ()

system() is only used in the iopipe test and the things it calls
(which are POSIX-y) are protected by an ifdef.

* Remove HD from HDposix_memalign() ()

The posix_memalign call is only used in the direct VFD, which can only
be built if posix_memalign() is available.

* Remove HD from memory allocate/free calls ()

* HDcalloc
* HDfree
* HDmalloc
* HDrealloc

* chore: fix grammar ()

* docs: remove redundancy in Data Transfer section of user guide ()

* Remove checks for setsysinfo, which is unused ()

* Autotools
* CMake

* Remove HD from protected POSIX calls ()

These calls are non-C99 but protected by ifdefs and have no Windows
equivalents:
* HDalarm
* HDasprintf
* HDclock_gettime
* HDfcntl
* HDgethostname
* HDgetrusage
* HDsymlink

* Rename HDato*() to ato*() ()

* Remove some "Programmer" comments ()

These are meaningless noise.

Removes the "Programmer" lines on comment start lines:

    /* Programmer: John Smith

These complicate my sed script that will rip out the rest of
the comments.

* Rename HDexit() and related to exit(), etc. ()

* HDatexit
* HDexit
* HD_exit

* Remove HD from strto* calls ()

* HDstrtod
* HDstrtol
* HDstrtoll
* HDstrtoul
* HDstrtoull
* HDstrtoumax

* Remove HD from C std lib file ops ()

* HDfclose
* HDferror
* HDfeof
* HDfflush
* HDfopen
* HDfread
* HDfwrite

* Remove programmer/date from comments ()

* Removes Programmer: and Date: fields
* Fixes a few Modifications: fields leftover from previous work

* Remove HD from HDmem* calls ()

* Remove HD from HDis* (e.g., isalpha) ()

* HDisalnum
* HDisalpha
* HDiscntrl
* HDisdigit
* HDisgraph
* HDislower
* HDisprint
* HDispunct
* HDisspace
* HDisupper
* HDisxdigit

* Update actions for release option, fix branch for daily build ()

* Update actions for release option, fix branch for daily build

* Scheduled workflows run on latest commit on the develop

* Add snapshots location

* docs: improve consistency in verb form () ()

* fix gh action if statements ()

* Adjust presets timeout and fix build script VS versions ()

* Several ros3vfd logging improvements

* Committing clang-format changes

* Update COPYING ()

Fixed old support URL.

* addresses compilation fortran warnings on Frontier ()

* Fix doc for H5allocate_memory ()

* merge bbrelease to release ()

* merge bbrelease to release

* Fix pre-req workflow

* Replace support.hdfgroup.org URLs for alternative COPYING file ()

* Replace support.hdfgroup.org URLs for alternative COPYING file
locations in copyright headers with https://www.hdfgroup.org/licenses.
Replace  support.hdfgroup.org URL for alternative COPYING_LBNL_HDF5
with github URL.
Tweak chkcopyright script for change from UICOPYRIGHTSTR to
THGCOPYRIGHTSTR.

* Replace 1_10 reference with develop branch ()

* Switch CI to use release script ()

* Subfiling VFD source cleanup ()

* Subfiling VFD source cleanup

Modularize Subfiling CMake code into separate CMakeLists.txt file

Update Mercury util code to latest version and update Copyright

Generate mercury_util_config.h header file instead of using
pre-generated file

Remove unnecessary Mercury functionality

Fix minor warning in Subfiling VFD code

* Remove Mercury headers from Autotools publicly-distributed header list

* install h5fuse.sh in bin dir. ()

* Disable h5py until fixed properly without spack ()

* ROS3: (feature) Temporary security credentials ()

- Implemented support for AWS temporary security credentials.
  For this kind of credentials also a session/security token
  should be included in the request by adding the
  x-amz-security-token header.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Avoid truncating at null byte when copying to std::string ()



---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix CMake builds when Subfiling VFD isn't enabled ()

* Fix CMake builds when Subfiling VFD isn't enabled

* Add Subfiling VFD entry to hdf5-config.cmake.in

* Fix some warnings in developer builds ()

* Fix some warnings in developer builds

* Switch approach to Winline flag

* Fixed more warnings about extra semicolons ()

* Require semi-colon after H5_CHECK_OVERFLOW calls



Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro ()

Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning
causing Werror Release builds to fail

* Update DEFAULT_API_VERSION documentation for CMake ()

* Update DEFAULT_API_VERSION documentation for CMake

* Fix hint

---------

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* changed the scope of #ifdef DOXYGEN to now include H5D multi-functions ()

* Option changed but not all references ()

* Option changed but not all references

* remove quotes from binary var

* Move 1.12.3 release to October ()

* Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized warning ()

* removed the use of encoded single apostrophe ()

* removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read

* updated sanitizer paragraph
* fixed brief description for H5Fget_info

* ROS3: (fix) Replaced HDfprintf ()

- Replaced the HDfprintf() functions by fprintf() to be consistent
  with other parts of the library.

* chore: make VRFY output consistent ()

* CMake: (fix) Threads dependency ()

- If the HDF5 library has been build with either thread-safety or
  subfiling VFD feature on it will have an additional dependency
  on a threading library. This dependency has been added to the
  hdf-config.cmake.in file.

* chore: fix grammar - get hang -> get hung ()

* Another round of fixing -Wextra-semi-stmt warnings ()



Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* chore: fix typo - persent -> present ()

* Remove py-pip from h5py action ()

* Update release schedule ()

* Move 1.12.3 to November
* Add 1.14.3 in October

* Update README.md w/ 1.4.3 info ()

* Switch parallel compression to use vector I/O ()

Updates parallel compression feature to use vector I/O instead of
creating and passing down MPI derived types to VFD

* Fix incorrect error check in H5Ofill.c for undefined fill values ()

* Fix H5Otoken_to_str call in h5dump and other minor cleanup ()

* Fix loading plugin fails with missing directory GH issue  ()

* Made HGOTO_ERROR a do-while loop ()

* Made HGOTO_ERROR a do-while loop

* Update files to skip list and ignore_words_list  ()

* Update files to skip list and ignore_words_list for codespell to not
check files generated by autotools.  Autotools generate misspellings
that can't be fixed in HDF5 code.

* Windows runtime items go into the bin folder ()

* A couple of documentation items to fix ()

* Fix h5repack for variable-length datatyped datasets ()

* Fix CVE-2018-11202 ()

A malformed file could result in chunk index memory leaks. Under most
conditions (i.e., when the --enable-using-memchecker option is NOT
used), this would result in a small memory leak and and infinite loop
and abort when shutting down the library. The infinite loop would be
due to the "free list" package not being able to clear its resources
so the library couldn't shut down. When the "using a memory checker"
option is used, the free lists are disabled so there is just a memory
leak with no abort on library shutdown.

The chunk index resources are now correctly cleaned up when reading
misparsed files and valgrind confirms no memory leaks.

* Fix CVE-2018-13867 ()

* Fixes the last of the -Wextra-semi-stmt warnings ()

* Fixed extra semi warning by adjusting alternative macro definitions

* Find-replace H5E_END_TRY; -> H5E_END_TRY

* Made H5Epush_goto a do-while loop, fixed indentation

* Made GOTOERROR and ERRMSG do-while loops

* Made Hgoto_error and Hgoto_done  do-while loops

* Made vrfy_cint_type and vrfy_ctype  do-while loops

* Made TEST_TYPE_CONTIG and others do-while loops

* Removed extraneous semi-colons

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix a typo in RELEASE.txt

* Fix assertion failure in H5D__mpio_collective_filtered_vec_io ()

* Make h5dump spacing consistent when printing VLEN datatype ()

* Fix for the bug exposed from running test/set_extent.c when selection… ()

* Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled.
This is a fix from Neil.
The test/set_extent.c is modified to test for selection I/O enabled.

* Add Fortran ES module to deploy list ()

* Add Fortran ES module to deploy list

* Change fortran mod file export to use a list of names

* test(parallel): verify FALSE case ()

* Implementation of the mpio driver with selection I/O. ()

* This changes the default selection I/O to on for MPIO.

* Work around a testphdf5 failure on Cray MPICH machines ()

* set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with ()

CMake to fix Fortran build failures.

* Add RELEASE.txt notes for recent selection I/O work. ()

* Fix possible performance regression introduced with in-place type conversion in 1.14.2 ()

* Correct script ()

* Correct CI settings ()

* Correct CI settings

* Correct plugin file name

* restore CI tarball name prefix to match bin/release ()

* Fix assertion failure during file close on error ()

* Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled ()

* Fix valgrind warning about write of uninitialized bytes ()

* Fix valgrind warning about write of uninitialized bytes in ScaleOffset filter ()

* Update presets, examples uncompress, szip cache ()

* Fix serial to parallel chunked dataset file space allocation bug ()

* chore: fix typo ()

* Fix for CVE-2016-4332 ()

This CVE issue was previously listed as fixed (via HDFFV-9950) back in
2016, but with no confirmation test. Now that test files exist for
the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an
assert in debug builds.

This fix replaces the assert with pointer checks that don't raise
errors or asserts. Since the function is in cleanup code, we do our
best to close and free things, even when presented with partially-
initialized structs.

Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)

* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 ()

* Enable szip by default in Autotools ()

Since libaec is so prevalent and BSD-licensed for both encode and
decode, we build the szip filter by default when the szip or aec
libraries are found.

* Re-enable SZIP default to ON in CMake ()

The Autotools were handled in a separate commit

* Fix Heap-buffer-overflow WRITE in H5MM_memcpy ()

* Add Intel oneAPI actions () ()

* ci: add Intel oneAPI actions ()

* ci: fix CMake installation

* ci: use absolute paths for libtool installation

* ci(oneAPI): update compiler versions and use cron

* Add RELEASE.txt entry for compound performance regression fix () ()

* chore: remove gubbins comment ()

* Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] ()

* Avoid H5Ocopy in h5repack for variable-length string types ()

* Skip atomicity tests for OpenMPI major versions < 5 ()

* Fix an issue with use of uninitialized memory in trefer_deprec.c test ()

* Add parallel examples in doxygen ()

* Fix use of uninitialized value in testpar/t_dset.c test ()

* Remove extraneous "33" in RELEASE.txt ()

* Revise file close assertion failure fix ()

* Remove intel oneapi warning ()

* Fix for CVE-2018-15671.  h5stat -S $POC will result in a crash with segmenetation fault. ()

It is because the object in the testfile points back to the root group.
When the tool tries to traverse the object, it goes back to the root group and then back again.

* chore: match function call and VRFY() output ()

* Fix the Fortran extension used in example links ()

* Put H5T_CONV_ab macros in do..while loops ()

Ever since a recent round of macro cleanup, bin/trace and clang-format
have been bickering over what H5Tconv.c should look like and neither
produces readable code.

This change puts the top-level H5T_CONV_ab macros in do..while loops,
adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF
and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros
clang-format recognizes. H5Tconv.c is now readable and both bin/trace
and clang-format are happy.

* Convert some H5MM calls to standard C equivalents ()

* H5MM_calloc and malloc are now mapped to stdlib C calls
* H5MM_memcpy now maps directly to memcpy in release builds
* H5MM_memcpy is still implemented as a separate function that
   checks for buffer overlap when H5MM_DEBUG is defined
   (default w/ debug builds)
* Switches many library memcpy calls to use H5MM_memcpy
* Fixes a possible zero allocation in H5Olayout.c

* Add 1.14.4 to the release schedule ()

* Output stderr file in CMake testing on failure ()

* Add Intel oneAPI badges ()

* Add a CVE regression test action ()

*

* Disable SZIP for Intel oneAPI Action ()

* Disable SZIP for Intel oneAPI Action

* Disable Fortran and parallel

* Update VOL CMake for REST VOL ()

* Update VOL CMake for REST VOL

* Prevent linking static libs to VOLs

* Add an h5py badge to README.md ()

* Removed all the ranks printing out testing information ()

* Fix Subfiling VFD IOC assignment bug ()

* Correct java test dimension ()

* Support CMake VOL builds with FetchContent from local directory ()

* Update VOL CMake for REST VOL

* Prevent linking static libs to VOLs

* index on fetch_local: 5c5c3f1505 Prevent linking static libs to VOLs

* index on (no branch): 9a36d3e7b1 On fetch_local: WIP:add source dir fetch option for vols

* Allow building of VOL from local source

* Move LOCAL_DIR option to HDF5_VOL_ALLOW_EXTERNAL

* Fix the Fortran include dir in install config files ()

* Convert hbool_t --> bool in examples ()

* Fix some minor formatting for consistency ()

* Create scorecard.yml ()

Bring in OSSF Scorecard code scanner as a GitHub action

* Convert hbool_t --> bool in testpar ()

* hbool_t/TRUE/FALSE --> bool/true/false in tools ()

* Convert hbool_t --> bool in test ()

* Convert hbool_t --> bool in src ()

* hbool_t --> bool in src

* Does not remove TRUE/FALSE
* Public header files are unchanged
* Public API calls are unchanged

* TRUE/FALSE --> true/false in src

* Add deprecation notice for hbool_t

* Added new Fortran API wrappers ()

* Added new wrappers for
h5get_free_list_sizes_f
H5Sselect_intersect_block_f
H5Sselect_shape_same_f
h5pget_no_selection_io_cause_f
h5pget_mpio_no_collective_cause_f
H5Lvisit_by_name_f
H5Lvisit_f
H5Fget_info_f
h5dwrite_chunk_f
h5dread_chunk_f

* added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests

* added fortran tests

* Update tH5F.F90

* misc. fortran fixes for failing CI dailty tests ()

* fixed H5Lvisit* interface

* changed integer type for direct write

* Consistent initialization of hid_t in the tests ()

* Fix windows cpack with debug ()

* Add missing row for the ROS3 VFD in table  ()

* fixed nvidia compiler issue ()

* Identify functions in a subgroup ()

* quiet warning on sunspot (gcc 11.2.0) ()

* Add API examples doxygen page ()

* removed C_INT32_T from Fortran APIs ()

* Add NVHPC 23.7 GitHub Actions ()

* Add NVHPC 27.3 GitHub Actions

* Address @derobins review

* Remove HD prefix from math functions ()

* Remove HD prefix from HDlog10 calls ()

Was missed in a previous commit and causes building subfiling to
fail.

* fixed arg to C H5Dwrite_chunk ()

* Strip HD prefix from string/char C API calls ()

* Strip HD prefix from string/char C API calls

* HD(f)(put|get)(s|c)
* HDstr*
* HDv*printf
* HD(s)(print|scan)f
* HDperror

But NOT:

* HDstrcase*
* HDvasprintf
* HDstrtok_r
* HDstrndup

As those are not C99 and have portability work-around
implementations. They will be handled later.

* Fix th5_system.c screwup

* Convert main.yml CI into callable workflows ()

* Fix broken URL. ()

* Fix grammar ()

* Update oneAPI-C/A badge yml links. ()

* Check return values from HDF5 API calls. ()

* Adds link to h5fuse.sh in testpar for autotools ()

* Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.

* Some minor formatting and text changes ()

* Fix typos and grammar in t_pread. ()

* Fix typo (givin->given) in test/testframe.c. ()

* Fix ifx unused variable hdferr warning. ()

* Correct comments about H5Z_FILTER_NONE ()

* Update release script. ()

* fixed function declaration ()

* Fixed GH-3554 ()

Removed the extra condition

* Remove h5dwalk.1 man page. ()

* Removed the use of -commons linking option on Darwin ()

Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used

* Fix docs for H5Pset_dxpl_mpio_collective_opt() ()

* Fix typo: arange->arrange in src/H5Cmpio.c. ()

* Fix docs for H5Acreate2 and H5Acreate_by_name ()

* Use HDoff_t with lseek consistently ()

lseek on Windows uses __int64 for both the offset and return type
instead of off_t like most POSIX systems. This changes ensures we
use HDoff_t (which is typdef'd correctly on Windows) w/ lseek.

* Replaces HDgetenv with getenv ()

* Develop tools move ()

Reorganizes the tools files to support the VOL tests

* Clean up Subfiling VFD header doxygen formatting ()

* Remove `sh` to run bash script. ()

* Correct path name of ddl file to be changed ()

* Fix potential uninitialized variable ()

Moves a union initialization up a bit so it's performed before code
that can jump to the cleanup target, where file descriptors could
be checked without being initialized.

This could only happen in test code and only in an out-of-memory
situation.

Fixes Coverity 1542254

* Remove unnecessary assignment in test generator ()

Fixes what looks like a copy/paste/modify error in the format convert
test file generator, where an array element is assigned one value
and them immediately overwritten by another value.

Fixes Coverity issue 1542285

* Remove useless define TRUE/FALSE statements. ()

* Fix typo behaviour and dependes. ()

* Fix typos ()

* Fixed unused variable in H5CS.c () ()

* Fixed 

* Fix grammar ()

* Cleanup unused statements () ()

Removed unnecessary assert statements and noise comments.

* Fix Intel oneAPI icc warning ()

* Fix several spelling/grammar issues ()

* Add HPC CDash to README.md ()

* Disable static + thread-safe on Windows w/ CMake ()

The thread-safety feature on Windows requires a hook in DllMain() and
thus is only available when HDF5 is built as a shared library.

This was previously a warning, but has now been elevated to a fatal
error that cannot be overridden with ALLOW_UNSUPPORTED.

Fixes GitHub 

* Remove unused member from H5D_shared_t struct. ()

* Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT ()

* Fix grammar ()

* Disambiguate error output messages. ()

* Disambiguate error output messages.

* Address @brtnfld review.

* Fail CMake on Windows when sub-filing VFD is enabled ()

* Improve consistency in past tense usage ()

* Split out test logic to separate file ()

* Drop MPI-2 support ()

* Switch IEEE flags for NAG Fortran ()

Default is -ieee=stop, which causes problems when the H5T
module performs floating-point type introspection.

The new mode is -ieee=full

* Remove 1.10.11 info from README.md ()

* Fixes GH#1027 compilation error ()

* Remove 1.10 badge ()

* Use real URLs and updated names for plugins ()

* synchronize TGZ naming convention/usage

* Update parallel compression feature to support multi-dataset I/O ()

* Add more tests for selection I/O. ()

* Adjust 1.14 files after merging

---------
 2023-10-12 11:32:23 -05:00
jhendersonHDF
d8dd57aba1
Fix incorrect error check in H5Ofill.c for undefined fill values () () 2023-08-02 13:14:22 -07:00
Dana Robinson
9ef2f993cf
Sync test dir w/ develop () 2023-07-28 09:08:44 -05:00
Dana Robinson
61186204c0
Remove "Programmer" lines () 2023-07-27 14:08:47 -07:00
Dana Robinson
1e91d96fa0
Brings over most of the HD prefix removal () 2023-07-27 15:43:30 -05:00
Dana Robinson
7707859279
Merge with develop () 2023-04-21 23:25:12 -07:00
Larry Knox
11dfa25910
Update copyright headers () 
* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
 2022-11-01 16:02:27 -05:00
Allen Byrne
ae414872f5
Develop clang 13 format () 
* Update format source to clang 13

* More format changes
 2022-07-26 14:45:46 -07:00
jhendersonHDF
27bb358f7a
Subfiling VFD () 
* Added support for vector I/O calls to the VFD layer, and
associated test code.  Note that this includes the optimization
to allow shortened sizes and types arrays to allow more space
efficient representations of vectors in which all entries are
of the same size and/or type.  See the Selection I/o RFC for
further details.

Tested serial and parallel, debug and production on Charis.
       serial and parallel debug only on Jelly.

* ran code formatter

quick serial build and test on jelly

* Add H5FD_read_selection() and H5FD_write_selection().  Currently only
translate to scalar calls.  Fix const buf in H5FD_write_vector().

* Format source

* Fix comments

* Add selection I/O to chunk code, used when: not using chunk cache, no
datatype conversion, no I/O filters, no page buffer, not using collective
I/O.  Requires global variable H5_use_selection_io_g be set to TRUE.
Implemented selection to vector I/O transaltion at the file driver
layer.

* Fix formatting unrelated to previous change to stop github from
complaining.

* Add full API support for selection I/O.  Add tests for this.

* Implement selection I/O for contiguous datasets.  Fix bug in selection
I/O translation.  Add const qualifiers to some internal selection I/O
routines to maintain const-correctness while avoiding memcpys.

* Added vector read / write support to the MPIO VFD, with associated
test code (see testpar/t_vfd.c).

Note that this implementation does NOT support vector entries of
size greater than 2 GB.  This must be repaired before release,
but it should be good enough for correctness testing.

As MPIO requires vector I/O requests to be sorted in increasing
address order, also added a vector sort utility in H5FDint.c  This
function is tested in passing by the MPIO vector I/O extension.

In passing, repaired a bug in size / type vector extension management
in H5FD_read/write_vector()

Tested parallel debug and production on charis and Jelly.

* Ran source code formatter

* Add support for independent parallel I/O with selection I/O.  Add
HDF5_USE_SELECTION_IO env var to control selection I/O (default off).

* Implement parallel collective support for selection I/O.

* Fix comments and run formatter.

* Update selection IO branch with develop ()

Merged branch 'develop' into selection_io

* Sync with develop ()

Updated the branch with develop changes.

* Implement big I/O support for vector I/O requests in the MPIO file
driver.

* Free arrays in H5FD__mpio_read/write_vector() as soon as they're not
needed, to cut down on memory usage during I/O.

* Address comments from code review.  Fix const warnings with
H5S_SEL_ITER_INIT().

* Committing clang-format changes

* Feature/subfiling ()

* Initial checkin of merged sub-filing VFD.

Passes regression tests (debug/shared/paralle) on Jelly.
However, bugs and many compiler warnings remain -- not suitable
for merge to develop.

* Minor mods to src/H5FDsubfile_mpi.c to address errors reported by autogen.sh

* Code formatting run -- no test

* Merged my subfiling code fixes into the new selection_io_branch

* Forgot to add the FindMERCURY.cmake file. This will probably disappear soon

* attempting to make a more reliable subfile file open which doesn't return errors. For some unknown reason, the regular posix open will occasionally fail to create a subfile.  Some better error handling for file close has been added.

* added NULL option for H5FD_subfiling_config_t in H5Pset_fapl_subfiling ()

* NULL option automatically stacks IOC VFD for subfiling and returns a valid fapl.
* added doxygen subfiling APIs

* Various fixes which allow the IOR benchmark to run correctly

* Lots of updates including the packaging up of the mercury_util source files to enable easier builds for our Benchmarking

* Interim checkin of selection_io_with_subfiling_vfd branch

    Moddified testpar/t_vfd.c to test the subfiling vfd with default configuration.
    Must update this code to run with a variety of configurations -- most particularly
    multiple IO concentrators, and stripe depth small enough to test the other IO
    concentrators.

    testpar/t_vfd.c exposed a large number of race condidtions -- symtoms included:

      1) Crashes (usually seg faults)

      2) Heap corruption

      3) Stack corruption

      4) Double frees of heap space

      5) Hangs

      6) Out of order execution of I/O requests / violations of POSIX semantics

      7) Swapped write requests

        Items 1 - 4 turned out to be primarily caused by file close issues --
    specifically, the main I/O concentrator thread and its pool of worker threads
    were not being shut down properly on file close.  Addressing this issue in
    combination with some other minor fixes seems to have addressed these issues.

        Items 5 & 6 appear to have been caused by issue of I/O requests to the
    thread pool in an order that did not maintain POSIX semantics.  A rewrite of
    the I/O request dispatch code appears to have solved these issues.

        Item 7 seems to have been caused by multiple write requests from a given
    rank being read by the wrong worker thread.  Code to issue "unique" tags for
    each write request via the ACK message appears to have cleaned this up.

        Note that the code is still in poor condtition.  A partial list of known
    defects includes:

     a) Race condiditon on file close that allows superblock writes to arrive
        at the I/O concentrator after it has been shutdown.  This defect is
        most evident when testpar/t_subfiling_vfd is run with 8 ranks.

     b) No error reporting from I/O concentrators -- must design and implement
        this.  For now, mostly just asserts, which suggests that it should be
        run in debug mode.

     c) Much commented out and/or un-used code.

     d) Code orgnaization

     e) Build system with bits of Mercury is awkward -- think of shifting
        to pthreads with our own thread pool code.

     f) Need to add native support for vector and selection I/O to the subfiling
        VFD.

     g) Need to review, and posibly rework configuration code.

     h) Need to store subfile configuration data in a superblock extension message,
        and add code to use this data on file open.

     i) Test code is inadequate -- expect more issues as it is extended.

        In particular, there is no unit test code for the I/O request dispatch code.
        While I think it is correct at present, we need test code to verify this.

        Similarly, we need to test with multiple I/O concentrators and much smaller
        stripe depth.

    My actual code changes were limited to:

          src/H5FDioc.c
          src/H5FDioc_threads.c
          src/H5FDsubfile_int.c
          src/H5FDsubfile_mpi.c
          src/H5FDsubfiling.c
          src/H5FDsubfiling.h
          src/H5FDsubfiling_priv.h
          testpar/t_subfiling_vfd.c
          testpar/t_vfd.c

    I'm not sure what is going on with the deletions in src/mercury/src/util.

    Tested parallel/debug on Charis and Jelly

* subfiling with selection IO ()

Merged branch 'selection_io' into subfiling branch.

* Subfile name fixes ()

* fixed subfiling naming convention, and added leading zero to rank names.

* Merge branch 'selection_io' into selection_io_with_subfiling_vfd ()

* Added script to join subfiles into a single HDF5 file ()

* Modified  H5FD__subfiling_query() to report that the sub-filing VFD supports MPI
This exposed issues with truncate and get EOF in the sub-filing VFD.
I believe I have addressed these issues (get EOF not as fully tested as it should be), howeer,
it exposed race conditions resulting in hangs.  As of this writing, I have not been able
to chase these down.

Note that the tests that expose these race conditions are in testpar/t_subfiling_vfd.c, and
are currently skipped.  Unskip these tests to reproduce the race conditions.

tested (to the extent possible) debug/parallel on charis and jelly.

* Committing clang-format changes

* fixed H5MM_free

Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Move Subfiling VFD components into H5FDsubfiling source directory

* Update Autotools build and add H5_HAVE_SUBFILING_VFD macro to H5pubconf.h

* Tidy up CMake build of subfiling sources

* Merge branch 'develop' into feature/subfiling ()

Merge branch 'develop' into feature/subfiling

* Add VFD interface version field to Subfiling and IOC VFDs

* Merge branch 'develop' into feature/subfiling ()

Merge branch 'develop' into feature/subfiling

* Merge branch 'develop' into feature/subfiling ()

Merge branch 'develop' into feature/subfiling

* Tidy up merge artifacts after rebase on develop

* Fix incorrect variable in mirror VFD utils CMake

* Ensure VFD values are always defined

* Add subfiling to CMake VFD_LIST if built

* Mark MPI I/O driver self-initialization global as static

* Add Subfiling VFD to predefined VFDs for HDF5_DRIVER env. variable

* Initial progress towards separating private vs. public subfiling code

* include libgen.h in t_vfd tests for correct dirname/basename

* Committing clang-format changes

* removed mercury option, included subfiling header path ()

Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests.

* added check for stdatomic.h ()

* added check for stdatomic.h with subfiling
* added H5_HAVE_SUBFILING_VFD for cmake

* fix old-style-definition warning ()

* fix old-style-definition warning

* added test for enable parallel with subfiling VFD ()

Fails if subfiling VFD is not used with parallel support.

* Subfiling/IOC VFD fixes and tidying ()

* Rename CMake option for Subfiling VFD to be consistent with other VFDs

* Miscellaneous Subfiling fixes

Add error message for unset MPI communicator

Support dynamic loading of subfiling VFD with default configuration

* Temporary fix for subfile name issue

* Added subfile checks ()

* added subfile checks

* Feature/subfiling ()

* Subfiling/IOC VFD cleanup

Fix misuse of MPI_COMM_WORLD in IOC VFD

Propagate Subfiling FAPL MPI settings down to IOC FAPL in default
configuration case

Cleanup IOC VFD debugging code

Change sprintf to snprintf in a few places

* Major work on separating Subfiling and IOC VFDs from each other

* Re-write async_completion func to not overuse stack

* Replace usage of MPI_COMM_WORLD with file's actual MPI communicator

* Refactor H5FDsubfile_mpi.c

* Remove empty file H5FDsubfile_mpi.c

* Separate IOC VFD errors to its own error stack

* Committing clang-format changes

* Remove H5TRACE macros from H5FDioc.c

* Integrate H5FDioc_threads.c with IOC error stack

* Fix for subfile name generation

Use number of I/O concentrators from existing subfiling configuration file, if one exists

* Add temporary barrier in "Get EOF" operation to prevent races on EOF

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix for retrieval of machine Host ID

* Default to MPI_COMM_WORLD if no MPI params set

* added libs rt and pthreads ()

* added libs rt and pthreads

* Feature/subfiling ()

* More tidying of IOC VFD and subfiling debug code

* Remove old unused log file code

* Clear FID from active file map on failure

* Fix bug in generation of subfile names when truncating file

* Change subfile names to start from 1 instead of 0

* Use long long for user-specified stripe size from environment variable

* Skip 0-sized I/Os in low-level IOC I/O routines

* Don't update EOF on read

* Convert printed warning about data size mismatch to assertion

* Don't add base file address to I/O addresses twice

Base address should already be applied as part of H5FDwrite/read_vector calls

* Account for 0-sized I/O vector entries in subfile write/read functions

* Rewrite init_indep_io for clarity

* Correction for IOC wraparound calculations

* Some corrections to iovec calculations

* Remove temporary barrier on EOF retrieval

* Complete work request queue entry on error instead of skipping over

* Account for stripe size wraparound for sf_col_offset calculation

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Re-write and fix bugs in I/O vector filling routines ()

* Rewrite I/O vector filling routines for clarity

* Fix bug with iovec_fill_last when last I/O size is 0

* added subfiling_dir line read ()

* added subfiling_dir line read and use it
* shellcheck fixes

* I/O request dispatch logic update ()

Short-circuit I/O request dispatch when head of I/O queue is an
in-progress get EOF or truncate operation. This prevents an issue where
a write operation can be dispatched alongside a get EOF/truncate
operation, whereas all I/O requests are supposed to be ineligible for
dispatch until the get EOF/truncate is completed

* h5fuse.sh.in clean-up ()

* Added command-line options

* Committing clang-format changes

* Align with changes from develop

* Mimic MPI I/O VFD for EOF handling

* Initialize context_id field for work request objects

* Use logfile for some debugging information

* Use atomic store to set IOC ready flag

* Use separate communicator for sending file EOF data

Minor IOC cleanup

* Use H5_subfile_fid_to_context to get context ID for file in Subfiling
VFD

* IOVEC calculation fixes

* Updates for debugging code

* Minor fixes for threaded code

* Committing clang-format changes

* Use separate MPI communicator for barrier operations

* Committing clang-format changes

* Rewrite EOF routine to use nonblocking MPI communication

* Committing clang-format changes

* Always dispatch I/O work requests in IOC main loop

* Return distinct MPI communicator to library when requested

* Minor warning cleanup

* Committing clang-format changes

* Generate h5fuse.sh from h5fuse.sh.in in CMake

* Send truncate messages to correct IOC rank

* Committing clang-format changes

* Miscellaneous cleanup

Post some MPI receives before sends

Free some duplicated MPI communicator/Info objects

Remove unnecessary extra MPI_Barrier

* Warning cleanup

* Fix for leaked MPI communicator

* Retrieve file EOF on single rank and bcast it

* Fixes for a few failure paths

* Cleanup of IOC file opens

* Committing clang-format changes

* Use plan MPI_Send for send of EOF messages

* Always check MPI thread support level during Subfiling init

* Committing clang-format changes

* Handle a hang on failure when IOCs can't open subfiles

* Committing clang-format changes

* Refactor file open status consensus check

* Committing clang-format changes

* Fix for MPI_Comm_free being called after MPI_Finalize

* Fix VFD test by setting MPI params before setting subfiling on FAPL

* Update Subfiling VFD error handling and error stack usage

* Improvements for Subfiling logfiles

* Remove prototypes for currently unused routines

* Disable I/O queue stat collecting by default

* Remove unused serialization mutex variable

* Update VFD testing to take subfiling VFD into account

* Fix usage of global subfiling application layout object

* Minor fixes for failure pathways

* Keep track of the number of failures in an IOC I/O queue

* Make sure not to exceed MPI_TAG_UB value for data communication messages

* Committing clang-format changes

* Update for rename of some H5FD 'ctl' opcodes

* Always include Subfiling's public header files in hdf5.h

* Remove old unused code and comments

* Implement support for per-file I/O queues

Allows the subfiling VFD to have multiple HDF5 files open simultaneously

* Use simple MPI_Iprobe over unnecessary MPI_Improbe

* Committing clang-format changes

* Update HDF5 testing to query driver for H5FD_FEAT_DEFAULT_VFD_COMPATIBLE
flag

* Fix a few bugs related to file multi-opens

* Avoid calling MPI routines if subfiling gets reinitialized

* Fix issue when files are closed in a random order

* Update HDF5 testing to query VFD for "using MPI" feature flag

* Register atexit handler in subfiling VFD to call MPI_Finalize after HDF5
closes

* Fail for collective I/O requests until support is implemented

* Correct VOL test function prototypes

* Minor cleanup of old code and comments

* Update mercury dependency

* Cleanup of subfiling configuration structure

* Committing clang-format changes

* Build system updates for Subfiling VFD

* Fix possible hang on failure in t_vfd tests caused by mismatched
MPI_Barrier calls

* Copy subfiling IOC fapl in "fapl get" method

* Mirror subfiling superblock writes to stub file for legacy POSIX-y HDF5
applications

* Allow collective I/O for MPI_BYTE types and rank 0 bcast strategy

* Committing clang-format changes

* Use different scheme for subfiling write message MPI tag calculations

* Committing clang-format changes

* Avoid performing fstat calls on all MPI ranks

* Add MPI_Barrier before finalizing IOC threads

* Use try_lock in I/O queue dispatch to minimize contention from worker threads

* Use simple Waitall for nonblocking I/O waits

* Add configurable IOC main thread delay and try_lock option to I/O queue dispatch

* Fix bug that could cause serialization of non-overlapping I/O requests

* Temporarily treat collective subfiling vector I/O calls as independent

* Removed unused mercury bits

* Add stubs for subfiling and IOC file delete callback

* Update VFD testing for Subfiling VFD

* Work around HDF5 metadata cache bug for Subfiling VFD when MPI Comm size
= 1

* Committing clang-format changes

Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
 2022-07-22 13:03:12 -07:00
Dana Robinson
838d050a63
h5test.h testing macros get enclosed in do..while loops () 
* h5test.h testing macros get enclosed in do..while loops

* Adds missed macro in hl C++ code

* Fixes macro in Windows code
 2022-05-04 08:49:01 -07:00
Scot Breitenfeld
f859cb732b
Fixed Spelling Errors () 
* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging

* Committing clang-format changes

* changed size_i in printf to reflect the I/O.

* Committing clang-format changes

* Fixed seg fault with xlf on BE with -qintsize=8

* fixed error function string

* spelling corrections via codespell, added new spell check github actions

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* work around for https://github.com/codespell-project/codespell/issues/2137

* misc

* added missing file

* misc

* misc.

* misc

* switch to using Codespell with GitHub Actions

* misc.

* misc.

* fixed more sp errors

* Fix new typos found by codespell.

* fixed proceed with precede

* fixed variable in fortran test

* fixed minnum

* updated spelling list

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
 2021-12-07 08:27:29 -06:00
jhendersonHDF
3da0802c40
VFD plugins () 
* Implement support for loading of Virtual File Drivers as plugins

Fix plugin caching for VOL connector and VFD plugins

Fix plugin iteration to skip paths that can't be opened

* Enable dynamic loading of VFDs with HDF5_DRIVER environment variable

* Temporarily disable error reporting during H5F_open double file open

* Default to using HDstat in h5_get_file_size for unknown VFDs

* Use macros for some environment variables that HDF5 interprets

* Update "null" and "ctl testing" VFDs
 2021-09-29 13:28:12 -05:00
Sean McBride
131402a92d
More various warnings () 
* Committing clang-format changes

* Fixed various -Wdouble-promotion warnings

* Fixed -Wshadow warning for `optopt` conflict

On macOS at least, there is a global various named `optopt` in unistd.h.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
 2021-08-24 23:05:23 -05:00
Quincey Koziol
c6e4e53546
Update clang config () 
* Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
 2021-03-17 10:25:39 -05:00
Sean McBride
d7b40604ef
Fixed all clang-tidy bugprone-suspicious-string-compare warnings () 
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings

This change was generated entirely by clang-tidy itself.

* Reformat code with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
 2021-03-10 12:42:35 -06:00
Sean McBride
c41a1cb209
Applied clang-tidy readability-non-const-parameter warning fixes auto… () 
* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes

Removes useless const declarations.

* Fixed most readability-non-const-parameter warnings

These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
 2021-03-09 10:59:44 -06:00
Larry Knox
4819f89d3f
Update license url () 
* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
 2021-02-17 08:52:04 -06:00
Dana Robinson
ca3659a014 HD prefix updates in src/ and test/ 
Adds missing HD prefixes to API calls in src and test.

Adds some extra processing to bin/checkposix to keep the noise
levels down when running the script (not comprehensive).
 2020-10-23 17:13:05 -07:00
Allen Byrne
b2d661b508 Clang-format of source files 2020-09-30 09:27:10 -05:00
David Young
d85cd245d2 Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experiment 2020-09-03 16:13:47 -05:00
Dana Robinson
b2d917437d Minor refactoring based on 1.10 normalization work 2020-08-17 09:12:59 -07:00
David Young
307cb5da48 Squash my changes on branch fprintf-experiment into one commit for 
reapplication to my new warnings branch, `warnings-again`.  These
changes are included:

commit 915551b7bf64e777dd2007386ec77b1d117770da
Merge: 63858c2 a8892bb
Author: David Young <dyoung@hdfgroup.org>
Date:   Mon Nov 25 17:39:49 2019 -0600

    Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment

commit a8892bb42d
Merge: 5c911d8 f907b51
Author: David Young <dyoung@hdfgroup.org>
Date:   Mon Nov 25 17:33:54 2019 -0600

    Merge pull request  in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop

    * commit 'f907b511d06612dafc7814a7c30f2f3d2b76d52b':
      Oops, remove more C99 designated initializers for VS 2010 compatibility.

commit 63858c22e168acaec0af8ced6641f26102cc6bb0
Merge: 20ae787 5c911d8
Author: David Young <dyoung@hdfgroup.org>
Date:   Mon Nov 25 17:04:42 2019 -0600

    Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment

commit 5c911d8baf
Merge: b8a5671 62208b0
Author: David Young <dyoung@hdfgroup.org>
Date:   Mon Nov 25 16:58:27 2019 -0600

    Merge pull request  in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop

    * commit '62208b056a09c01855fbac7f75146be58ad6bfe5': (44 commits)
      Add an #include to get a function declaration.
      Don't use C99 designated initializers, they're not compatible with Visual Studio 2010.
      Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*.  This is more code that may not compile with VS2010, *sigh sigh*.
      Always warn on maybe-uninitialized.  -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using.
      Only promote maybe-uninitialized warnings to errors on GCC 8.  Even on GCC 8, there may be false positives at low optimization levels?  I need to check.
      Only use -Werror=cast-function-type with GCC 8 and later.
      Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags.
      Add new source files to CMakeLists.txt.
      Mention the -Werror= flags in libhdf5.settings.in.
      free -> HDfree
      Promote decleration-after-statement warnings to errors.
      Quiet decleration-after-statement warnings.
      Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements.
      Document H5D__chunk_mem_xfree_wrapper().
      Undo accidental test deletion.
      Oops, delete a debug printf that snuck in here.
      Undo my changes to the HD macros, hadn't really intended those to be on this branch....
      Make errors of some more warnings.  Move disabled warnings to DEVELOPER_WARNING_CFLAGS.  Put just one warning option on a line, and sort some of the options.
      Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *.
      Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays.  Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc.
      ...

commit 20ae7877e33931b95e8c3502b027d6c3fe94a11f
Merge: 46f8c61 edd5297
Author: David Young <dyoung@hdfgroup.org>
Date:   Fri Nov 22 15:34:09 2019 -0600

    Merge remote-tracking branch 'origin/add-werror-and-squash-some' into fprintf-experiment

commit 46f8c613d5117a8be5bc8385a072daa0b4262f06
Author: David Young <dyoung@hdfgroup.org>
Date:   Fri Nov 22 15:29:00 2019 -0600

    GCC really wants us to use `ll` to format `long long`, so try to make that work
    before any other format modifier.  Seems like we're not compiling the autoconf
    test program with -Werror=format ?  Probably should.

commit eee35b8ef3759c391327cd48a9b3c56b6f8abc99
Author: David Young <dyoung@hdfgroup.org>
Date:   Fri Nov 22 15:28:05 2019 -0600

    It's hard to know just how wide an HDoff_t will be, and I don't think POSIX or
    C standards provide a PRI macro for it, so cast to intmax_t and format using
    PRIdMAX.

commit 86eab12df7a89b546a38e99f8178dd2adbcb3433
Author: David Young <dyoung@hdfgroup.org>
Date:   Fri Nov 22 15:26:25 2019 -0600

    URemove some casts.se the right format string for the argument.  Here and there
    stop casting a printf argument.

commit f722f7cbecbaa99449941484b014426f62f1bed5
Merge: 58e3743 6d5ec83
Author: David Young <dyoung@hdfgroup.org>
Date:   Fri Nov 22 14:44:16 2019 -0600

    Merge branch 'add-werror-and-squash-some' into fprintf-experiment

commit 58e3743b7faa9836606ee91798fe80dfc0040da7
Author: David Young <dyoung@hdfgroup.org>
Date:   Wed Nov 20 21:07:21 2019 -0600

    Remove custom HDfprintf implementation, using the standard library's,
    instead.  Take a swipe at repairing fprintf format strings, mainly
    replacing "%Hu" with "%" PRIuHSIZE, "%a" with "%" PRIuHADDR, "%Zu" with
    "%zu".

    Here and there remove an awkward cast of a printf argument to `long
    long` and use PRI[doux]8, PRI[doux]32, or PRI[doux]64, instead.

    Change occurrences of "%t" to "%s" and perform a suitable change of
    argument, `cond` -> `cond ? "TRUE" : "FALSE"`.

    Some occurrences of %Hu, %a, and %t remain, they just weren't flagged by
    the compiler because of #ifdef'age.

commit d4366909293fa970c23512ac80e5d865d76cddbf
Author: David Young <dyoung@hdfgroup.org>
Date:   Wed Nov 20 20:54:32 2019 -0600

    Promote format-string warnigns to errors.
 2020-07-07 10:49:55 -05:00
Dana Robinson
55844f79e9 Misc warning fixes. 2020-05-10 09:48:30 -07:00
David Young
f19e06b59e testpar/t_2Gio.c: Fix a typo that I think was introduced by a 
previous warnings PR.  An array element was assigned to
        itself---shape[2]Â =Â shape[2];---instead of being assigned to
        chunk[2].

fortran/src/H5Pf.c: move conditional compilation controlled by
        H5_NO_DEPRECATED_SYMBOLS outside of a function for readability.

fortran/src/H5match_types.c: put a variable's declaration under the same
        conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its
        use.

For now, skip compilation of some unused debug dump routines in the JNI.
While I'm in the JNI, delete a set-but-unused variable.

src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS
        so that it's not declared but unused or vice versa.

test/cache_common.h: add an #include in to get some symbols we need to
        avoid implicit declaration warnings.

test/dsets.c: use a more conventional conditional-compilation syntax.

test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized
        variables before use.

test/vfd.c: pass the expected type of `void **` to posix_memalign(3)
        instead of `int **`.

testpar/t_bigio.c: explicitly compare with 0 instead of using ! when
        "equal to 0?" is the question not "is false?"  Repair some
        indentation while I'm here.

testpar/testpar.h: repair misaligned line-continuation backslashes in a
        macro that probably should be a function so that we don't have
        to fiddle with the line continuation to begin with.

tools/src/h5repack/h5repack_main.c: fix some compiler fussing about
        enums.

tools/test/perform/pio_engine.c: the compiler fusses if you cast a
        function call returning double directly to off_t.  It's ok if
        you cast a variable that's a double to off_t, however.  Write
        and use a new function, sqrto(), to avoid the cast warnings.
 2020-01-29 11:44:39 -06:00
Dana Robinson
a92c735c9b Squashed commit of the token_refactoring branch: 2020-01-16 13:29:34 -08:00
David Young
0108072f7a Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings level and fixing some code.' (commit 5c911d8baf)" 2019-11-27 11:26:02 -06:00
David Young
8fb9fb5d4d Revert "Oops, remove more C99 designated initializers for VS 2010 compatibility." 
This reverts commit f907b511d0.
 2019-11-27 11:16:52 -06:00
David Young
f907b511d0 Oops, remove more C99 designated initializers for VS 2010 compatibility. 2019-11-25 17:30:08 -06:00
David Young
42cd35b717 GCC isn't smart enough to realize that fill_c is always initialized 
and exclusively used in `datatype == H5T_COMPOUND` branches, so just
initialize it at its declaration so that GCC doesn't warn.
 2019-11-13 12:03:18 -06:00
Jerome Soumagne
c13078a0ed Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() 2019-10-08 14:30:24 -05:00
Allen Byrne
64e6665b54 Add HD prefix to tests 2019-08-15 16:46:15 -05:00
Dana Robinson
67a126c7ba Normalization with vol_integration (test code and H5Xtest.c) 2018-09-20 10:40:51 -07:00
Dana Robinson
734aebc395 Rework of the POSIX file open permissions and macros to clean up 
HDopen() calls.

Also fixed a minor const warning in the core VFD.
 2017-04-28 18:13:22 -04:00
Dana Robinson
d3b664b6a7 Changed the Windows POSIX open() file permissions to be correct 
according to MSDN. Partial fix for HDFFV-9630.
 2017-04-28 08:11:29 -07:00
Larry Knox
89fbe00dec Merge pull request in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10 
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
  Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
  Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
  Merge pull request  in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
  Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
 2017-04-25 16:05:36 -05:00
Quincey Koziol
5df52404bc Misc. small cleanups to sync against incoming page buffering changes. 2017-03-02 06:24:46 -08:00
Frank.Willmore
526bcc242d Changes to be committed: 
modified:   bittests.c
	modified:   cmpd_dset.c
	modified:   dsets.c
	modified:   dt_arith.c
	modified:   dtypes.c
	modified:   extend.c
	modified:   fillval.c
	modified:   filter_fail.c
	modified:   flush1.c
	modified:   gen_cross.c
	modified:   hyperslab.c
	modified:   istore.c
	modified:   links.c
	modified:   links_env.c
	modified:   objcopy.c
	modified:   plugin.c
	modified:   tcheck_version.c
	modified:   unlink.c
	modified:   unregister.c

Minor fixes to replace numeric exit codes with MACRO declarations. Not all codes found were boolean, and those cases were not changed.
 2016-10-25 09:53:44 -05:00
Quincey Koziol
f40381b0ea [svn-r30285] Description: 
More warning cleanups, bringing the build down to 25 unique types of
warnings, with 550 warnings in 122 files (down from 28, 770, and 134).

Tested on:
    MacOSX/64 10.11.5 (amazon) w/serial & parallel
    (h5committest forthcoming)
 2016-08-13 04:23:53 -05:00
Jerome Soumagne
2094d86461 [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if available 
Fix tests accordingly and fix misuse of hbool_t in various places

Fix initialization of H5Pgcpl/ocpl structs in property decoding routines

Tested on:
    Linux/32 (jam)
    Linux/64 (platypus)
    Linux/PPC64 (ostrich)
    MacOSX/64 10.11
 2015-10-20 01:28:17 -05:00
Dana Robinson
c226e58005 [svn-r27626] Various minor warning fixes before major SWMR and VDS merges. 
gcc 4.9.2 was used to create the warning list

- implicit casts
- shadowed variables
- various enum issues
- other minor fixes (comments, unused macros, etc.)

Tested on: h5committest
 2015-08-31 14:04:23 -05:00
Jerome Soumagne
ab7d724ffd [svn-r27548] Revert r27545 2015-08-21 17:44:22 -05:00
Jerome Soumagne
7ce2d52cf6 [svn-r27545] Add first support for _Bool and make hbool_t a "real" _Bool if available 
Fix tests accordingly
 2015-08-21 13:52:30 -05:00
Mohamad Chaarawi
fc45d5fcb0 [svn-r27133] - Add a new attribute function characterstic for format: 
* H5_ATTR_FORMAT(X,Y,Z)  __attribute__((format(X, Y, Z)))
- Rename UNUSED attribute characterstic to H5_ATTR_UNUSED.
- Rename NORETURN attribute characterstic to H5_ATTR_NORETURN

tested with h5committest.
 2015-06-01 14:38:09 -05:00
Dana Robinson
7659506fa8 [svn-r26438] Fixed some double promotion warnings from gcc 4.9.2. Most were in 
format strings.

Tested on: h5committest
 2015-03-11 17:51:14 -05:00
Dana Robinson
d8e3d8e908 [svn-r26333] Eliminates gcc warnings due to -Wunsuffixed-float-constants. 
- Adds 'F' suffixes for most float constants.

- A few constants MUST be of type double. These now receive the long
  double L suffix and are then cast to double. I do this via a new
  H5_DOUBLE() macro which was added to H5private.h.

Fixes: HDFFV-9148

Tested on: h5committest
 2015-03-01 13:48:54 -05:00
Quincey Koziol
33ea1ada24 [svn-r25496] Description: 
Merge 64-bit ID changes from branch to trunk.  (Plus a few minor cleanups
that aren't on the branch)

Tested on:
    Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
    (h5committested on branch already for a week)
 2014-07-30 15:55:14 -05:00
Quincey Koziol
f97d63cb95 [svn-r24869] Description: 
Clean up more compiler warnings, plus merge a few Coverity bug fixes from
the hdf5_1_8_coverity branch back to the trunk:

r20877:
Purpose: Fix coverity issue 1723

Description:
Modified test_generate in hl/test_image to close file "f" before exit, even if
an error occurs.

r20879:
Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go
futher if call fails as well as empty.

r20881:
Coverity  in Run 46: I changed the Line 442 where it tries to check whether
FLAG_PRINTED is TRUE.  But it had just been set to FALSE.  I took out the
condition check in the print statement.

Tested on:
    Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel
    (too minor to require h5committest)
 2014-03-23 01:27:57 -05:00
Joel Plutchak
30f904dbe9 [svn-r23667] Removed H5E call. 2013-05-03 10:39:44 -05:00