szip (or libaec) is currently not tested in CI. This adds szip to the
the Autotools GitHub CI actions on Linux when building with the
Autotools.
This PR also cleans up a few warnings that remained in the szip-
related code so the -Werror check will pass.
* Include shlwapi.h explicitly
* Add shlwapi library to LINK_LIB when header is detected
Looking for StrStrIA in the shlwapi library is not reliable due
to stdcall on mingw32.
* HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a committed datatype. Added a test case for the fix that Quincey checked in.
* Committing clang-format changes
* Fixed a typo in a comment.
* Fixed a typo in a comment.
* Minor change: changed H5Tcommit to H5Tcommit2.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
* Allow spaces (and tabs) in VOL connector info string from environment variable.
* Parse connector name from HDF5_PLUGIN_PATH environment variable better
* Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an
error message to the failure return value from not finding a plugin.
* Play nice with existing plugin paths
* Use API routine to determine if native connector is terminal.
* Committing clang-format changes
* Make string size larger, to allow for connectors with longer names.
* Be more flexible about testing external pass through connectors, especially if
they have registered new optional operations.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
* Allow spaces (and tabs) in VOL connector info string from environment variable.
* Parse connector name from HDF5_PLUGIN_PATH environment variable better
* Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an
error message to the failure return value from not finding a plugin.
* Play nice with existing plugin paths
* Use API routine to determine if native connector is terminal.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
* Allow spaces (and tabs) in VOL connector info string from environment variable.
* Parse connector name from HDF5_PLUGIN_PATH environment variable better
* Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an
error message to the failure return value from not finding a plugin.
* Play nice with existing plugin paths
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
* Allow spaces (and tabs) in VOL connector info string from environment variable.
* Parse connector name from HDF5_PLUGIN_PATH environment variable better
* Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an
error message to the failure return value from not finding a plugin.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Updates release schedule for 2023
* Fixes broken build badge
* Another build badge tweak
* Even more badge tweaking
* More branch tweaking
* More badge tweaking
* More badge tweaks
* Even more badge tweaking
* Adds badges for other branches
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
* Allow spaces (and tabs) in VOL connector info string from environment variable.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Fix for Autotools --disable-deprecated-symbols
When we added v116 as a valid option, we left the default as v114 so
using --disable-deprecated-symbols leads configure to complain that you
can't set a default API that was deprecated.
The GitHub action didn't catch this because it explicitly specifies v116
This only affects develop w/ the Autotools when
--disable-deprecated-symbols is requested.
* Added v116 & default to the --with-default-api-version help string
The Autotools --with-default-api-version help string was missing v116.
This has been added, as well as a "default" target so the CI can catch
version problems when we forget to update the defaults upon creating
a new major version.
The GitHub CI also now uses "default" as the target for the deprecated
symbols build.
* Fixes the 1.14 API GitHub CI threadsafe/build_mode
This action still had the bug we fixed where we set the build mode
and threadsafety using an array of size one instead of an object.
* Partial work towards cleaning up the onion VFD code
* Committing clang-format changes
* A few minor tweaks to the onion VFD public header
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5F_LIBVER_LATEST changes for move to 1.15
* Add new default api check
* Format fixes
* Fix default configure
* fix lib version tests
* Fix another version variable
* Add 1.14 doc link
* Fix up the H5Pencode2 test for virtual layout.
* Committing clang-format changes
* Remove VERIFY and use TEST_ERROR.
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine. The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table. When the library finally exits, it will try to close the
file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().
* Committing clang-format changes
* Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291.
* Committing clang-format changes
* Add the test file to Cmake.
* Skip test_misc37() for drivers that is not default compatible as it is using a pre-generated file.
* Committing clang-format changes
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Converts the YAML build mode arrays to objects in special runs
* Adds a dump of the matrix context for each test
This would have made it a LOT easier to debug the build_mode issues...
* Disable the mirror VFD in the -Werror checks
We can re-enable this after we fix the warnings, but I don't want to
conflate code and GitHub changes, so this is a better way to get the
CI to pass for now.
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine. The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table. When the library finally exits, it will try to close the
file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().
* Committing clang-format changes
* Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291.
* Committing clang-format changes
* Add the test file to Cmake.
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump.
When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the
closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value"
all the way till the end of the routine. The user-provided corrupted file has an illegal
file size causing failure when reading the image during the closing process.
At the end of this routine it sets f->shared to NULL and then frees "f".
This is done whether there is error or not in "ret_value".
Due to the failure in reading the file earlier, the routine then returns error.
The error return from H5F__dest() causes the file object "f" not being removed from the
ID node table. When the library finally exits, it will try to close the
file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f).
Fix:
a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine.
b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before.
c) h5debug.c main(): track error return from H5Fclose().
* Committing clang-format changes
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Compound datatypes may not have members of size 0
A member size of 0 may lead to an FPE later on as reported in
CVE-2021-46244. To avoid this, check for this as soon as the
member is decoded.
This should probably be done in H5O_dtype_decode_helper() already,
however it is not clear whether all sizes are expected to be != 0.
This fixes CVE-2021-46244 / Bug #2242.
Signed-off-by: Egbert Eich <eich@suse.com>
* Rework error recovery code in H5O__dtype_decode_helper() and
H5O__dtype_decode().
* Format changes for src/H5Odtype.c.
Signed-off-by: Egbert Eich <eich@suse.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Add compound and refactor out atomic types
* Add Array String tests back
* Convert Attribute version of compound example
* Update transfer atom8ic read to return object
* When evicting driver info block, NULL the corresponding entry
Since H5C_expunge_entry() called (from H5AC_expunge_entry()) sets the flag
H5C__FLUSH_INVALIDATE_FLAG, the driver info block will be freed. NULLing the
pointer in f->shared->drvinfo will prevent use-after-free when it is used in other
functions (like H5F__dest()) - as other places will check whether the pointer is
initialized before using its value.
This fixes CVE-2021-46242 / Bug #2254
Signed-off-by: Egbert Eich <eich@suse.com>
* When evicting the superblock, NULL the corresponding entry
The call to H5AC_expunge_entry() will free the corresonding structure,
to avoid a use-after-free, the corrsponding pointer entry will be NULLed.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
For Data Layout Messages version 1 & 2 the specification state
that the value stored in the data field is 1 greater than the
number of dimensions in the dataspace. For version 3 this is
not explicitly stated but the implementation suggests it to be
the case.
Thus the set value needs to be at least 2. For dimensionality
< 2 an out-of-bounds access occurs as in CVE-2021-45833.
This fixes CVE-2021-45833 / Bug #2240.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Commit afc54d75a1 to the test suite to eliminate a separate
shell script did not take into account that there may be
multiple dependent test scripts which resulted in the
message:
`/bin/sh: line 7: [: too many arguments`.
when running the test suite.
Beware that this new version still makes use of non-posix GNU
extensions to `test`.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
* Use ubuntu-20.04 for github autotools parallel tests until parallel
configure is fixed on ubuntu 22.04.
* Remove inactive developers from CODEOWNERS.
* Temporarily cat config.log for autotools build in github actions.
* Try ubuntu-latest.
* Attempt to cat config.log even when configure fails.
* Fix syntax.
* Try again
* Try again
* Try again.
* Back to original temporary fix.
* Install libopenmpi-dev with openmpi-bin, which was installed as a
dependency prior to ubuntu-22.04.
* Jira HDFFV-10881: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application. A quick and simple fix to make it fail with a relevant error message.
* Format changes.
* Committing clang-format changes
* Minor change: split one condition check into two for clarity.
* Adding doxygen comment for H5VLwrap_register.
* Minor change: adding a little more detail to the Doxygen comment for H5VLwrap_register.
Return the result rather than setting the exit code. "return" is a
language keyword whereas "exit" is a function for which the <stdlib.h>
header has to be included which it wasn't in this test, therefore the
test would previously fail to identify that the encoder was enabled if
"-Werror=implicit-function-declaration" was used, which it is by default
with clang from Xcode 12 and later.
Fixes#2262
The size of the enumeration values is determined by the size of the parent.
Functions accessing the enumeration values use the size of the enumeration
to determine the size of each element and how much data to copy. Thus the
size of the enumeration and its parent need to match.
Check here to avoid unpleasant surprises later.
This fixes CVE-2018-14031 / Bug #2236.
Signed-off-by: Egbert Eich <eich@suse.com>
According to the specification, the information block for external links
contains 1 byte of version/flag information and two 0 terminated strings
for the object linked to and the full path.
Although not very useful, the minimum string length for each (with
terminating 0) would be one byte.
Checking this will help to avoid SEGVs triggered by bogus files.
This fixes CVE-2018-16438 / Bug #2233.
Signed-off-by: Egbert Eich <eich@suse.com>
Initially, the accumulated metadata location is initialized to HADDR_UNDEF
- the highest available address. Bogus input files may provide a location
or size matching this value. Comparing this address against such bogus
values may provide false positives. This make sure, the value has been
initilized or fail the comparison early and let other parts of the
code deal with the bogus address/size.
Note: To avoid unnecessary checks, we have assumed that if the 'dirty'
member in the same structure is true the location is valid.
This fixes CVE-2018-13867 / Bug #2230.
Signed-off-by: Egbert Eich <eich@suse.com>
When decoding a file space info message in H5O__fsinfo_decode() make
sure each element to be decoded is still within the message. Malformed
hdf5 files may have trunkated content which does not match the
expected size. Checking this will prevent attempting to decode
unrelated data and heap overflows. So far, only free space manager
address data was checked before decoding.
This fixes CVE-2021-45830 / Bug #2228.
Signed-off-by: Egbert Eich <eich@suse.com>
Additions
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Malformed hdf5 files may provide more dimensions than the array dim[] in
H5IMget_image_info() is able to hold. Check number of elements first by calling
H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
This will cause the function to return only the number of dimensions.
The fix addresse a stack overflow on write.
This fixes CVE-2018-17439 / HDFFV-10589 / Bug #2226.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
* Removes MPE instrumentation support.
The Autotools will no longer accept --with-mpe= and the logging commands
have been removed from the FUNC_ENTER macros. CMake has never supported
instrumenting for MPE.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Malformed hdf5 files may have trunkated content which does not match
the expected size. When this function attempts to decode these it may
read past the end of the allocated space leading to heap overflows
as bounds checking is incomplete.
Make sure each element is within bounds before reading.
This fixes CVE-2019-8396 / HDFFV-10712 / github bug #2209.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.com>
This has not been used to debug the library in a very long time. Most
developers use valgrind, -fsanitize=address, or some other memory checker
instead of this library.
This removes:
* dmalloc.h include from H5private.h
* --with-dmalloc= Autotools configure option
* HDF5_ENABLE_USING_DMALLOC CMake option
* Bug fix: make sure the test case supports the pass_through connector.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Change how HPC tests are executed
* Move ctest_test commands for serial and parallel tests into cmake files.
* Update checks for uploading Test.xml to CDash.
* Correct cmake scripots.
* Remove extraneous characters.
* Add ctest_start (APPEND).
* Add binary directories to scripts running ctest_test.
* Correct parameters for appending Test.xml.
* Set CTEST_SITE and CTEST_BUILD_NAME.
* Try to pass site and build_name to ctest_test sripts.
* Add site name and build name for ctest_test commands vi environment.
* Revert "Try to pass site and build_name to ctest_test sripts."
This reverts commit d364aaf0fa.
* Correct typo in src/CMakeLists.txt.
* Update batch scripts to run ctest_test scripts.
Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
* Update link for Software Changes in RELEASE.txt.
Add RELEASE.txt contents from 1.13.3 release to HISTORY-1_13.txt.
* Reverse order of entries in HISTORY-1_13.txt to match the order in previous HISTORY
files.
* 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.
* Added a test case for H5VLget_connector_name.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
* Committing clang-format changes
* Update main.yml
* Update HISTORY-1_13.txt
Missing release note added for changed location of CMake configuration files.
* Update HISTORY-1_13.txt
Fix typo
* Update main.yml
revert change
* Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3
release.
Added new version to exceptions in lines 74-5 of src/H5.c
* Cleared RELEASE.txt entries following HDF5 1.13.3 release.
Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean.
* format fixes
* fixed DOXYGEN_PREDEFINED
* Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args
* format fixes
* Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN
* reordered multidataset declarations
* alt. for H5Aclose_async and H5Acreate_async
* made doxgyen API into seperate blocks
* updated codespell
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added a test case to verify the VOL capacity flags work correctly.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix bug with cross platform compatibility of references within vlens.
No testing yet.
* Merge from multi_rd_wd_coll_io to a more recent branch from develop.
Untested, probably does not work yet.
* Committing clang-format changes
* Committing clang-format changes
* Fix many bugs in multi dataset branch. Mostly works, some issues in
SWMR tests.
* Committing clang-format changes
* Disable test in swmr.c that was failing due to bug in HDF5 unrelated to
multi dataset.
* Committing clang-format changes
* Fixed fortran multi-dataset tests
* Fixed xlf errors
* Added benchmark code for multi-datasets
* loops over datasets
* added missing error arg.
* Added gnuplot formatting
* Jonathan Kim original MD benchmarking code
* updated MD benchmarking code
* code clean-up
* Only make files in feature test mode
* misc clean-up
* removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option
* Committing clang-format changes
* Change multi dataset API to use arrays of individual parameters instead
of the parameter struct.
* Committing clang-format changes
* Update to new multi dataset Fortran API and tests. (#1724)
* Update to new multi dataset Fortran API and tests.
* Sync Fortran with develop.
* skipping h5pget_mpio_actual_io_mode_f for now
* Fixed issue with dxpl_id, changed to variable size dim. (#1770)
* Remove "is_coll_broken" field from H5D_io_info_t struct
* Committing clang-format changes
* Minor cleanup in multi dataset code.
* Committing clang-format changes
* Clean up in multi dataset code.
* Committing clang-format changes
* Committing clang-format changes
* Fix speeling
* Fix bug in parallel compression. Switch base_maddr in io_info to be a
union.
* Committing clang-format changes
* Implement selection I/O support with multi dataset. Will be broken in
parallel until PR 1803 is merged to develop then the MDS branch.
* Committing clang-format changes
* Spelling
* Fix bug in multi dataset that could cause errors when only some of the
datasets in the multi dataset I/O used type conversion.
* Committing clang-format changes
* Integrate multi dataset APIs with VOL layer. Add async versions of
multi dataset APIs.
* Committing clang-format changes
* Spelling fixes
* Fix bug in non-parallel HDF5 compilation.
* Committing clang-format changes
* Fix potential memory/free list error. Minor performance fix. Other minor
changes.
* Committing clang-format changes
* Fix memory leak with memory dataspace for I/O.
* Committing clang-format changes
* Fix stack variables too large. Rename H5D_dset_info_t to
H5D_dset_io_info_t.
* Committing clang-format changes
* Remove mem_space_alloc field from H5D_dset_io_info_t. Each function is
now responsible for freeing any spaces it adds to dset_info.
* Committing clang-format changes
* fixed _multi Fortran declaration
* Refactor various things in (mostly) the serial I/O code path to make
things more maintainable.
* Committing clang-format changes
* updated to array based, doxygen, and examples
* Reinstate H5D_chunk_map_t, stored (via pointer) inside
H5D_dset_io_info_t.
* Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t.
Switch temporary dset_infos to be local stack variables.
* Committing clang-format changes
* format cleanup
* format cleanup
* added coll and ind
* Modify all parallel I/O paths to take dset_info instead of assuming
dset_info[0].
* Committing clang-format changes
* fixed output
* Rework parallel I/O code to work properly with multi dataset in more
cases. Fix bug in parallel compression.
* Committing clang-format changes
* Prevent H5D__multi_chunk_collective_io() from messing up collective opt
property for other datasets in I/O. Other minor cleanup. Add new test
case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now
due to failures apparently unrelated to multi dataset code.
* Fix spelling
* Committing clang-format changes
* Replace N log N algorithm for finding chunk in
H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of
io_info->sel_pieces in that function.
* Committing clang-format changes
* Replace sel_pieces skiplist in io_info with flat array of pointers, use
qsort in I/O routine only when necessary.
* Committing clang-format changes
* Add new test case to mdset.c
* Committing clang-format changes
* Fix spelling
* Very minor fix in H5VL__native_dataset_read()
* Fix bug that could affect filtered parallel multi-dataset I/O.
* Add RM entries for H5Dread_multi(), H5Dread_multi_async(),
H5Dwrite_multi(), and H5Dwrite_multi_async()
* Unskip test in swmr.c
* Committing clang-format changes
* Eliminate H5D__pre_read and H5D__pre_write
* Remove examples/ph5mdsettest.c. Will fix and re-add as a test.
* Enable hyperslab combinations in mdset test
* Committing clang-format changes
* Clarify H5Dread/write_multi documentation.
* Fix bugs in multi-dataset I/O. Expand serial multi dataset test.
Update macro in parallel multi dataset test.
* Committing clang-format changes
* Spelling
* Remove obsolete entry in bin/trace
* Rework type conversion buffer allocation. Only one buffer is shared
between datasets in mdset mode, and it is malloced instead of calloced.
* Committing clang-format changes
* Fix bug in error handling in H5D__read/write
* added multi-dataset fortran check with optional dataset creation id (#2150)
* removed dup. dll entry
* Address comments from code review.
* Remove spurious changes in H5Fmpi.c
* Fix issue with reading unallocated datasets in multi-dataset mode.
Address other comments from code review.
* Committing clang-format changes
* Delay chunk index lookup from io_init to mdio_init so it doesn't add
overhead to single dataset I/O.
* Committing clang-format changes
* Fix inappropriate use of piece_count
* updated copyright on new file, removed benchmark from testing dir.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fix for HDFFV-10840: Instead of using fill->buf for datatype conversion
if it is large enough, a buffer is allocated regardless so that the element
in fill->buf can later be reclaimed.
Valgrind is run on test/set_extent.c and there is no memory leak.
* Add information of this fix to release notes.
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
* Added empty "getting started" markdown file
* Added title and brief tour of source code
* Moved platform-independence text to markdown
* Added anatomy of a function documentation
* Adds information on public/private/package calls and macros
* Adds much getting started guide text
* Fixed typos
* Fixed codespell issues
* Fix a sporadic failure in Subfiling VFD tests
* Subfiling VFD - add note to H5Pget_fapl_subfiling documentation
Adds note about how H5Pget_fapl_subfiling only returns the original
settings on a FAPL and those settings could have been modified by the
Subfiling VFD's environment variables
* Use case-inseneitive comparison for headers
HTTP headers should be case-insensitive. Use case-insensitive string
comparisons when working with HTTP header responses to ensure
compatibility.
* Revert "Use case-inseneitive comparison for headers"
This reverts commit a02f591723506b62b7208449be6eef7122120398
* Ignore case when searching HTTP header responses
Looking up the Content-Length in the header returned by S3 storage
endpoints should ignore case. To guarantee portability implement a
function for case-insensitive string search, because it is non-standard.
* Add an _ after H5 for the strcasestr implementation
It is a private function and should sport that underscore.
* Remove author comment from the doc comment
* Use search function defined by system if available
Check whether the system provides a function implementing case
insensitive string searches. Only use the custom implementation if the
system does not provide the functionality.
* Add tests for case-insensitive search
Basic tests:
- Search for empty string
- Search with exact match
- Search with case-insensitive match
- search with no match
* Enforce clang-format style
Some variable definitions in the th5_system tests did not conform to
clang-format's expectations. Updated the offending lines.
* Correct comment describing test case
* Added some spaces to please clang-format
* Ignore discarding const
Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr
Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
* Added feature/vol_cap_flags branch to GitHub actions
* Convert unsigned cap flag field to uint64_t and add flags
* Committing clang-format changes
* Convert unsigned cap flag field to uint64_t and add flags
* Committing clang-format changes
* Updates the VOL struct version number
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the module directory from the Automake flags as this
generated a large number of "missing include directory" warnings
and is unecessary
* Adds the module path to libhdf5.settings
* Moves -Wunused-dummy-arguments to the developer warnings since this
generates a lot of spurious, unfixable noise due to things like
callback wrappers
* Changes the return cast in h5fget_fileno_c, fixes a comment, and comment
on potential badness
* Initializes a variable in tH5L_F03.F90 to quiet a 'maybe
uninitialized' warning
* Cleans up main GitHub workflow(s)
* Combines main.yml and pr-check.yml, which differed trivially
* Reduces config redundancy via proper use of the matrix scheme
* Adds build-only configs for:
- Version 1.6 default API
- No deprecated symbols
- Parallel HDF5
* The -Werror config was converted to build-only
* Makes the naming scheme more uniform
* Spaces out the code and adds comments
* Typo fix
* Fix mirror VFD CMake configure typo
* Debugging hack
* Undo debug hack and fix CMake build mode
* Set CC=mpicc for parallel builds
* Another attempt to fix parallel builds
* Updates comments in main.yml
* Fixes a v16 API bug in the mirror VFD test code
* Committing clang-format changes
* Added checks for v1.8 - 1.12 APIs
* Manually specify Windows configs
Java debug builds time out when running tests on Windows. We'll disable
them in debub mode while we investigate.
* Revert "Manually specify Windows configs"
This reverts commit d710d8d219.
* Skip Debug Windows configs while we investigate Java H5L timeouts
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes ST from the list of debug packages
The ST package (ternary search trees) was removed from the library a while ago
* Replaced B2 package
I did some crude timing with and without the B2 debug code enabled
and it doesn't seem to make much of a difference.
* Add Developer build mode to CMake
* Set a few CMake variables for Developer build modes
* Refactor enabling of debug and developer-level compile definitions
* Convert cache debugging macros to normal ifdef style
Normal ifdef-style instead of if-style allows build system to define macros
without warning about redefining macros with different values (0 vs. 1)
* Add HDF5 Developer compile definitions to testing files
* Temporarily disable -fanalyzer flag for GCC 12+ Developer builds
* Fix bug in attribute type conversion where the background buffer would
not be initialized with the destination contents when necessary. Other
minor simplification.
* Committing clang-format changes
* Fix warnings.
* Address review comments.
* Add RELEASE.txt note for PR #2016
* Add GitHub number to release note
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix test failure
Description:
- Added two H5File constructors to open file with non-default fapl
- Added non-default fapl to test functions
- Commented certain renaming attribute tests because of the unexpected
behavior in renaming an attribute (HDFFV-11327)
Platform tested:
Linux/64 (jelly)
* Committing clang-format changes
* Update H5File.cpp
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix bug in attribute type conversion where the background buffer would
not be initialized with the destination contents when necessary. Other
minor simplification.
* Committing clang-format changes
* Fix warnings.
* Address review comments.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix test failure
Description:
- Added two H5File constructors to open file with non-default fapl
- Added non-default fapl to test functions
- Commented certain renaming attribute tests because of the unexpected
behavior in renaming an attribute (HDFFV-11327)
Platform tested:
Linux/64 (jelly)
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix typos found in the rest of the hdf5 code-base
* Typo in tool.cmake
* Revert "Typo in tool.cmake"
This reverts commit 06b8403d99.
* Fix clang-format styling
Found via `codespell -q 3 -S ./release_docs,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c -L isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn\'t,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ake,gord,numer,ro,oce`
* Rename Subfiling IOC "thread_pool_count" field to "thread_pool_size"
* Add simple HDF5 example for Subfiling VFD
* Subfiling VFD - never cache app topology as it may change
* Subfiling VFD - cleanup unused funtionality and tidy up some TODOs
* Subfiling VFD - tidy up subfiling error handling in H5subfiling_common.c
* Subfiling VFD - show number of failed I/O requests on close
* Subfiling VFD - Update file cmp callback after switching to MPI I/O VFD
* Amend RELEASE.txt with info about h5fuse.sh and Subfiling limitations
* Subfiling VFD - switch to using H5_basename and H5_dirname
* H5Dchunk_iter now passes chunk dimension scaled offsets, fix#1419
* Update docs for H5Dchunk_iter, H5Dget_chunk_info*
Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following
* offset Logical position of the chunk’s first element in units of dataset elements
* filter_mask Bitmask indicating the filters used when the chunk was written
* size Chunk size in bytes, 0 if the chunk does not exist
* Adds platform-independent basename and dirname
* Tidy up H5_dirname and H5_basename implementations and add tests
* Committing clang-format changes
* Fix misspelling
* Several fixes for H5_dirname/H5_basename from review
* Committing clang-format changes
* Add reason to VERIFY_STR macros in th5_system.c
* Use H5MM_free instead of HDfree in H5_dirname/H5_basename tests
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Sanity checks for H5Xcreate_anon functions to make sure the IDs passed in are valid.
* Removed unnecessary sanity checks.
Co-authored-by: songyulu <songyulu@jelly.ad.hdfgroup.org>
* Remove generated file h5fuse.sh
* Link pthreads library when Subfiling VFD is built
* Switch to MPI I/O driver for Subfiling HDF5 stub file
* Rough first implementation for Subfiling file deletion
* Subfiling VFD - get file dirname for file deletion
* Subfiling VFD - set lock callback to NULL for now to avoid performance
issues
* Committing clang-format changes
* Minor tidying up of Subfiling testing
* Fixups for Subfiling VFD support in tools
* Tidy up Subfiling public interface and add Doxygen
* Respect Subfiling configuration settings from application
* Add release note for Subfiling VFD
* Committing clang-format changes
* Committing clang-format changes
* Shorten some Subfiling environment variable names
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD feature
* Fixes onion VFD errors with non-sec2 backing store VFDs
* Disables the onion VFD tests w/ ph5diff
* Disables non-sec2 VFDs as onion VFD backing stores
* Committing clang-format changes
* Formatted source
* Typo
* Adds onion VFD tools tests to CMake
* Fixes for v16 API compatibility
* Memset structs to avoid bad frees on errors
* H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE
* Properly decodes checksums on BE machines
* Be more careful about uint64_t to haddr_t/hsize_t conversions
* Another fix for BE data comparison
* Removed double underscores from onion constants
* Replace hard-coded onion header string w/ constant
* Fixes cleanup paths in H5FD__onion_ingest_history()
* Fixed use of size_t revision numbers
* Fix h5dump revision count format string
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
This is causing issues with the NAG Fortran compiler in our daily
testing due to -shared getting inappropriately added. Reverting while
we investigate.
* Updates uthash from 2.1.0 to 2.3.0
* Moves uthash include and related to H5private.h
* Defines HASH_NONFATAL_OOM so that out-of-memory doesn't abort()
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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 (#1215)
Merged branch 'develop' into selection_io
* Sync with develop (#1262)
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 (#1464)
* 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 (#1034)
* 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 (#1219)
Merged branch 'selection_io' into subfiling branch.
* Subfile name fixes (#1250)
* fixed subfiling naming convention, and added leading zero to rank names.
* Merge branch 'selection_io' into selection_io_with_subfiling_vfd (#1265)
* Added script to join subfiles into a single HDF5 file (#1350)
* 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 (#1539)
Merge branch 'develop' into feature/subfiling
* Add VFD interface version field to Subfiling and IOC VFDs
* Merge branch 'develop' into feature/subfiling (#1557)
Merge branch 'develop' into feature/subfiling
* Merge branch 'develop' into feature/subfiling (#1563)
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 (#1577)
Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests.
* added check for stdatomic.h (#1578)
* added check for stdatomic.h with subfiling
* added H5_HAVE_SUBFILING_VFD for cmake
* fix old-style-definition warning (#1582)
* fix old-style-definition warning
* added test for enable parallel with subfiling VFD (#1586)
Fails if subfiling VFD is not used with parallel support.
* Subfiling/IOC VFD fixes and tidying (#1619)
* 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 (#1634)
* added subfile checks
* Feature/subfiling (#1655)
* 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 (#1673)
* added libs rt and pthreads
* Feature/subfiling (#1689)
* 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 (#1703)
* 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 (#1714)
* added subfiling_dir line read and use it
* shellcheck fixes
* I/O request dispatch logic update (#1731)
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 (#1757)
* 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>
* Fix HDFFV-11308 - dataset access properties disappear when using
H5Fstart_swmr_write.
* Committing clang-format changes
* Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs
in the library exposed by this test.
* Committing clang-format changes
* Replace accidental use of double_t in swmr.c with double.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix HDFFV-11308 - dataset access properties disappear when using
H5Fstart_swmr_write.
* Committing clang-format changes
* Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs
in the library exposed by this test.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes a stack overflow in the h5dump test generator
The opaque type size was declared to be the size of the "buffer of two
opaque elements", causing a memcpy call in H5Dwrite to read outside
the buffer, dumping garbage into the file.
Note that this only affected the test generator and not h5dump itself.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes warnings when the deflate filter is not built
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the small perf tool
This tool doesn't really do anything special and installed, which
conflicts with gnu's perf tool.
* Adds suggestions from code review
* Fix for a tools compile issue when deprecated symbols are disabled
Introduced in #1811, also uses VOL token instead of addr
* Fix for similar compile issues in java when deprecated symbols are
disabled.
* Committing clang-format changes
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Oflush causes H5Fclose to trigger an assertion failure in metadata cache for parallel. This commit makes sure H5Oflush fails for parallel until this problem is solved in the future.
* Committing clang-format changes
* Changed the use of H5F_get_driver_id to H5F_HAS_FEATURE.
Co-authored-by: songyulu <songyulu@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
LLONG_MAX and ULLONG_MAX are defined in limits.h in C99. SIZET_MAX
should be SIZE_MAX, which has been around forever. SSIZET_MAX should
be SSIZE_MAX, which is defined whereever ssize_t is found. I've kept
the definition for SSIZE_MAX (renamed from SSIZET_MAX) for platforms
where ssize_T is not present (e.g., Windows).
* Fixes for warnings identified by MSVC
* Committing clang-format changes
* Moves the casts in H5Binternal.c to the other side
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Rework java vl check in read/write. Handle old refs in h5dump
* Committing clang-format changes
* Java changes allow default VL reads
* Fix JNI utility for old refs
* HDFFV-11310 - implement vlen read/write for atomic types.
* format check fix
* Mostly format fixes
* More format issues
* Two format changes
* Use JNI names for sizeof
* format change
* fix size typo
* Change to older method to initialize list
* remove unused var
* format fix
* switch writeVL functions to use datatype instead of java type
* Add VL option to generic read/write check
* Correct function name typo
* Add JIRA issue
* Correct note to match change in code.
* HDFFV-11318 add VL references as byte arrays
* Add release note and format changes
* Another format update
* Fix unreleased allocations
* Fix format
* format correction
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Initial implementation for supporting UnifyFS in HDF5 with MPI_File_sync after write
* Committing clang-format changes
* Fix format
* Fix env variable and return value check
* Fix flag retrieve
* Fix issues with getting/setting the flag
* Fix merge conflicts
* Update
* Committing clang-format changes
* Update based on suggestions
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Minor clang warning fixes in src and test
* Fixes clang warnings in high-level library
* clang format-nonliteral warning fixes
* Committing clang-format changes
* Fixed int -> float clang cast warnings in h5diff
* Quiets some warnings in flex/bison generated code
* Suppress overlong string warning for libinfo on clang
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for production mode gcc warnings
With the strict-overflow changes, this brings the number of warnings
in the C library w/ gcc 12 to zero.
* Fix typo
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds format attribute to (s|p)io_perf code
* Added gcc format attribute to additional test code
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
GitHub issue #732 claims that mallocing a particular buffer can
trigger undefined behavior and that callocing the buffer fixes
the issue.
I did not confirm this, but the fix is trivial and better anyway.
Very new versions of Autoconf complain about our Java macros. Since they
work well enough and there is no obvious upgrade path, we're suppressing
the category for now.
When the filename was flipped from being a static array to being
dynamically allocated, the sizeof(filename) call wasn't updated.
This always returns the size of the pointer, truncating the
filename.
* Adds a -Werror debug Autotools test and updates build modes
* Un-excludes the workflow files
* Strip out -Werror from CFLAGS when running configure tests
This causes spurious test failures when the configuration test
programs raise warnings.
Ubuntu 22.04 complains about AC_HAVE_LIBRARY being deprecated. This
updates the macro to AC_CHECK_LIB, where the specified function
is GetUserName().
This change only affects MinGW
* Quiets size warning in large library setting string
If the size of this string is a problem, people can build with the
embedded library info disabled.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Straightforward conversion of sprintf to the safer snprintf
* Trickier conversion of sprintf to safer snprintf
This involved minor changes to private function signatures to take the size of the buffer.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed -Wreserved-id-macro warnings from header include guards
* Removed all __int64 and LL suffix stuff now that C99 is minimum requirement
* Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings
Double underscore is reserved in C++ and this public header should be C++ compatible.
* Never define __STDC_FORMAT_MACROS anymore
Defining it causes a -Wreserved-id-macro.
Happily, according to the C++11 standard:
"The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++."
https://cplusplus.github.io/LWG/issue984
So looks like it's not necessary to define it with reasonably new toolchains.
* Fixed some -Wunused-macros warnings, removed dead code
* Fixed all -Wdouble-promotion warnings in C++ files
* Fixed remaining -Wsuggest-destructor-override warnings
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Promote some GCC warnings back to errors and deal with build breakage.
I tested configuring and building with GCC 8.3.0 with
`.../configure --prefix=$HOME/wrk/install/manydsets --enable-build-mode=production --enable-symbols=-gdwarf-4 --enable-warnings-as-errors --enable-java --enable-hl --enable-fortran --enable-cxx --enable-mirror-vfd --enable-ros3-vfd --enable-direct-vfd`
and with the same options but `--enable-build-mode=debug`.
* Promote -Wrestrict to -Werror=restrict to help catch overlapping
arguments to strcpy, memcpy, et cetera, at compile time.
* NFCI: sort lines.
* Committing clang-format changes
* NFCI: remove whitespace at EOL.
* Re-use temporary variable `shared`.
* Remove merge oopsie.
* Mention that no op codes are understood per review comment.
* Change this back to the develop branch's way, since this change isn't
integral to the PR.
* Committing clang-format changes
* NFCI: reduce differences with `develop` branch in the hope that that
also kicks off CI.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fixes a bug where t_cache fails due to a string size being too small
Recent warning reductions led to an incorrect string size being passed
to h5_fileaccess, causing the test to silently fail. In addition to
fixing the bug, the test will now fail noisily on setup failures.
* Updates the t_cache test to fail noisily on setup errors
* Fix various warnings
* Move HDfree_const to H5private.h for wider use
* Print output from all ranks in parallel tests on allocation failure
* Move const pointer freeing macro to h5test.h for now
* Avoid a signed overflow: check the range of `entry_ptr->age` before
increasing it instead of increasing it and then checking the range.
This quiets a GCC warning.
* Avoid the potential for signed overflow by rewriting expressions
`MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`.
This change quiets some GCC warnings.
* Change some local variables that cannot take sensible negative values
from signed to unsigned. This quiets GCC warnings about potential
signed overflow.
* In a handful of instances, check the range of a signed integer before
increasing/decreasing it, just in case the increase/decrease overflows.
This quiets a handful of GCC signed-overflow warnings.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.
* HDFFV-11306,
* Fixed it so both h5open_f and h5close_f can be called multiple times.
* Fixed an issue with open objects remaining after h5close_f was called.
* Added additional tests.
* comments clean-up
For more information:
https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* Use the FAPL that was created earlier in the test (and delete an unused
variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd.
* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.
* Committing clang-format changes
* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.
* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.
This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.
* Committing clang-format changes
* Per discussion, use HD and add comments.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.
* First stab at a Github status bar
* Adds a .tokeignore file for counting lines of code accurately
* Yanks lines of code calculation since it wildly overcounts
* Fix MPI version check for MPI_Aint_diff usage
* Add H5_CHECK_MPI_VERSION macro
Adds new H5_CHECK_MPI_VERSION macro to check for MPI library version/subversion pair of at least the specified pair
* 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
* 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
* Minor optimization to vector I/O request sort routine.
Tested parallel / debug on Jelly.
* 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.
* Added "ctl" callback to the VFD interfance, and the associated
H5FDctl() and H5FD_ctl() calls.
Modified the MPIO VFD accordingly -- specifically:
Added ctl() call with op-code support to expose rank, size,
and communicator.
Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(),
and H5FD_mpi_get_comm() to use the new ctl() callback. In passing
removed the const qualifier from the file parameter of these
functions, as the file parameter of the ctl callback is not
const.
Deleted the old H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and
H5FD__mpio_communicator() calls from the MPIO VFD.
Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the
MPIO VFD accordingly. Note that all VFDs now use H5FD_class_t,
with no special class for VFDs that that support MPI.
Some minor touch ups to the Neil's selection I/O mods in passing.
Tested serial and parallel, debug and production on charis and
jelly.
* 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.
* 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.
* Committing clang-format changes
* Run formatter
* Update selection IO branch with develop (#1215)
Merged branch 'develop' into selection_io
* Sync with develop (#1262)
Updated the branch with develop changes.
* Committing clang-format changes
* fixed spelling (#1353)
* Implement big I/O support for vector I/O requests in the MPIO file
driver.
* Committing clang-format changes
* Update dummy file driver in h5test.c to match new struct.
* Fix another outdated H5FD_class_t struct.
* Free arrays in H5FD__mpio_read/write_vector() as soon as they're not
needed, to cut down on memory usage during I/O.
* Committing clang-format changes
* Address comments from code review. Fix const warnings with
H5S_SEL_ITER_INIT().
* Committing clang-format changes
* Fix warnings in selection I/O code
* Refactor H5FD__mpio_read/write_vector() to bring common code for
constructing MPI Datatype into a shared function.
* Committing clang-format changes
* Fix bugs in selection I/O code.
* Fix bugs in selection I/O code
* Address comments from review. Add "version" field to H5FD_class_t
struct and accompanying H5FD_CLASS_VERSION macro.
* Committing clang-format changes
* Committing clang-format changes
* Address comments from selection I/O PR
* Committing clang-format changes
* Fix spelling
* Fix bugs int test/vfd.c
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
From Vailin:
Fix the FSM bug when setting the FSM threshold to a non-default value.
Check for smaller or larger section size after merging and shrinking a
section, for this case is the section that is smaller than threshold
(see H5MF_xfree() in H5MF.c). It is possible for the section to be
smaller after merging/shrinking (see H5MF__sect_large_shrink() in
H5MFsection.c).
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
* Committing clang-format changes
* Update main.yml
* Update HISTORY-1_13.txt
Missing release note added for changed location of CMake configuration files.
* Update HISTORY-1_13.txt
Fix typo
* Update main.yml
revert change
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Committing clang-format changes
* Spelling of preceed was corrected to proceed, but should have been
corrected to precede.
* Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'.
* Update version to 1.13.2-1 after 1.13.1 release.
Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk.
* Update VERS_RELEASE_EXCEPTIONS with new incompatible release version.
* Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to
HISTORY-1_13.txt.
Clean entries from RELEASE.txt.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
* fixed buf definition in h5dfill_f
* Committing clang-format changes
* Spelling of preceed was corrected to proceed, but should have been
corrected to precede.
* Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'.
* OESS-168: Remove clang warnings.
* OESS-168: Address @lrknox and @gnuoyd reviews.
* Eliminate clang warnings listed in PR #1310 without adding new ssize_t
variables.
* Committing clang-format changes
* Add H5_ATTR_UNUSED to wait_for_child call.
Remove unneeded casts in mirror_log calls.
* Keep ssize_t in mirror_server.c line 479.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Hyo-Kyung Lee <hyoklee@hdfgroup.org>
* Correct some conversion specifications.
* Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few
instances where PRIdHSIZE was appropriate. Remove a couple of casts and
use correct format strings, instead.
* Copy values from a possibly unaligned buffer to aligned local variables
instead of casting and dereferencing pointers into the buffer.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Implement big I/O support for independent reads. Add test for this.
* Committing clang-format changes
* Update big I/O code in H5FD__mpio_write() to match that in
H5FD__mpio_read().
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updated plugins project required adjustments
* Updated plugins need to distinguish external libs
* Fix missed rename
* Use same name for windows as linux - avoid name clash
truncated because the recipient buffer was too small, and the warning is
one that we promote to an error. Now there is a warning that the buffer
is too big (-Wlarger-than=), but we don't promote those to errors, yet.
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
* fixed handling size 0 datasets
* fixed handling size 0 datasets
* format
* Implement H5ESget_requests() to retrieve request pointers and
corresponding connector IDs from an event set. Add tests for this
function.
* Add "order" parameter to H5ESget_requests, to allow the user to specify
the order in which requests are returned.
* Fix bugs with H5ESinsert_request()
* Change H5ESget_requests() API to have separate input and output
parameters for the allocated array length(s) (in) and the number of events in
the event set (out).
* Fix issue with H5_now_usec() with 32 bit systems. Also improve event
set test.
* Committing clang-format changes
* Add comments to H5_now_usec() explaining rationale for uint64_t casts.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This would
cause H5C_resize_entry to mark the entry as dirty and make
H5AC_resize_entry think that it doesn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needs to allocate a new entry for insertion into the dirty
entry skip list, since the entry doesn't exist on that list.
This causes an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
* Implemented suggestion in #1380
* fix typo
* Use differently named files in tests
* format fix
* Revise comments
* fic typos
* Change test display and file name
* Avoid using a non-literal formatting string with sprintf in begin_test.
Use snprintf. Don't duplicate a string on the heap unnecessarily.
* Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format
string any more.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Replaced many uses of sprintf with safer snprintf
Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable.
* Removed unnecessary use of static on small buffers
This improves thread safety.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove const from the argv tools/tests main sig.
* also remove const from H5_get_option and parse_command_line.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Commit 61464d7e was a fix for a compiler error on OpenBSD where
int_fast8_t is in fact larger than 1 byte. However, the changes broke
H5detect.c generation of H5Tinit.c on Power8 big-endian, and probably on
all big-endian machines. Switching DETECT_BYTE to DETECT_I for 8 byte types doesn't work on our big-endian Power8 machine because switching the last parameter of DETECT_I_BYTE_CORE from "int" to the 8 byte type incorrectly sets dt->shared->u.atomic.order = H5T_ORDER_LE on a big-endian machine. A different fix to accomodate both big-endian and OpenBSD is needed. See commit 61464d7e for OpenBSD info.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix several places where rank 0 can skip past collective MPI operations on failure
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
* Converted README.txt to README.md and updated files referring to README.txt to README.md.
* removed references to README.txt
* updated MANIFEST
* From gitlab.kitware.com/third-party/hdf5 rework custom commands
commit/757aa42ebff8c9819c054f5e00559143c60f653d
* Correct stamp file generation
* Needs to support pregenerated H5Tinit.c file
* Adjust custom command for all build systems types
* Custom target only depends on OUTPUT of custom command
* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
* Add tests for H5Ocopy of new object refs
* Correct class name
* Skip test because of issue with debug assertions
* Update reference file
* Fix object examples for new refs
* Fix testswmr scripts with utils/test variable
* Change format of configure var assignment
* quote the variable value in configure
* Use sh.in expected var pattern
* Only ref builddir in script
* Create vars for utils/test and test as H5_<path>_BUILDDIR
* Use abs_top_builddir in test scripts
* Change script var to make it easier to read.
* Use @abs_top_builddir@ directly in paths
* Correct typos/comment
* Convert SWMR shell scripts to Windows powershell.
* Use $LastExitCode instead of $? in script
* Prevent execution in a different window
* Github #969 Use stdout instead of file for configure check (#1089)
* Use stdout instead of file for configure check
* Make change requested by #1157
* Change fortran to use stderr for configure
* Correct typo
* remove obsolete file check
* Fortran statement fix
* Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201)
* Fixes const warnings in H5ES package (#1211)
* Quiets a 'set but not used' warning in h5diff_array.c (#1210)
* Convert vds swmr test script to powershell
* Enable vdsswmr powershell test
* Add configure vdsswmr statement
* Correct powershell script vars
* Convert SWMR shell scripts to Windows powershell.
* Use $LastExitCode instead of $? in script
* Prevent execution in a different window
* Github #969 Use stdout instead of file for configure check (#1089)
* Use stdout instead of file for configure check
* Make change requested by #1157
* Change fortran to use stderr for configure
* Correct typo
* remove obsolete file check
* Fortran statement fix
* Convert vds swmr test script to powershell
* Enable vdsswmr powershell test
* Add configure vdsswmr statement
* Correct powershell script vars
* Cleanup review issues
* Fix variable assignment
* Change the wait function to pass in the path
* Disable actual test execution until programs fixed
* Adjust copyright text
* Fix spelling
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Adds tool h5dwalk and configure options to enable building it.
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs
Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the
library due to missing ID range checks in H5Pget_filter_by_id1/2.
The library now returns a normal error code when filter IDs are
out of range. Fixes HDFFV-11286.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Create 2D arrays on the heap by malloc'ing `struct { TYPE arr[ROWS][COLS];
}`. This avoids the double-indirection through pointers and the
additional memory of H5TEST_ALLOCATE_2D_ARRAY().
This change will safely quiet the cast warning that PR #1129 was
intended to fix.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the
raw H5R_ref_t bytes to a heap buffer that's known to have the right
alignment.
* Committing clang-format changes
* Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and
initialize the H5R_ref_t to all-0s so that arbitrary stack content
doesn't foul things up. Bail out with an error if `size` exceeds
`sizeof(H5R_ref_t)`.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Hyperslabs can be reworked inside several H5S callbacks, making H5S_t
non-const in some places where it is marked const. This change switches
these incorrectly const H5S_t pointer parameters and variables to
non-const where appropriate.
* Use stdout instead of file for configure check
* Make change requested by #1157
* Change fortran to use stderr for configure
* Correct typo
* remove obsolete file check
* Fortran statement fix
pointer or from pointer to integer (-Werror=int-conversion). Also,
make it an error if the library explicitly converts to pointer from an
integer of a different size (-Werror=int-to-pointer-cast).
* Take a stab at using constructors to initialize instead of
function-entry macros. This is a work in progress. It's good enough to
run `many_dsets`.
* Committing clang-format changes
* Add the `many_dsets` benchmark and some scripts I used on jelly for
setting up the build/test environment and for recording/flame-graphing
profiles.
* Committing clang-format changes
* Change my Makefile and environment script to work both on jelly
and on mayll (and probably on Summit).
* Disable clang-format "fix."
* Replace the `if (!H5_TERM_GLOBAL)` test in each FUNC_ENTER_ macro with
`if (true)`.
* Fix bad grammar in a comment.
* Instead of labeling the H5*__init_package routines constructors, fold
each into an initialization routine, H5*_init(), and call each of
the H5*_init() routines. Call most of the H5*_init() routines from
H5_init_library() in an explicit order that I found out earlier by
instrumenting each __init_package routine and running the library
tests. Roll H5FD*__init_package routines into H5FD*_init() routines.
This change ends just-in-time initialization of package dependencies by
package initializers.
Don't track in per-package variables (H5_PKG_INIT_VAR) whether each
package has been initialized. Instead, track in a single library
variable whether the whole library is initialized or not.
Drive the initialization of packages by H5_init_library() with a table
of initializer routines. Also drive the termination of packages by
H5_term_library() with a table.
Perform initialization as needed from FUNC_ENTER_API_INIT(err). This
basically restores the old behavior of that macro.
Delete a bunch of #definitions in H5private.h that have fallen out of
use with these changes.
* Committing clang-format changes
* Undo the bad auto-formatting that appears to have occurred in spite
of my disabling it. Bracket some code in /* clang-format off */ /*
clang-format on */ to prevent a recurrence.
* Remove a diagnostic abort().
* Fix a logic error: print a comma between every package terminator run,
and don't print an initial comma.
* Complete the changes I started in H5_term_library() that undo the bad
auto-formatting.
Stop tracking whether package "tops" were initialized in per-package
variables H5*_top_package_initialize_s. H5_term_library() takes care of
that for them.
Remove H5R_top_term_package() and H5R_term_package(), they don't do
anything.
* Committing clang-format changes
* NFCI. Simplify macro text: replace `if (true) {` with `{`.
* Fix formatting and suppress clang-format on a longer range.
* Quiet some unused label, unused variable complaints that cropped up
after I simplified the FUNC_ENTER_ macros for the sake of performance.
* Committing clang-format changes
* Delete some programs and scripts that don't belong in the pull request.
* Use the right function-entry macro.
* Use a sensible format and disable auto-formatting.
* Stop calling do-nothing initializer H5FS_init(). Delete it.
* Document what changes to make if the default VFD changes.
* While I am here, change an `await_prior` flag on the terminator table
to `true` to match the previous, non-table-driven code that was here.
Found the oversight making the following changes:
NFCI: insert an empty line and copy over slightly-edited comments from
the previous version, where those comments still correctly explained how
library termination operated.
* NFCI: lower a staircase.
* Replace every occurrence of FUNC_ENTER_NOAPI_INIT(...) with H5_PUSH_FUNC
since that is all that that macro does any more.
Quiet a bunch of new warnings by changing FUNC_ENTER_NOAPI(...) to
FUNC_ENTER_NOAPI_NOERR and removing disused `done:` labels.
* NFCI: add curly braces around a multiline statement.
* Quiet a signed/unsigned comparison warning.
* Add some documentation about library initialization and shutdown.
* Make sure that the library is initialized, or else that initialization
is already underway, before performing any VFD's initialization.
* Committing clang-format changes
* Committing clang-format changes
* Reduce differences from `develop` branch.
* Always initialize `tot_init`.
* Committing clang-format changes
* Fix typo: H5SL_init initializes skip lists, not VOL.
* Remove H5_TERM_GLOBAL test in H5T_init. H5T_init was unusual in that
it tested H5_TERM_GLOBAL and exited early if it was set. No other
module initializers did that, and I cannot find any reason that should
be necessary. Tests still pass when I remove it, so away it goes.
* Use HD prefix.
* Add function header comments.
* Drop the intermediate variable, it's only used once.
* Extract subroutine `H5FDperform_init(hid_t (*init)(void))` that
initializes the library, if necessary, before calling its VFD-initializer
argument. Use H5FDperform_init in the definition of the symbols
H5FD_<vfd> (e.g., H5FD_SEC2), which may be evaluated before the library
is initialized, like so:
```
```
I implement H5FDperform_init in its own source file, H5FDperform.c,
and exclude that file from trace processing because the `bin/trace`
cannot deal with the function-pointer type.
* Straggler from last: add new source file src/H5FDperform.c.
* Committing clang-format changes
* Add a missing file to the MANIFEST.
* Switch to FUNC_ENTER_API_NOINIT in H5FDperform_init() and hbool_t in
H5_term_library().
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Assume C99 fixed sized ints exist, use them
* Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89
Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Enable usage of new-style references with dimension scale APIs
* Add API to check if an object ID represents a native connector object
* Modified code to use new function H5DSwith_new_ref to determine if new references should be used with
Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF
varible is define at configure time (--enable-dimension-scales-with-new-ref).
Tested on jelly.
ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references.
* Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library.
test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5
for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further
investigation; but current implementation of the new references is not portable between LE and BE systems,
and 32 and 64-bit systems.
* Minor fixes for testing issues
* Update test_ds.c
Enabled broken test; tests pass now.
* Update RELEASE.txt
Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*).
* Update MANIFEST for new 32-bit new-style references test file for H5DS APIs
* Update 'dimension scales w/ new-style refs' feature based on review
Co-authored-by: Elena <epourmal@hdfgroup.org>
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the "try free" behavior from the skip lists
This was only used in the ID code when iterating and a callback
could delete IDs. It is not used anywhere else in the library and
is now pointless overhead.
Also quiets the const warnings when returning stored elements. They
only need to be const with respect to the skip list code, which should
never modify them. The library can do whatever it wants with the elements
it stored.
* Formatted source
* Move test utilities to utils/test folder
* Fix makefile assignment
* Add new dir
* add new folder
* Correct copied makefile
* Fix dir typo
* Add missing include dir
* Remove unnecessary lib link
* Correct dependent dirs
* Fix conditional checks
* Disable test if not built
* fix path to executable
* Use fixture for swmr_vfd check
* Add release note
* Correct shell tests and c++ flag warning
* Update autotools c++ warning
* Fix typo
* Avoid maintenance headaches: delete the `noerror-` variants of the
compiler flags files, since they essentially duplicate the `error-`
files modulo the replacement of `-Werror=` with `-W` and any changes in
comments. (I verified the duplication with a script.)
For autoconf, reinstate the use of the `demote_errors` shell function to
derive the `noerror-` content from the `error-` content. `demote_errors`
replaces `-Werror=` with `-W` when `WARNINGS_AS_ERRORS` is `no`.
Slightly reorder `configure.ac` so that the setting of
`WARNINGS_AS_ERRORS` takes effect before the `error-` files are sourced.
* Take a stab at updating the CMake files to match the changes I made to
the autoconf files to remove `noerror-` files. I'm not much of a CMake
user so these changes are quite rough.
Looks like the duplication can be reduced with the introduction of a new
macro.
* Delete `noerror-` files from the MANIFEST.
* Reduce duplication in the CMake files: perform the
HDF5_ENABLE_WARNINGS_AS_ERRORS test once in the ADD_H5_FLAGS macro.
* Add a release note.
* Update compact dataset I/O routines to handle driver-level memory copy
* Combine compact I/O read/write struct into single I/O struct
Rename CTL memory copy flag and H5Fquery routine to get file driver
structure
* Add RELEASE.txt entry for new "ctl" memory copy operation
* 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
This patch will remove clang warnings on Mac:
``` warning: implicit conversion increases floating-point precision:
'float' to 'double' [-Wdouble-promotion]
```
* Update Platforms Tested in RELEASE.txt.
Remove Tested Configuration Features Summary for updated replacement.
* Set version to 1.13.0-6 for rc6 snapshot.
* Added "ctl" callback to the VFD interface, and the associated
H5FDctl() and H5FD_ctl() calls.
Modified the MPIO VFD accordingly -- specifically:
Added ctl() call with op-code support to expose rank, size,
and communicator.
Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(),
and H5FD_mpi_get_comm() to use the new ctl() callback. In passing
removed the const qualifier from the file parameter of these
functions, as the file parameter of the ctl callback is not
const.
Deleted the old H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and
H5FD__mpio_communicator() calls from the MPIO VFD.
Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the
MPIO VFD accordingly. Note that all VFDs now use H5FD_class_t,
with no special class for VFDs that that support MPI.
Some minor touch ups to the Neil's selection I/O mods in passing.
Tested serial and parallel, debug and production on charis and
jelly.
* Reserve a range of VFD "ctl" opcodes for library and experimental usage
* Add "ctl" callbacks to passthrough VFDs
* Add RELEASE.txt entry for "ctl" callback
* Use H5FDopen with H5F_ACC_RDWR flag instead of H5F_ACC_TRUNC in vfd test
* Remove handling of passthrough "ctl" flag from multi VFD
* Move logic for testing H5FD_CTL__TEST_OPCODE into a testing VFD
Revise description of "ctl" callback in RELEASE.txt
Remove unused H5FD_CTL__NUM_OPCODES definition
Fix some warnings in multi VFD
Co-authored-by: mainzer <mainzer#hdfgroup.org>
* Committing clang-format changes
* Fixed GCC warning suppression pragmas to also work with clang
H5_GCC_DIAG_ON remains gcc-only.
Added a new H5_CLANG_DIAG_ON that's clang-only, but it's not used anywhere currently.
Added a new H5_GCC_CLANG_DIAG_ON that works with both compilers, which afterall support mostly the same warnings. Changed almost all uses of H5_GCC_DIAG_ON to use H5_GCC_CLANG_DIAG_ON, with the exception of a couple, where they really were suppressing gcc-only warnings.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() function
- Made a small improvement for H5Z_xform_noop() function. Now,
the function will also return TRUE if the data transform function
expression = "x". For this case, the HDF5 library behaves in a
similar fashion as the case when no data transform function has been
specified.
- Improved the inline documentation of the function
H5Z_xform_create() such it is more inline with the rest of the
code.
* Committing clang-format changes
* H5Ztrans: (feature) Added 3 tests for improved H5Z_xform_noop() function
- Added serial test with data transform expression = "x" to
verify the improved H5Z_xform_noop() function behaves as expected.
- Added 2 parallel tests with data transform expression = "x"
in combination with a filter. Before, these tests will fail but
with the improved H5Z_xform_noop() function they work and result
in the expected behavior.
- Small bug fix for one of parallel filter tests.
* Committing clang-format changes
* H5Ztrans: (feature) Added release note about detection of the
simple data transform function "x".
- Added a brief explanation about the implemented improvement
of the detection of the simple data transform function "x"
to the RELEASE.txt file.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* add ULL attr set/get signatures to LT public API
* add LT implementation of ULL set/get attribute
* fix copy-paste typo in test comment
* add ULL test data
* define ullong attr name global variable
* add LT tests for ULL attr set/get
* Committing clang-format changes
* correct type passed to lt get attr test for ULL
* update RELEASE.txt with added ULL set/get functionality
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update copyright headers with reproduction notice in 5 files that did
not match terms in COPYING file
.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Create a tag file for permalinks.
* Added DOXYGEN_TAG_FILE.
* Added Doxygen life-cycle examples for different modules.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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>
* Pacify clang-analyzer-unix.cstring.NullArg
* Apply some bugprone-suspicious-string-compare
* Apply some readability-simplify-boolean-expr
* Apply some readability-make-member-function-const
* Apple some bugprone-macro-parentheses
* Changed an f suffix to L for `long double`
* Applied some readability-uppercase-literal-suffix automatically
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Instead of looking at `MATCHES 0` which runs a regex and returns a false
positive for any result such as `10`, check if they are equal to `0`.
Also quote `0` to avoid looking it up as a variable (which was left
behind prior to the fix to use `${RETURN_VAR}` in the `c_run` macro).
Ensure that the used number of processes times an integer number
is equal to SPACE1_DIM1 and SPACE_DIM2. These variables are
equal to 24 and are defined in ph5example.c. If this is not the
case the ph5example test will fail.
* Committing clang-format changes
* Fix issue #924, ${HDF5_CXXLINKER} does not work in h5c++.
2 instances of CLINKER corrected to CXXLINKER
comment border aligned
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes a bad memory read and unfreed memory in fsinfo code
The segfaul from CVE-2020-10810 was fixed some time ago, but the
illegal memory read and unfreed memory were not.
This fix tracks some buffer sizes and errors out gracefully on errors,
ensuring buffers are cleaned up and avoiding the H5FL infinite loop +
abort on library close.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
* Reorg tools perform to provide h5perf for installation
* Correct file paths
* Correct path
* Add new src folder to makefile list
* Remove bin_PROGRAMS from TEST_PROG
* Default h5perf executables to static build
* Remove test lib dependency from h5perf
* format adjustments
* Remove test lib from autotools makefile
* Add note
* h5perf needs the math library
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Some of the command-line tools would allow partial long options (e.g.,
--datas instead of --dataset). These were inconsistently implemented,
difficult to maintain, and occasionally blocked useful long options.
They have been removed from all the tools.
NOTE: This change should NOT be merged to 1.12 or earlier.
* Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid
warning that unsigned comparison < 0 is always false, which is known,
but for later versions the comparison can possibly be true.
* Better solution for avoiding warning that unsigned comparison < 0.
* Remove version-check for relnum in H5check.
* Add in release exception code check
* Fix typos
* Fix more typos
* Rework comments
* format change
* format whitespace
* Library version must be less than or equal to headers
* Need the NOT version of the compare
* Enable release+1 check for PASS
* Add release note
* Update note
- warn_unused_result warnings from h5jamgentest and j5stat_gentest
that were triggered by write(2) calls where we didn't check the
return value
- A missing callback in the NULL VOL connector
- A possibly uninitialized property list pointer
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
* Fix static perform tools compile for arg options
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* CMake: (feature) libaec
Implemented better support for the compression library libaec.
Especially, for the new version 1.0.5:
- The CMake config files of this version 1.0.5 now set certain
SZIP variables which can be used in the existing
CMake structure.
- Both static and shared SZIP compatible libaec library contains
all required objects such it can be easily used when building
HDF5 from scratch.
- Introduced the USE_LIBAEC_STATIC option to make use of the static
version of SZIP compatible libaec library.
* CMake: (fix) libaec
Implemented the fallback option for the case if version 1.0.5
of libaec could not be found.
* Docs: Added description about libaec implementation.
Added short description about the libaec improvement to the Bug Fixes
section in the Configuration sub-section.
* Moves get_option from the tools library to the C library
* Adds H5 prefix to get_option call and variables
* Renames the H5_get_option long options struct and enum
* Cleans up POSIX/C bits in H5private.h
* Assume difftime exists (C89)
* Reorg AC_CHECK_HEADERS so headers are in alphabetical order
* Split off networking-related AC_CHECK_HEADERS
* Remove unused UNAME_CYGWIN from configure.ac
* Remove checks for unused sys/timeb.h
* Tidying pass over H5private.h HD prefix macros
* Tidy H5win32defs.h
* Add HD prefix to various scanf calls
* Committing clang-format changes
* Fixes to the alarm(2) code used in the tests to make Windows happy
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Assume the library has C99 types in C++ type code
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Reorganization of C and POSIX headers in H5public.h & H5private.h
Consolidated and removed duplicates
* It turns out Windows has sys/types.h
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Mostly just moving things around and changing the comments to keep the
delta small. The only symbol change is that for curl/curl.h which I
changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol
is not used in the library and is just an artifact of the checks.
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Removes C++ dependency on H5private.h
Most C API calls have been removed, aside from a few uses of free,
where we just dropped the 'HD'. A couple of H5_ATTR_UNUSED macros
were also replaced with (void) statements.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
This is extremely slow and generates a LOT of false positives. It's also
not really a warning flag, but an analysis feature and thus belongs in
a separate configure option, not lumped in with the warnings.
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++
Allows C++ library to be built on older versions of gcc.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Removes clang-format comments from H5O.c call
* Fixes bin/trace to correctly wrap lines near the clang-format limit
* Removed unused variable from bin/trace
* Update API tracing for new H5VL_request_status_t typedef
* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure
* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation
* Remove 'canceled' event status from Java constants
* Be safer about releasing resources when inserting a newly opened/created object or file into an event set
* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".
* Remove H5ES_STATUS_CANCELED from Java wrappers also
* Apply patch for dynamically registering optional VOL operations
* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.
* Corrections based on PR feedback.
* Further changes to make based on PR feedback.
* Remove H5Dwait & H5Fwait (moved to the async connector). Added H5atclose
routine. Updated 'optional op' operations.
* Fix missed merge marker, and reformatted line
* Update API tracing infrastructure for H5atclose callback
* Clean up some warnings
* Normalize against develop branch
* Correct level of indirection
* Add doxygen info for H5is_library_terminating and regression tests for it and H5atclose
* Relocate prototype (and doxygen info) for H5Aclose
* Align w/changes on develop
* Move group package initialization code to H5Gint.c, and update tracing macros
* Change non-static function declarations to be static
* Correct GCC diagnostic macro
* Ensure that H5TSpublic.h header gets installed (#129)
* Finish moving API routines that invoke VOL framework to main source files.
* Fix position of H5Fmount and H5Funmount
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Add wrappers for dynamically registered optional operations
* Fix typo
* Update doxygen comment for H5atclose with additional detail.
* Add H5VL\*_vararg versions of H5VL routines that use va_list parameters
* Implement and test H5S_BLOCK
* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c.
* Add H5Iregister_future routine and tests.
* Correct return value for H5Lexists_async
* Add H5_DLL macro to public H5ES API routines
* Update supported -> flags parameter for introspect_query callback
* Remove my email address. Update passthrough VOL connector ID.
* Fix comment for post_open_api_common
* Remove unused non-blocking VOL connector
* Minor cleanup in async branch in preparation for merge to develop
* Update CMake and the Autotools to use the new pass-through VOL ID
* Finish another iteration on public H5ES routines, along with running the code reformatter
* Another round of reformatting
* Fix for SWMR daily test failures (#160)
The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.
* Added selective async APIs (#150)
* Added selective async APIs
Description:
Added the following APIs:
H5Ropen_attr_async
H5Ropen_object_async
H5Ropen_region_async
H5Mcreate_async
H5Mopen_async
H5Mput_async
H5Mget_async
H5Mclose_async
H5Tcommit_async
H5Topen_async
H5Tcopy_async
H5Tclose_async
- Updated an expected output file to include a new internal function
in the error stack for the failure case.
* Updated async APIs per reviews, including removing async version of
H5Tcopy.
* Removed statements that were added by mistake in the previous commit.
* Fix compile issues in H5M and warnings elsewhere
* Reformat code
* Brings VOL_LIST changes from develop. (#163)
* Remove H5Dwait and H5Fwait calls, which were incorrectly brought back in
* Tiny cleanup of H5Lcreate_hard_async
* Run source formatter
* Allow for canceled operation in wait_cb
* Attempt to fix switch on string value
* Re-run source formatter
* Add H5S_BLOCK testfile to CMake clean target
* Add H5Pset_vol_async API routine and 'get_cap_flags' VOL introspection callback
* Clean up warnings
* Add H5P(set\|get)_vol_implicit_async API routines to allow \/ disallow implicit asynchronous operations (default is disallowed)
* Run formatting script
* Remove H5VL_REQUEST_WAIT\*
* Warning cleanup
* Eliminate strdup()s on statically allocated strings
* Warning cleanup
* Split H5VLrestore_lib_state into H5VLstart_lib_state and H5VLrestore_lib_state, and rename H5VLreset_lib_state to H5VLfinish_lib_state.
* Duplicate strings when building err_info to return to applicatin
* Move connector author routines into seperate header files, all included in the new hdf5dev.h header
* Run bin/trace to add TRACE macros
* Allow H5ES_NONE as a valid, but no-op, parameter to all H5ES API routines that accept an event set ID
* Clean up formatting
* Remove H5Pset/get_vol_implicit_async
* Clean up warning
* Remove H5Pget_vol_async and replace with more generic H5Pget_vol_cap_flags
* Clean up warnings
* Add H5ESfree_err_info convenience routine
* Fix typo
* Correct matching for cached VOL plugins
* Add developer header file
* Update for C99 compatibility
* Add missing trace macro
* Stop clang-format from messing with the trace macros. Don't set up VOL wrappers for 'infrastructure' objects like requests and blobs
* Fix warning about formatting a directory
* Clean up formatting for H5E_BEGIN_TRY / H5E_END_TRY
* Reduce scope of H5ES__close
* Enable CMake checks for various types on MacOS
* Clean up properly when H5CX_retrieve_state() fails. Also clean up many compiler warnings.
* Committing clang-format changes
* Merge from develop
* Fix mis-placed assert
* Remove commented-out code
* Re-add macro for unsetenv on Windows (I think it accidentally was merged out)
* Strengthen sanity check from error report to assertion
* Committing clang-format changes
* Add units to the comments for a few fields
* Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it.
* Committing clang-format changes
* Remove H5ESget_time_estimate
* Committing clang-format changes
* Create developer header for datatype routines and move type conversion register/unregister routines there.
* Simplify internal H5VL_setup_name_args and H5VL_setup_idx_args routines
* Add H5VLlink_optional_op, allowing dynamicly registered optional operations for the link VOL subclass, also added H5VL_loc_params argument to the link 'optional' callback to allow them to work correctly.
* Run bin/format_source on current code
* Add H5VLobject_optional_op, allowing dynamicly registered optional operations for the object VOL subclass, also added H5VL_loc_params argument to the object 'optional' callback to allow them to work correctly.
* Run bin/format_source on current code
* Committing clang-format changes
* Revert "Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it."
This reverts commit 5ac92014da.
* Committing clang-format changes
* Convert attribute 'get' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Update tracing macros
* Convert attribute 'specific' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert dataset 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to attribute 'get' and 'specific' operation parameters.
* Convert datatype 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to H5O_refresh_metadata arguments.
* Reduce warnings
* Reduce warnings
* Track change to datatype 'get' callback
* Fix bug with file pointer getting invalidated when object closed
* Reformat source
* Convert file and group VOL classes 'get' and 'specific' operations to use
struct-of-tagged-union pattern for VOL callback arguments, instead of using
varargs. Also small cleanup to the attribute get name operation. Also moved
'mount' and 'unmount' operations to be group specific operations, instead of
file specific, to better align with their behavior (mounted files are on
groups, so a group is what is operated on).
* Remove remainder of merge conflict marking
* Convert link VOL class 'create' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Remove some unused local variables
* Convert link VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor 'get name by idx' routines to return actual length of name with a parameter instead of the return value, and move some callback context structs for the link interface from the private header file into the source code module, to reduce their visibility scope.
* Update tracing macros
* Convert link VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert object VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert object VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor H5G_loc_exists, et al, to return 'exists' flag in a parameter and errors with the function return value, instead of overloading both into the return value. And, corrected logic error in test/links.c around non-existant objects in a file.
* Convert request VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert blob VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also removes the H5VL_BLOB_GETSIZE operation, as it's unused in the library and the blob ID size for a container is now returned with H5VL_FILE_GET_CONT_INFO.
* Add 'const' to several parameters that are only queried.
* Convert all VOL classes' 'optional' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Convert several 'get' routines to return the length of an array in a parameter instead of combining it into the return value. Move several routines to be in less public namespace. Correct direct_chunk test to verify that parameters aren't modified on error.
* Switch get/specific/optional VOL callback argument structures to be 'async-friendly'. Also other minor cleanups and bug-fixes.
* Add H5Pset_dataset_io_hyperslab_selection / H5S_PLIST feature, to allow skipping H5Dget_space + H5Sselect_hyperslab for async operation
* Add dynamic optional operations for request objects
* Update dynamic operation test for optional request operations
* Update a comment for an operation argument
* Run trace and format_source scripts
* Committing clang-format changes
* Committing clang-format changes
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* C++ build and warning updates
* Fixes all warnings on C++ (with gcc 9.3)
* Updates CMake and Autotools C++ builds
* Undo warning clobber
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Splits internal parts of H5L.c to H5Lint.c
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER
* Rips out the BEGIN_FUNC, etc. macros
* Removes 'end if', etc. comments from H5HL package
* Committing clang-format changes
* Fixes an H5EA iterate issue
* Fixes an issue in the H5FA iterator code
* Further cleanup in bin/trace after macro removal
* Iterator changes in H5EA and H5FA
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Removes pre-C99 build and header cruft
* Assumes ANSI C headers exist
* Assumes stdbool.h, stdint.h, and inttypes.h are present
* Assumes the C++ compiler can handle stdint.h
* Removes all work-arounds for missing functionality, especially stdbool.h
* Formats source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Requires a C++11 compiler to build the C++ wrappers
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Runs the flush1/flush2 tests in their own directory
Avoids file deletions by other tests.
* Revert "Runs the flush1/flush2 tests in their own directory"
This reverts commit 746c048824.
Also pulls the flush files from the clean list, which is a simpler fix.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Makes the event_set test a single-source target
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Several CMake updates:
* Removes unused HDF5_ENABLE_HSIZET
* Switches TEST_SHELL_SCRIPTS to ON
* Sets SH_PROGRAM to bash instead of sh
* Set default build type back to RelWithDebInfo
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Fixes a minor valgrind issue in the chunk_info test (#675)
* Fixes a minor valgrind issue in the chunk_info test
The chunk_info test incorrectly set the number of bytes in a compressed
buffer, which caused valgrind to complain about writing uninitialized
bytes.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Add H5Dchunk_iter method for iterating over chunks
This method iterates over all chunks in dataset, calling a user-supplied
callback with the chunk information and optional user supplied data.
The iterator is stopped when ITER_STOP is returned by the user-supplied
callback or the iterator is exhausted.
Existing methods to get chunk_info performs an iteration each time, so
to get many or all chunks causes SUM(i) for i = 0 -> N operations for N
chunks, as opposed to N operations when using this iterator for this use case.
* H5Dchunk_iter: test iterating all chunks, some chunks and failing iteration.
* H5D: move H5Dchunk_iter private methods to specific
* trace: add H5D_chunk_iter_op_t and trace H5D.c
* chunks-iter: document chunk_iter
* chunk-iter: chunk add FUNC_ENTER/FUNC_LEAVE macros
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* BUG: DataSet assignment operator is missing
* Some compilers complain if the copy constructor is given explicitly
but the assignment operator is implicitly set to default.
* Explicitly defining the assignment operator allows us to properly
handle reference counters for shared resources.
* BUG: DataSet assignment operator is missing.
* Mimicking code of H5DataType::operator() as suggested by @bmribler.
* Added test
Description:
Added test for DataSet::operator= that Leengit added
Platform tested:
Linux/64 (jelly)
* Removed Author field.
* Commit clang format changes.
* Entry for Leengit's github PR #503
* Removed lines left by mistake
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed HDFFV-11223 (CVE-2018-14460)
Description
- Added checks against buffer size to prevent segfault, in case of data
corruption, for sdim->size and sdim->max.
- Renamed data files in an existing test to shorten their length
as agreed with other developers previously.
Platforms tested:
Linux/64 (jelly)
* Committing clang-format changes
* Updated for test files
* Updated for HDFFV-11223
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Adds consts to a few global variables
* Cleans up a const warning left over from previous constification
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Brings over hash table code from Bitbucket
* Can be switched between skip list and hash table implementation
with H5_USE_ID_HASH_TABLE #define
* Not yet updated to use iterate-safe delete
* Fixes a warning and changes where the problematic test is
commented out.
* Adds mark-and-sweep flags and members
* Final fixes for hash table ID code
* Removes skip list ID code
* Committing clang-format changes
* Formatted source
* Adds a comment about the mark-and-sweep scheme.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Adds consts to a few global variables
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed use of null pointer identified by UBSan
UBSan warned:
runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t')
with these two tests:
H5REPACK-committed_dt_DFF
H5REPACK-committed_dt
Reformulated per @gnuoyd suggestion.
* Fixed undefined float -> unsigned char conversion in HL_test_image
* Removed dead skip_overflow_tests_g global
The global `skip_overflow_tests_g` was being set but never read.
* Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5`
* Committing clang-format changes
* Remove extra ']' in line 730.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removed mentions of Wdeclaration-after-statement now that C99 is required
* Remove -Werror=declaration-after-statement from error-general file.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Committing clang-format changes
* Fixes incorrect size_hint handling in H5Gcreate1
* Updates the size hint type for group creation
* Updates the RELEASE.txt note
* Revert "Updates the RELEASE.txt note"
This reverts commit 3df386acca.
* Reverts previous behavior to use a uint32_t struct field
* Updates RELEASE.txt
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.
Fixes HDFFV-11239
* Fixes typos
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID
This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.
This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed warnings and started H5Epublic.h.
* Include H5FD* headers to correctly resolve references.
* Doxygen2 (#330)
* H5Eauto_is_v2.
* Added a few more calls.
* Added a few more H5E calls.
* First cut of H5E v2.
* Added the deprecated v1 calls.
* Updated spacing.
* Once more.
* Taking some inspiration from Eigen3.
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)
* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.
* doxygen work. fixs format by using clang-format.
* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.
* added documentation for H5P APIs (#350)
* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios
* format corrections
* fixed grammer
* fixed herr_t
* Better name.
* A fresh look.
* add doxygen to H5Ppublic.h
* use attention instead of warning
* Add doxygen comments in H5Ppublic.h (#375)
* Add doxygen comments in H5Ppublic.h
* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops
* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt
* Fix clang-format errors
* Fix filenames in doxygen/examples
* add doxygen to H5Ppublic.h (#378)
* add doxygen to H5Ppublic.h
* use attention instead of warning
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
* Revert "add doxygen to H5Ppublic.h (#378)"
This reverts commit 2ee1821b13.
* Updated Doxygen variables.
* I forgot to copy two images.
* Enable desktop search by default.
* Add my assigned Doxygen documentation.
* Remove whitespace at EOL. Appease clang-format.
* Addressed Chris' comments.
* Added an alias for asynchronous functions.
* One space is enough for all of us.
* Slightly restructured RM page.
* address some issues
* reformatting
* Style external links.
* reformatting
* reformatting
* Added "Metadata Caching in HDF5" as a technical note example.
* Revise this soon!
* Added specification examples.
* Fixed references.
* Added H5AC cache image stuff and file format study.
* Added older FMT versions. Where did 1.0 go?
* Updated C/C++ note and replaced ambiguous labels.
* Reformat source with clang v10.0.1.
* Added the VFL technical note.
* Added what I believe might be called version 1.0 of the format.
* Added the remaining specs.
* Added H5Z callback documentation and fixed a few mistakes.
* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.
* clang-format happy?
* Ok?
* Bonus track: Deprecated H5D functions.
* Carry over the more detailed group description.
* Added documentation for the missing and deprecated H5R calls.
* Life is easier and less repetitive w/ snippets. Use them!
* Eliminate the snippet block ID artifacts in the HTML rendering.
* Fixed snippet HTML artifacts and added a few missing calls.
* Under 20 H5Ps to go!
* Almost complete!
* "This is a form of pedantry up with which I will not put." (Churchill)
* Let's not waste as much space on bulleted lists!
* First complete (?) draft of the Doxygen-based RM.
* Completeness check and minor fixes along the way.
* Pedantry.
* Adding missing H5FD calls checkpoint.
* Pedantry.
* More pedantry.
* Added H5Pset_fapl_log.
* First draft of H5ES.
* Fixed warnings.
* Prep. for map module.
* First cut of the map module.
* Pedantry.
* Possible H5F introduction.
* Fix the indentation.
* Pedantry.
* Ditto.
* Thanks to the reviewers for their comments.
* Added missing images.
* Line numbers are a distraction here.
* More examples, references, and clean-up. Don't repeat yourself!
* Clang pedantry.
* Ditto.
* More reviewer comments...
* Templatized references and cleaned up \todos.
* Committing clang-format changes
* Fixed MANIFEST.
* Addressed Quincey's comments. (OCPLs)
* Fixed a few more \todo items.
* Fixed more \todo items.
* Added attribute life cycle.
* Forgot the examples file.
* Committing clang-format changes
* Pedantry.
* Live and learn!
* Added a sample H5D life cycle.
* Committing clang-format changes
* Pedantry.
Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING (license) file.
* Add release_docs/code-conventions.md file.
* Add script to test h5py.
* Fix script error.
* Add file h5pytest.yml.
* Test declaration of counter variables in for loops.
* Committing clang-format changes
* Committing clang-format changes
* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.
* Revert "Added [] to line 126 of H5LTanalyze.l."
This reverts commit e4a9cee441.
* Revert extra commits to match canonical develop.
* Update top-level COPYING file and remove COPYING files from
subdirectories.
* Remove subdirectory COPYING files from MANIFEST.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Brings the native VFD H5Fdelete() implementation from Bitbucket
Only brings the 'del' callbacks, not the 'open/close' scheme.
* Formatter changes
* Committing clang-format changes
* Fixes direct VFD callback name
* Removes UNUSED macro from family API call
* Adds barrier and rank 0 check to MPI-I/O VFD delete
* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"
This reverts commit 909765f759.
* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""
This reverts commit 9b04bef115.
* Adds a second barrier after the delete in MPI-I/O VFD
* Only delete files in the core VFD when the backing store flag is set
* Fixes string issues in multi VFD
Also, h5test.c cleanup code now uses H5Fdelete().
* Formatted source
* Rework fapl checks for MPI-I/O VFD delete callback
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Removes my_strdup() from the multi VFD
* Use strdup directly when memory sanity checks are off
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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
* added H5fortkit dependency for H5VLff.F90, HDFFV-11232
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Updates the accum test to work on Windows
Uses CreateProcess() on Windows
* Source formatting
* Fix for Unix child result
* Fixes process return code bug on Windows
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING (license) file.
* Add release_docs/code-conventions.md file.
* Add script to test h5py.
* Fix script error.
* Add file h5pytest.yml.
* Test declaration of counter variables in for loops.
* Committing clang-format changes
* Committing clang-format changes
* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.
* Revert "Added [] to line 126 of H5LTanalyze.l."
This reverts commit e4a9cee441.
* Revert extra commits to match canonical develop.
* Add cmake variable HDF5_LIB_INFIX (#7)
* Add cmake variable HDF5_LIB_INFIX
This infix is added to all library names after 'hdf5'.
e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
This name is used in packages on debian based systems.
(see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)
This option is useful when testing projects on debian based systems with
custom builds of hdf5 while trying to minimize differences between the
custom setup and the environment created by installing system packages.
* Added RELEASE.txt entry for HDF5_LIB_INFIX.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Committing clang-format changes
* Removes c99_(v)snprintf from standalone code
These internal API calls were removed in a previous commit but were
missed in the sio/pio_standalone code.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING (license) file.
* Add release_docs/code-conventions.md file.
* Add script to test h5py.
* Fix script error.
* Add file h5pytest.yml.
* Test declaration of counter variables in for loops.
* Committing clang-format changes
* Committing clang-format changes
* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.
* Revert "Added [] to line 126 of H5LTanalyze.l."
This reverts commit e4a9cee441.
* Revert extra commits to match canonical develop.
* Added [] to H5LTanalyze.l line 126 to eliminate warning "rule could not be
matched".
Ran bin/genparser hl/src with flex v2.6.4 and Bison v3.0.4 on jelly.
* Added HD to strdup in H5LTparse.y line 338.
Ran bin/genparser hlsrc again.
* Removed line 126 from H5LTanalyze.l - previous line matches.
Added previously removed line 318 of H5LTparse.y to fix hl_test_lite
failure.
Ran bin/genparser.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* File locks now work on Windows
Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial).
* Committing clang-format changes
* Committing clang-format changes
* Fixes commenting in h5repack
* Reworks H5Fis_accessible()
H5Fis_accessible() created a new file handle and attempted to read
through it, which will fail when a file has been opened with an
exclusive lock on operating systems that have mandatory locks.
This change uses the same scheme we use in H5Fopen() to check if
the file is already open and only tries to read the file signature
if the file has not already been opened.
Also adds a test for this behavior.
* Committing clang-format changes
* Trivial change to force github to run actions
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds an implementation for nanosleep on Windows
* Committing clang-format changes
* Fix insane formatter issue
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Some of the uniniitialized bits in the buffer may get carried through
all the way to disk, creating a risk for leaks.
We observed an msan error during the floating point output conversion.
Due to the encoding certain bits could remain untouched during the conversion.
In this draft we zero initialize the dbuf used by every convertor.
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033)
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode
Platforms tested:
Linux/64 (jelly)
* Accidentally left in another occurrence of the previous patch from user
after a more correct fix was applied, that is the check now accounted
for the previous advance of the buffer pointer. Removed it.
* Typo
* Fixed format issues.
* Added test.
* Changed arguments to ADD_H5_TEST
* Fixing arguments to ADD_H5_TEST again.
* Fixing arguments again.
* Took out the CMake changes until Allen can help.
* Added files:
tCVE_2018_11206_fill_old.h5
tCVE_2018_11206_fill_new.h5
* Revert "Took out the CMake changes until Allen can help."
This reverts commit c21324d6e0.
* Revert "Fixing arguments again."
This reverts commit 5832a70674.
* Revert "Fixing arguments to ADD_H5_TEST again."
This reverts commit b45de823c2.
* Revert "Changed arguments to ADD_H5_TEST"
This reverts commit 16719824f5.
* Added first argument to ADD_H5_TEST for HDFFV-10480 fix.
* Changed argument 0 to 1
* Revert "Changed argument 0 to 1"
This reverts commit b343d6613b.
* Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix."
This reverts commit b8a0f9a9e8.
* Added first argument and corrected the second.
* Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049
* Improved error messages.
* Added description of the current HDF5 branches.
* Removed capitalization in from Develop, Release, Feature to reflect the real naming schema
* Added a draft of contributions guidance document.
* Fixed typos.
* Fixed section title.
* Fixed typo.
* Fixed typos and formatting.
* Fixed many typos and simplified the text (e.g., removed testing instructions and left pointers to where to find them, etc.)
* Fixed a typo.
Please enter the commit message for your changes. Lines starting
* Added contributing.md file and rearranged doc entries in alphabetical order.
* ddressed Gerd's review comments; found and fixed more typos.
* Addressed comments from Larry and Scot.
* Suppresses the tcheck_version test's abort dialog on Windows
Windows raises a modal abort/retry/ignore dialog box when CRT
calls abort(). This change installs a report hook that suppresses
the dialog so that the CMake tests don't time out waiting for a
nonexistent user to click a dialog box.
* Committing clang-format changes
* Removes __cdecl from callback
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes a few testhdf5 warnings raised in Visual Studio
Visual Studio is grumpier about treating pointers like integers than
gcc.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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>
* Stop using global variables to share parse context with the lexer.
The lexer uses an unconventional strategy for parsing lexical categories
NUMBER (decimal numbers) and STRING (double-quoted strings) that involves
sharing the parse context with the lexer using global variables. There
are a couple of problems with that. First, the lexer is too complicated
for the simple tokenization it performs—it's hard to tell if it is
correct. Second, as @seanm points out, the shared global variables
spill into the namespace shared by other libraries and application
programs—e.g., VTK.
* Regenerate source files from *.[yl].
* Replace strndup, which isn't available on Windows, with a custom
routine, `trim_quotes`, that produces a copy of its `const char *`
argument with leading and trailing double quotes ('"') removed.
While I am here, remove the unnecessary statement `BEGIN INITIAL;`,
which I should have deleted in a previous commit.
* Regenerate .c from .l.
* You haven't programmed in C until you have programmed in High-Definition
(HD) C.
* \#include "H5private.h" for HD* definitions.
* Regenerate *.[ch] from *.[yl].
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Replaces checks for fork, etc. with H5_HAVE_UNISTD_H
Code previously checked for individual POSIX API calls using
H5_HAVE_FORK, etc. The calls we use have been standardized for
decades and available via unistd.h.
Some test messages that were missing when tests are skipped
due to a lack of unistd.h were also added.
The configure checks for individual POSIX API calls will be
removed in a later commit.
* Stupid formatter
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* 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>
* Fixed clang-tidy bugprone-reserved-identifier warnings
* Fixed clang-tidy bugprone-assert-side-effect warnings
* Fixed clang-tidy bugprone-copy-constructor-init warning
* Fixed clang-tidy readability-redundant-preprocessor warning
For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.
Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.
* Fixed clang-tidy readability-redundant-string-init warnings
* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings
* Fixed clang-tidy performance-unnecessary-value-param warnings
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* 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>
* Removed bad function pointer casts
In one case fixed the actual function signature to be correct.
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixes various warnings noticed on Windows
- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()
* Fixes clang-format issues
* Fixed -Wunused-local-typedef warning
* Fixed -Wformat warnings
In one case also removed a `z` character. There was a `z%d` that I think was supposed to be `%zd`
* Fixed -Wshorten-64-to-32 warnings
* Fixed -Wself-assign warnings
* Fixed -Wreserved-id-macro warnings
* Commit format changes from clang-format, clang version 10.0.1.
* Fixed -Wself-assign warnings
* Fixed -Wunused-local-typedef warning
* Fixed -Wformat warnings
In two cases also removed a `z` character. There was a `z%d` that was supposed to be `%zd`.
* Fixed -Wshorten-64-to-32 warnings
* Fixed -Wreserved-id-macro warnings
* Fixed -Wself-assign warnings
* Format source.
* Remove blank lines to pass format check.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Use do-while trick to force H5Epush_ret() to require trailing semi
Fixed ensuing compiler errors.
* Commit format changes from running clang-format with clang version 10.0.1.
* Use do-while trick to force H5Epush_ret() to require trailing semi
Fixed ensuing compiler errors. Updated RELEASE.txt.
This change was made to allow clang-format to correctly format the code.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* Drop the export attribute on forward declaration
They don't mean anything on forward declarations anyways.
* Fixed -Wunused-parameter warnings in some C++ files
Allowed all the attribute #defines to work in C++ also.
* Fixed -Wunused-variable warnings by removing dead code
* Fixed all -Wshorten-64-to-32 warnings by adjusting casts
There was no truncation in fact, since the unsigned result was upcast to size_t then implicitly downcast to uint32_t.
* Fixed all -Wcomma warnings by spliting statements onto own lines
* Fixed all -Wself-assign warnings with different unused param suppression
* Fixed all -Wextra-semi warnings
* Fixed all -Wswitch-enum warnings
Just added new explicit cases with the existing default case.
* Fixed all -Wmissing-prototypes warnings
Just made functions static. Moved them into an extern "C" block.
* Reformatted source with bin/format_source using clang version 10.0.1
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling
Removed leading underscore(s) from header guard spelling. Used 2 regexes:
` _H5(.*)_H`
` __H5(.*)_H`
Applied case-insensitively to only .h files.
* Modified scripts that generate header files to not use underscore prefix
Interestingly, there was already no leading underscore in the trailing comment at the end of the file
* Fixed remaining -Wreserved-id-macro warning not caught by regex
* Fixed various -Wincompatible-pointer-types-discards-qualifiers warnings by adding const
* Fixed various -Wincompatible-pointer-types-discards-qualifiers warning by removing extraneous consts
There were casts with const, but the function parameter doesn't actaully take const, so just modified the casts.
In the other case, a local variable was const that should not have been, becuase its source wasn't const either.
* Fixed a -Wincompatible-pointer-types-discards-qualifiers warning by strdup-ing a string
Create a duplicate string instead of mutating a supposedly const one.
Description
Replaced an HDassert with a check for null pointer in H5O_dec_rc() to
catch null pointer in corrupted data situation.
As a result, removed the null check prior to H5O_dec_rc() calls.
Platforms tested:
Linux/64 (jelly)
* Fixed all -Wsometimes-uninitialized warnings by initializing variables
* Fixed all -Wconditional-uninitialized warnings by initializing variables
* Commit alignment changes from running bin/format_source with clang
version 10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
* 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.
Although clang defines __GNUC__ and supports most gcc warnings, it doesn't support all, and will in fact even warn about an unknown pragma.
Guard appropriately.
On macOS on x86_64, long double is 16 bytes; on macOS on arm64, it's 8 bytes.
Use the same existing technique used to properly detect other sizes to now also properly detect the size of long double.
For bug #311.
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Whitespace fixes except for H5Tprivate.h typo fix
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Small changes plus merge of tools arg parse from 1.12
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Fixed problems with vlens and refs inside compound using H5VLget_file_type()
* Fix date in RELEASE.txt
* Add assertions
* Move some manipulation of H5VL_object_t struct fields into the H5VL
package.
* Cache the pointer to the next point to process after the last call to
H5S__get_select_elem_pointlist. This allows the normal process of
iterating over the points in batches to be much more efficient, as the
library does not need to traverse the entirety of the preceding points
every time the funciton is re-entered.
* Update RELEASE.txt for point selection iteration performance fix.
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Removes no-op callback stubs from read-only VFDs
Also changes VFD registration to allow read-only VFDs with no
write callback to be registered.
* Adds a RELEASE.txt note for HDFFV-11205
For the read-only VFD registration change
* Revert "Removes no-op callback stubs from read-only VFDs"
This reverts commit a7a9549730.
* Removes lock callbacks from ros3 and hdfs VFDs
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* Removes no-op callback stubs from read-only VFDs
Also changes VFD registration to allow read-only VFDs with no
write callback to be registered.
* Adds a RELEASE.txt note for HDFFV-11205
For the read-only VFD registration change
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* Fixes Autotools detection of the st_blocks field in stat
The Autotools and CMake will now both correctly determine if the
stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS
appropriately.
* Fixes a typo in configure.ac
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Remove duplicate setting
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Pkgconfig fix - #218
* Update all pkgconfig settings with version
* Detect coredumps, and avoid printing a warning when creating a directory that already exists
* Retrieve the actual datatype object correctly, in the face of possible pass-through VOL connectors
* Detect more core dumps, and tiny formatting cleanup
* Revert error status checks for mirror VFD test script
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* OESS-98 fix hdf5 link target
The H5ARGS_TRACE macro was added during the async merge. These macros
are updated by the bin/trace script, but conflict with the formatter
so formatted code gets dirtied when autogen.sh is run.
This change enshrines the bin/trace output as canonical and adds
comments to turn clang formatting off for those lines containing
H5ARGS_TRACE.
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* Update other test machines
* OESS-98 fix tools test for plugins
* HDFFV-10865 performance improvement for java array
All outputs depenancies need to be listed for
the custom command.
ninja: error: 'cmake_object_order_depends_target_hdf5-shared_DEBUG', needed by 'Modules/ThirdParty/HDF5/src/itkhdf5/shared/H5Tinit.c', missing and no known rule to make it
* Add H5Fwait, H5Dwait, and other changes for async vol connector
* Revert temporary testing changes
* Add H5Fwait to header file
* Add H5VLreset_lib_state() routine.
* Correct VOL wrap context when retrieving library state for file open & create.
* Manage the API context's VOL connector state as part of the library state.
* Set the 'VOL connector property valid' flag when restoring the library state.
* Don't push new API context on stack when retrieving "current" one.
* Check for NULL VOL wrap context before decrementing refcount on it, when
freeing the API context state.
* Manage recount of underlying connector for VOL wrap context.
* Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and
release the global lock on the HDF5 library.
* Update library with new functions related to library global lock
* Add asynchronous token API
* Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the
threadsafety (H5TS*) routines.
* Sync w/develop
* Initial event set code framework.
* Elaborate on the H5ES routines, starting to add API routines.
Update the "close ID" callbacks to allow asynchronous request tokens to be
passed in from an asynchronous close API call.
Refactor current asynchronous API routines (H5Fopen/H5Fclose and
H5Dread/H5Dread) to use event sets instead of directly working with request
tokens from the application.
Clean up a few other minor warnings & code style issues.
* Implement H5EScreate, H5ESget_count, and H5ESclose.
It should be possible to write a simple application that creates an event
set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and
H5Fclose_async, then calls H5ESclose (which waits for all async events to
complete).
* Add source file for event set test.
* Refactor sync & async API routines to call common routine.
Move dataset API read / write routines to src/H5D.c, along with all the other
API routines.
Progress on "fake" async VOL connector, for testing.
* Modify async implementation to wrap async requests in a H5VL_object_t
struct so the VOL layer can find the connector when accessing the
request at a later point.
* Free the requests is H5ESclose. Remove comments implying that request
wait, notify, and cancel callbacks should free the request.
* Fix bug in error handling in H5Fclose.
* Fix bugs in async file routines. Rename H5VL_create_object_generic to
H5VL_create_object.
* Add explicit async version of H5Fcreate.
* Add more _async routines
* Correct typo for return value from H5Awrite changes
* Add H5EStest and H5ESwait routines
* Updated with API tracing info
* Fix NULL pointer dereference in H5ES__wait
* Add H5is_library_terminating() routine, so that VOL connectors can detect
when the library is shutting down.
* Fix typo
* Remove event from event set's linked list
* Move block of code so that vol_obj is valid
* Avoid setting properties in the DXPL when reseting the library state (and in
the test code).
* Refactor argument tracing to implement new capability for tracing arguments
of non-API routines, with the H5ARG_TRACE macro. This macro is updated
automatically with the bin/trace script that runs as part of the autogen.sh
process. Major changes were in src/H5trace.c and bin/trace, with the other
changes being cleanups to the argument lists, to improve their presentation
in the tracing output.
Also - added the "managed string" routines, which can dynamically allocate
strings, appending printf-formatted output to the string efficiently.
* Release memory for managed strings
* Fix printf() formats.
* More printf() format fixes.
* Add H5Eappend_stack routine and regression tests
* Clean up a few missed merge conflicts and update the error stacks.
* Remove unnecessary fork() operations and ten second sleep().
* Restore commented out attribute out, to better enable tracking down the previous failure
* Allow multiple H5ARG_TRACE macros within a routine to be updated
* Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert.
* Merge "managed" string routines into "ref-counted" strings, and refactor code to use them.
* Add missing file.
* Add caller's name and arguments to event, for error reporting
* Refactor event set setup for "API common" internal routines
* Checkin async API routines for H5A* and H5G* modules as listed in ID-283.
Fix couple h5dump expected output files due to the changes.
* Add some of the error query routines needed for event sets.
* Refactor to make async setup / teardown and "common" routines cleaner
* (1) Add async APIs to H5L, H5F, and H5D modules
(2) Fix errors in previous checkins of async APIs in H5A and H5G modules
(3) h5dump expected output changes
* Enhance event info, for better error handling
* Change name of temporary vol_obj variable, to help reduce coding errors
* Fix oversight with vol_obj pointer
* Minor code cleanup
* Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state
* Run source formatter
* Change H5TSmutex lock and release to include a lock count
* Update error reporting ideas
* Minor updates to improve sanity checking for retrieving / restoring library state
* Updated with feedback from h5py team members
* Refactor internal event set list and event handling, add implementation for H5ESget_err_info
* Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines.
* Update API tracing for new H5VL_request_status_t typedef
* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure
* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation
* Remove 'canceled' event status from Java constants
* Be safer about releasing resources when inserting a newly opened/created object or file into an event set
* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".
* Remove H5ES_STATUS_CANCELED from Java wrappers also
* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.
* Corrections based on PR feedback.
* Further changes to make based on PR feedback.
* Fix missed merge marker, and reformatted line
* Clean up some warnings
* Correct level of indirection
* Relocate prototype (and doxygen info) for H5Aclose
* Change non-static function declarations to be static
* Ensure that H5TSpublic.h header gets installed (#129)
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c.
* Add H5Iregister_future routine and tests.
* Correct return value for H5Lexists_async
* Add H5_DLL macro to public H5ES API routines
* Update supported -> flags parameter for introspect_query callback
* Remove my email address. Update passthrough VOL connector ID.
* Fix comment for post_open_api_common
* Remove unused non-blocking VOL connector
* Minor cleanup in async branch in preparation for merge to develop
* Update CMake and the Autotools to use the new pass-through VOL ID
* Fix for SWMR daily test failures (#160)
The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.
* Added selective async APIs (#150)
* Added selective async APIs
Description:
Added the following APIs:
H5Ropen_attr_async
H5Ropen_object_async
H5Ropen_region_async
H5Mcreate_async
H5Mopen_async
H5Mput_async
H5Mget_async
H5Mclose_async
H5Tcommit_async
H5Topen_async
H5Tcopy_async
H5Tclose_async
- Updated an expected output file to include a new internal function
in the error stack for the failure case.
* Updated async APIs per reviews, including removing async version of
H5Tcopy.
* Removed statements that were added by mistake in the previous commit.
* Fix compile issues in H5M and warnings elsewhere
* Reformat code
* Brings VOL_LIST changes from develop. (#163)
Co-authored-by: Houjun Tang <htang4@lbl.gov>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
The VOL_LIST variable used in the Autotools was duplicated in many
subdirectories. It's been moved to config/conclude.am to avoid
duplication. VFD_LIST was also moved to conclude.am.
* (fix) Segmentation fault when using a compound type.
In the case when a compounded attribute is written to dataset
followed by writing the data with a data transform function
to the dataset will result in a segmentation fault. It turns out
the data is classified as compounded while it is not. Now, the
state is always reset first to not compounded followed by the
existing check if the variable is compounded.
* (fix) Removed undesired comment lines.
* (fix) Segmentation fault when using a compound type: added test.
* (fix) Added the missing cmpd_transform.c file to MANIFEST.
* (fix) cmpd_dtransform test: autotools and source header.
Added the cmp_dtransform test to the autotools configuration and
updated the HDF Group copyright header.
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Fixes clang debug optimization level w/ Autotools
NOTE: This was only released in HDF5 1.10.7, so only the 1.10
branch needs a note in RELEASE.txt.
* Updates the clang -Og setting with a version check w/ autotools
* Sets -Og when clang >= 4.0 or Xcode >= 9.0
* Older versions get -O1
* Autotools only
* (fix) H5Z_xform_create function and scientific notation
Implemented a more sophisticated check to support scientific notation
in the expression of the H5Zset_data_transform function.
* (fix) H5Z_xform_create and scientific notation: Added test.
Added a test to demonstrate that the parsing of expression
which includes scientific notation works correctly. Improved
inline comment.
Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Add H5atclose and H5is_library_terminating routines.
* Add brief Doxygen comment for H5_atclose_func_t typedef.
* Added /*out*/ flag to parameter list, for the tracing script.
* Update doxygen comment for H5atclose with additional detail.
* Return FAIL for H5is_library_threadsafe and H5is_library_terminating when their parameters are NULL.
* Expand ID dec_ref and close callbacks to allow for asynchronous close operations.
* Fix typo
* Rename token -> request, remove programmer name
* H5E_ATOM to H5E_ID
* Renames H5I_ATOM to H5I_ID, among other related changes
* Java has been updated.
* Fortran is failing on my VM, even though I don't touch that.
* Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes
* Fixes typos in comments
* Updates to allow autotools builds on recent FreeBSD
* Switches the default C compiler to cc from gcc
(this may need a version string check if we want to support
FreeBSD 9 and earlier. FreeBSD 10 was released in 2014)
* Makes the default C++ compiler c++ (no previous setting)
* Both of these resolve to Clang on FreeBSD 10+
* Added a note about flang being unsuitable on FreeBSD
(the port uses an ancient build of flang that lacks Fortran
2003 support)
* Autotools only - CMake appears to use different CPP flags
which cause compilation errors
* Adds a RELEASE.txt note for new FreeBSD autotools changes
Enhance API tracing to handle more types, and to put tracing info in a string, allowing it to be used when reporting errors. Also refactor ref-counted strings (H5RS) module to add capabilities needed for the tracing. Refactored H5Gname.c routines to use new H5RS routines also. Added /*out*/ tags to API routines that are returning information to the application. Updated H5TRACE macros from running updated trace script over library code. Added tests for new H5RS routines.
* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Migrated documentation for SWMR functions.
* Catching up on MDC functions.
* Integrated the H5F MDC function documentation.
* Added MDC and parallel H5F functions.
* Slightly updated main page.
* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Revert "Switch ID code to use a hash table instead of a skip list (#52)"
This reverts commit a50d211755.
* H5I_id_type_t and H5I_class_t are no longer managed via free lists
* Fixed commenting issues
* Naming and commenting cleanup in H5I.c
* H5I cleanup
* Header cleanup
* Commenting
* More uniform naming
* Renames H5I_id_type_t and related in H5I.c
* Adds gcc pragmas to ignore H5I const casting
* Split H5I code into multiple files
* Rename id_type to simply type in H5I code
* Minor typo in H5Itest.c
* First cut of the H5 public API documentation.
* Added H5Z "bonus track."
* Applied Quincey's patch.
* Added the missing patches from Quincey's original patch.
* H5PL (complete) and basic H5VL API documentation.
* Added H5I API docs.
* Added H5L API docs.
* First installment from Elena's H5T batch.
* Second installment of Elena's H5T batch.
* Final installment of Elena's H5T batch.
* Brings hash table ID code over from Bitbucket branch
* Includes reformatting via clang.
* Excludes uthash.h from reformatting.
* Still has the failing test issue in tid.c. This should only be a
problem if a custom ID type is used and its free function deletes
other IDs.
* Fixes munged H5_GCC_DIAG_ON/OFF macros in H5I.c
The H5_GCC_DIAG_ON/OFF macros used to turn off fallthrough warnings
in uthash.h (external code) were munged when formatting with clang
due to their lack of quotes.
e.g.;
H5_GCC_DIAG_OFF(implicit-fallthrough)
was munged to:
H5_GCC_DIAG_OFF(implicit - fallthrough)
which compiles, but is useless. So, with quotes, this is now:
H5_GCC_DIAG_OFF("implicit-fallthrough")
which survives reformatting with clang.
* Fixes issues with user callbacks in the ID hash tables
The skip lists (previously) used to handle IDs use a mark-and-sweep
scheme to deal with user-defined ID delete callbacks which themselves delete
other IDs in the list. The uthash hash table implementation used to manage
the IDs in this feature branch does not have this ability.
This commit restores the skip lists for non-library ID types in lieu of
significantly modifying the uthash code. The hash tables are used to
manage the library IDs as those do not delete other IDs when they are
closed.
* Adds uthash.h to MANIFEST
* Removes implicit-fallthrough diagnostic disable
Removing -Wimplicit-fallthrough=5 means that the uthash code
no longer raises warnings so the H5_GCC_DIAG_OFF/ON macros
that disabled those warnings have been removed from H5I.c.
* Adds a test to ensure you can delete IDs in the H5Iiterate() callback
- HDFS VFD files now ignored in the Autotools when the HDFS VFD is not
being built.
- All VFD init code uses idiomatic H5I_INVALID_HID instead of -1
or FAIL.
- The HDFS VFD now includes H5FDdrvr_module.h in the right place.
- The HDFS tests in test/hdfs.c no longer pass NULL to VERIFY macros, which
raised warnings.
- Minor tweaks to fix const, unused variables, etc. warnings in
several VFDs.
Description
This is to fix the CVE issue CVE-2018-17432.
h5repack produced a segfault on a corrupted file. This fix modified the
dataspace encode and decode functions per Quincey's suggestion to prevent
the segfault and h5repack only failed for the corrupted file now.
Platforms tested:
Linux/64 (jelly)
Description
This is to fix the CVE issue CVE-2018-17432.
h5repack produced a segfault on a corrupted file. This fix modified the
dataspace encode and decode functions per Quincey's suggestion to prevent
the segfault. h5repack only failed for the corrupted file now.
Platforms tested:
Linux/64 (jelly)
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).
-Wimplicit-fallthrough=3 is added by -Wextra, which we already set.
Bumping the warning level only changes how fall-through comments are
parsed, with level 5 turning off fall-through comments entirely.
This is unnecessary and results in having to do extra work to squash
warnings when included external code uses fall-through.
This change also adds /* FALLTHROUGH */ comments where
H5_ATTR_FALLTHROUGH is used so compilers that don't use attributes
but do respect fall-through comments don't raise spurious warnings.
* Add BEGIN_FUNC / CATCH / END_FUNC to macros
* Remove incorrect trailing '{'
* Update trace script to wrap H5TRACE macros at 110 characters and improve
comments for code that performs this operation.
* Clean up printf-formatting in H5public.h and correct some oversights in the code.
* Reformat with BEGIN_FUNC / END_FUNC handled correctly by clang-format
* Run clang-format on changes.
* Correct H5_SIZEOF_HSIZE_T/H5_SIZEOF_HSSIZE_T macros to match typedef.
* And make the undef value match also.
* Update comment
* Update clang-format actions to exclude generated files.
* Post-process generated H5LTparse.h file as well as H5LTparse.c file.
* Fix formatting
* Update version of github clang-format action
* h5repacktest VFD fix and formatting changes
* Fix memory leak in H5PL__find_plugin_in_path
When encountering a directory, the current loop iteration was skipped
without freeing the memory allocated for the path.
* Refactor parser GCC diagnostic statements
* genparser on jelly with default bison/flex
Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de>
* commit 'c0fbc5c086566d5d3c1d1ef26baa81a53d59fc08': (24 commits)
Use the right format string, "%zu", for size_t.
Repair more format strings.
Fix a bunch of format string errors reported by Larry.
Fix some HDfprintf compilation errors: use the right format strings ("zu", PRIuHSIZE), avoid casting some printf arguments, pass the right number of arguments.
Test the format string "ll" before "l", "L", and "q", like the ./configure script does. This ought to fix the compilation failure in test/dt_arith.c that Allen told me about:
Cast a non-void pointer to void pointer for "%p".
Use PRIu32 and "zu" formats. Delete some casts from `size_t`.
I'm taking a guess that this code intended to point the 2-digit wide hexadecimal octet values, not 2 character-wide pointers to the bytes. The %02p format, which is a GNU-ism, disagreed with GCC 8.3.0 and the option flags we use.
%08p is not portable, it's a GNU-ism. Use %8p, instead. Squashes a GCC error.
Add format string macros PRI[doxX]HID for hid_t and use PRIdHID.
Use HDva_copy() and introduce a bunch of compatbility format-string constants for uppercase hexadecimal strings, `PRIX...`. Should fix the VS2010 errors that Allen mentioned:
Always #define HDfprintf as fprintf in this header. I believe this will fix the Windows build error that Allen reported.
Provide an HDvasprintf implementation only if it isn't #defined. This should fix the mingw compilation issue that Allen reported.
Fix va_list usage in the vasprintf(3) implementation.
Promote format-string warnings to errors.
Use the portable `-eq` operator instead of the bash-ism `==`. Fixes the tests on NetBSD, where /bin/sh != bash.
Restore a literal percent sign ("%%") that I accidentally deleted.
Fix code that made GCC complain about a NULL or `unsigned char *` arguments for "%s".
Take pains to provide UINT64_MAX in all conditions.
Correct a couple of format strings.
...
* commit '088014bef4216eede409d103876a9fd3efadd358':
More info for building plugins with library
Remove setting from cacheinit file
OESS-98 add release note for option
OESS-98 merge with clang-format changes
* commit '571a5e9250ca69adb54ef956361a5cf77059f67c':
Add h5ls test plugin format target
Fix manifest
Add code owners file
Update actions - split push/pull-request commits
Change to executable
Change to based on LLVM format
Fix comment formatting due to tabs conversion
Disable formatting for file
File changes to affect formatting
CMake and script changes for clang-format
* commit '9b3a3445dbb72a95b2b9355e0196efdaa5b0f452':
Add release note for new H5Ssel_iter_reset function
Add H5Ssel_iter_init API call to reset a selection iterator
./configure script does. This ought to fix the compilation failure
in test/dt_arith.c that Allen told me about:
/home/buildbot/bb-workers/centos8-vm01/hdf5trunk-StdShar-code-centos8/build/hdfsrc/test/dt_arith.c: In function ‘test_conv_int_1’:
/home/buildbot/bb-workers/centos8-vm01/hdf5trunk-StdShar-code-centos8/build/hdfsrc/test/dt_arith.c:2500:34: error: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Werror=format=]
HDfprintf(stdout," %29"H5_PRINTF_LL_WIDTH"d\n", *((long long*)aligned));
* commit '49e01e594eb2d0c25455e7ff71eed3de074fd15b':
Adds RELEASE.txt note about HDFS VFD stubs being removed
Removes inappropriate file locking call
Trivial whitespace change to H5Pencdec.c
Minor refactoring based on 1.10 normalization work
Trivialities noticed while normalizing 1.10
* commit 'ec1c324a0d184d2778e9155140367a7d3a307fa1':
Revert H5_VERS_SUBRELEASE check
Add special case when H5_VERS_SUBRELEASE is 0
Condition if (H5_VERS_SUBRELEASE) is incorrectly false when H5_VERS_SUBRELEASE is 0, a valid value for H5_VERS_SUBRELEASE. Updated to if (${H5_VERS_SUBRELEASE} STREQUAL "") with corresponding reversal of action statements to avoid NOT.
Add hypen to subrelease regex
Fix S3/HDFS test
H5_VERS_SUBRELEASE is 0, a valid value for H5_VERS_SUBRELEASE.
Updated to if (${H5_VERS_SUBRELEASE} STREQUAL "") with corresponding
reversal of action statements to avoid NOT.
* commit '4c43ff0b8b015ccfc1f4aeab18f189d629a5beb9':
Simplify default use of MPI_BYTE
Don't free builtin MPI_BYTE MPI type
Simplify code to avoid using a boolean to free MPI types
Avoid creating MPI datatypes on ranks with 0 chunks to write'
* commit '7b48e3409a8c3ba1e83c929656e84196a6dc2e6d':
Fix a bug in H5D__virtual_write_one to stop an assertion from failing deep in H5Dwrite---project the *clipped* virtual selection instead of the virtual selection:
Description
Added initialization to local structs in the src function
H5MF_settle_raw_data_fsm() and the test function test_bt2_hdr_fd()
to prevent the following error in two different occurrences:
MemorySanitizer: use-of-uninitialized-value
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
* commit 'd00bab96fb4da12a18b5de528c96469978c4c927':
Minor copy edits to comments -- no code changes.
Tab to space conversions.
When flushing, the metadata cache attempts to flush entries in increasing address order. To facilitate this, the metadata cache needs a list of of dirty entries in increasing address order. This is implemented via a skip list of all dirty entries in the cache.
* commit '0d14414ddd860f24f1386771ed3ba8d2f5e2710d':
1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] after AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling
H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS.
2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in
utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools
disabled.
Description:
Updated the original fix by Kent Y. in commit
200a77d8c3
- used internal functions instead of public API
- moved some code into the subroutine for a cleaner look.
- added test to dsets.c
Platforms tested:
Linux/64 (jelly)
Re-applied tab to space conversions accidentally reverted in the
commit of the metadata cache skip list optimization, and performed
some additional tab to space conversions in passing.
Tested parallel / debug on Jelly.
* commit 'c6248cfb6975a6ecadf0259390247ce05dc13c4b':
Addresseda Dana's comments from the pull request.
Fixed several typos in the comments found by Larry during the review.
The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification (HDFFV-10436).
* commit '3f46a380e084d83a84783383bdfbbd9a443e9f27':
Correct typos w/HGOTO_DONE & HGOTO_ERROR
Move H5T_vlen_reclaim to package scope
Switch H5VM inline routines back to single underscope and put a comment in their header about this naming
Clean up private / package / static namespace issues (function naming, which header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* commit 'baf7ebc4ca4eeecb11a607f420a5d5b95169eed5':
Cleans warnings and cruft from ttsafe_attr_vlen.c
Fixes Windows issues due to exposed pthread code
* commit '04b24163f7f08248a58d256371e088c8cc7816c8':
Cleans warnings and cruft from ttsafe_attr_vlen.c
Fixes Windows issues due to exposed pthread code
* commit '4f0283db788fc1a0db94e7825567210021b3b594':
Fixes a size mismatch when copying old-style to new-style references
Fixes memory leads in trefer.c
* commit '5ce2a178043d9749d30076a2e62249d9998c40ec':
Removes staff email addresses from the repository Removes redundant C library headers from hl library
* commit '47ad0ac7237b464e939fe54dd129a151944d9706':
Renames BEST-EFFORT to BEST_EFFORT for file locking env var
Updated the file locking Fortran property list wrappers and added a test.
Fixed missing parens in VFDs
Minor change to header comments in file locking C++ changes.
Squash merge of file locking fixes
* commit '91ca481ff152e7a6b0326fcdb59e506141d2d32a':
Reverts H5FDsplitter.c changes so they don't conflict with Quincey's big cleanup patch
Fixes -Wnull-dereference warnings around the cache logging calls
Fixes -Wnull-dereference warning in hl/src/H5DS.c
Adds -Wnull-dereference to the warnings we ignore in flex/bison generated code (that we have no control over).
Fixes warnings in the splitter VFD and tests
address order. To facilitate this, the metadata cache needs a list of
of dirty entries in increasing address order. This is implemented via a
skip list of all dirty entries in the cache.
To date this skip list has been maintained at all times.
However, profiling indicates that we can avoid significant overhead by
constructing the skip list of dirty entries just before a flush, taking
it down afterwareds, and not maintaining it during normal operation.
This commit implements this optimization for both serial and parallel.
Tested serial and parallel, debug and production on charis and jelly.
* commit 'f59bb712dec221a076728b6c582818bcf814d71a': (55 commits)
Fixes indenting in tools test scripts
Minor normalizations with 1.12 branch
Fixed bad parens in H5trace.c
Minor normalizations with hdf5_1_10
Mingw copy disabled
Warnings reduction in tools
Correct reference file
Correct h5diff filenames
Fixed typos in error messages.
Updated the Java tests to deal with H5Sset_extent_none changes
Fixed additional typos in tselect.c comments.
Fixes typo in tselect.c
Updates H5Sset_extent_none() to set H5S_NULL
Only one line needed to compare
Revert err file
Minor normalization with 1.10 branch
Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
revert error-stack enable
Minor normalization with 1.10.
Add release notes for tools
...
hexadecimal octet values, not 2 character-wide pointers to the bytes. The %02p
format, which is a GNU-ism, disagreed with GCC 8.3.0 and the option flags we
use.
for uppercase hexadecimal strings, `PRIX...`. Should fix the VS2010 errors
that Allen mentioned:
H5system.obj : error LNK2019: unresolved external symbol va_copy referenced in function HDvasprintf [C:\autotest\hdf5trunk-StdShar-code-vs10\build\ctest\hdfbld\src\hdf5-shared.vcxproj] 2 ..\..\..\hdfsrc\test\h5test.c(2103): error C2146: syntax error : missing ')' before identifier 'PRIX64' [C:\autotest\hdf5trunk-StdShar-code-vs10\build\ctest\hdfbld\test\hdf5_test-static.vcxproj]
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: 5c911d8f907b51
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:33:54 2019 -0600
Merge pull request #2055 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: b8a567162208b0
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 16:58:27 2019 -0600
Merge pull request #2030 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.
The HDF Group encourages community members to contribute to the HDF5 project. We accept and are very grateful for any contributions,
from minor typos and bug fixes to new features. The HDF Group is committed to work with the code contributors and make contribution
process enjoyable and straightforward.
This document describes guiding principles for the HDF5 code contributors and does not pretend to address any possible
contribution. If in doubt, please do not hesitate to ask us for guidance.
***Note that no contribution may be accepted unless the donor agrees with the HDF Group software license terms
found in the COPYING file in every branch's top source directory.***
> We will assume that you are familiar with `git` and `GitHub`. If not, you may go through the GitHub tutorial found at
[https://guides.github.com/activities/hello-world/](https://guides.github.com/activities/hello-world/). This tutorial should only take
around 10 minutes.
## Table of Contents
* [Workflow](#workflow)
* [Acceptance criteria for a pull request](#criteria)
* [Release Note](#releasenote)
* [Check List](#checklist)
# Workflow <A NAME="workflow"></A>
The process for contributing code to HDF5 is as follows:
* Open an issue on [HDF5 GitHub](https://github.com/HDFGroup/hdf5/issues).
> This step is ***required*** unless the change is minor (e.g., typo fix).
* Fork the [HDF5](https://github.com/HDFGroup/hdf5) repository.
* Make the desired changes to the HDF5 software.
* New features should always go to _develop_ branch first and later should be merged to the appropriate maintenance branches.
* Bug fixes should go to all appropriate branches (_develop_ and maintenance).
* Build and test your changes. Detailed instructions on building and testing HDF5 can be found in the `INSTALL*` files in the `release_docs` directory.
* Push your changes to GitHub.
* Issue a pull request and address any code formatting and testing issues reported.
Once a pull request is correctly formatted and passes **ALL** CI tests, it will be reviewed and evaluated by The HDF Group developers and HDF5
community members who can approve pull requests. The HDF Group developers will work with you to ensure that the pull request satisfies the acceptance
criteria described in the next section.
# Acceptance criteria for a pull request <A NAME="criteria"></A>
We appreciate every contribution we receive, but we may not accept them all. Those that we *do* satisfy the following criteria:
* **The pull request has a clear purpose** - What does the pull request address? How does it benefit the HDF5 community?
If the pull request does not have a clear purpose and benefits, it will not be accepted.
* **The pull request is documented** - The HDF5 developers must understand not only *what* a change is doing, but *how* it is doing it.
Documenting the code makes it easier for us to understand your patch and maintain the code in the future.
* **The pull request passes HDF5 regression testing** - Any issue fixed or functionality added should be accompanied by the corresponding
tests and pass HDF5 regression testing run by The HDF Group. We do not expect you to perform comprehensive testing across multiple platforms
before we accept the pull request. If the pull request does not pass regression testing after the merge, The HDF Group developers will work
with you on the fixes.
* **The pull request does not compromise the principles behind HDF5** - HDF5 has a 100% commitment to backward compatibility.
* Any file ever created with HDF5 must be readable by any future version of HDF5.
If your patch's purpose is to modify the HDF5 data model or file format,
**please** discuss this with us first. File format changes and features required by those changes can be introduced only in a new major release.
* HDF5 has a commitment to remaining *machine-independent*; data created on one platform/environment/architecture **must** remain readable by HDF5 on any other.
* For binary compatibility, no changes are allowed to public APIs and data structures in the maintenance releases; new APIs can be added.
* **New features are documented** - Any new features should have proper documentation; talk to us if you have any questions.
* **When to Write a Release Note** - Generally, a release note must be written for every change that is made to the code for which
users might see a change in the way the software works. In other words, if a user might see a difference in the way the software works,
a note should be written. By code we mean the text that will be compiled into one of the company's software products. The code includes
configuration changes and changes to tools users might work with to configure and build our software.
* Notes should be added for known problems. Known problems are issues that we know about and have not yet been able to fix.
* Any change made to address a user-reported problem should be described in a release note.
* A release note does not need to be written for changes to the code that users will not see. Here are some examples. If you add a
comment, you do not need to write a release note describing the comment you added. If you rewrite some code to make it read more
clearly and if there is no change in functionality or performance, then you do not need to write a release note. If you change the
process by which user software is made, you may not need to write a release note since the change was not made to the code.
* Users. We have different kinds of users. A release note may be written to be helpful to
application developers and not system administrators. Users who may find the RELEASE.txt file helpful include the following:
application developers, library developers, and system administrators.
# Release Note <A NAME="releasenote"></A>
* **Entry Syntax**
The release note entry syntax is shown below.
```
- Title/Problem
Problem/Solution
Signature
```
* **Entry Elements** - The elements of the entry - title, problem, solution, and signature - are described in more detail in the table
below. Descriptions of the problem and the solution should be clear without any ambiguities and should be short without losing clarity or specifics.
* **Title** - The title or tag should identify one or more categories that will help readers decide if the entry is something they need to study. Can be combined with the `Problem` element
* **Problem** - Describe the problem and how users might see the problem in a paragraph.
You might also consider the following as you describe the problem:
* Under what specific conditions does this issue arise?
* Under what specific conditions are we sure this issue will not arise?
* For a performance issue, instead of saying something is a performance issue, describe what the performance impact of issue is?
* **Solution** - Describe the solution in another paragraph.
You might also consider the following as you describe the solution:
* What was done to resolve the issue?
* What is the functional impact?
* Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround?
* For a performance fix, how has the performance improved? Links to published documentation would be good.
* **Signature** - Each entry must be signed with the initials of the author, the date in YYYY/MM/DD format, and the JIRA ticket number. The
following is an example entry written by developer Xavier Zolo on April 16, 2014 about JIRA ticket HDFFV-5555: (XYZ - 2014/04/16, HDFFV-5555). The
signature is enclosed in parentheses. JIRA or Github numbers should not be used in the description of the problem or the solution. They are like
abbreviations that customers and external users will not be able to interpret.
# Checklist <A NAME="checklist"></A>
Please make sure that you check the items applicable to your pull request:
* Code
* [ ] Does the pull request have a corresponding GitHub issue and clear purpose?
* [ ] Does the pull request follow HDF5 best practices (naming conventions, code portability, code structure, etc.)? <<TODO: link to the document>>
* [ ] If changes were done to Autotools build, were they added to CMake and vice versa?
* [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
* [ ] Is the new code sufficiently documented for future maintenance?
* [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros)
* Documentation
* [ ] Was the change described in the release_docs/RELEASE.txt file?
* [ ] Was MANIFEST updated if new files had been added to the source?
* [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://docs.hdfgroup.org/hdf5/develop/_r_m_t.html)?
* [ ] Was new functionality documented for the HDF5 community (the level of documentation depends on the feature; ask us what would be appropriate)
* Testing
* [ ] Does the pull request have tests?
* [ ] Does the pull request affect HDF5 library performance?
We want as many contributions as we can get, and we are here to help. Feel free to reach out to us if you have any questions
The daily tests run copies of some of the scripts in this directory from another repository, notably snapshot and runtest. The copies in this directory should work, but are not used in daily tests, though they should be tested occasionally.
Programs run via `autogen.sh` (or the equivalent in CMake) are indicated.
|Program|Purpose|
|-------|-------|
|`buildhdf5`|Convenience script to build HDF5 using the Autotools|
|`checkapi`|Checks if public API calls are used in internal functions|
|`checkposix`|Checks if C/POSIX calls are prefixed with `HD`|
|`chkcopyright`|Checks if files have appropriate copyright statements|
|`cmakehdf5`|Convenience script to build HDF5 using CMake|
|`debug-ohdr`|Examines debug output from `H5O_open/close` to look for open objects|
|`format_source`|Runs `clang-format` over the source files, applying our rules|
|`genparser`|Creates the flex/bison-based parser files in the high-level library|
|`h5cc.in`|Input file from which h5cc is created|
|`h5redeploy.in`|Input file from which h5redeploy is created|
|`h5vers`|Updates the library version number|
|`make_err`|Generates the H5E header files (called in `autogen.sh`)|
|`make_vers`|Generates H5version.h (called in `autogen.sh`)|
|`make_overflow`|Generates H5overflow.h (called in `autogen.sh`)|
|`output_filter`|Used in the tools test code to strip extraneous output before we diff files|
|`restore.sh`|Removes files generated by `autogen.sh`|
|`runbkprog`|Used by CMake to run test programs in the background|
|`switch_maint_mode`|Switches maintainer mode on/off in `configure.ac`|
|`trace`|Adds `TRACE` macros to HDF5 C library source files (run by `autogen.sh`)|
|`warnhist`|Generates compiler warning statistics for gcc/clang when fed output of make|
## TODO
* chkcopyright is currently semi-broken as it doesn't handle the full variety of copyright headers we need. We're leaving it in place, though, in the hopes that someone will update it in the future.
* Extending warnhist to better understand the output of additional compilers/languages would be nice.
# Process each source file, rewriting API functions with updated
# tracing information.
#
my $total_api = 0;
for $file (@ARGV) {
$file_api = 0;
$file_args = 0;
# Ignore some files that do not need tracing macros
unless ($file eq "H5FDmulti.c" or $file eq "src/H5FDmulti.c" or $file eq "H5FDstdio.c" or $file eq "src/H5FDstdio.c") {
unless ($file eq "H5FDmulti.c" or $file eq "src/H5FDmulti.c" or $file eq "H5FDstdio.c" or $file eq "src/H5FDstdio.c" or $file eq "src/H5TS.c" or $file eq "src/H5FDperform.c") {
# Snarf up the entire file
open SOURCE, $file or die "$file: $!\n";
$Source = join "", <SOURCE>;
close SOURCE;
# Make modifications
# Make a copy of the original data
my $original = $Source;
my $napi = $Source =~ s/\n([A-Za-z]\w*(\s+[A-Za-z]\w*)*\s*\**)\n #type
// catch failure caused by the DataSpace operations
catch(DataSpaceIExceptionerror)
{
catch(DataSpaceIExceptionerror){
error.printErrorStack();
return-1;
}
return0;// successfully terminated
return0;// successfully terminated
}
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