* commit 'f4015bed9e7ee43468240e734232f9114b749d4f':
Updated the Java attribute test so that attribute access property lists are created and used correctly.
* commit 'f6ddfd7dda8aa95b33ae89b87c70493d5c644dbe':
Add test cleanup
Need to shift off two arguments
HDFFV-9407 add autotools test
HDFFV-9407 Add test
* commit 'e35effff7da40fa8b0dda273be9bbdfa9c8c3624':
Move pragma statements outside of routines, to make older compilers happy.
Updated H5Tcopy() to get the dataset's datatype through the VOL when that is passed in as the object ID.
* commit '8b00d921d7313cd21947992ab4a007d593c49207':
Updated H5Tcopy() to get the dataset's datatype through the VOL when that is passed in as the object ID.
Updated CMake bulids, too.
* commit '17ae90917856e4cbab5a2f1c597197ee98802fc7':
Update GCC 6 & 7 flags for CMake builds
Move -Wnormalized down into GCC 6.x flags
Add support for GCC 7.x warnings, update warnhist script to account for them, clean up warnings.
* commit 'c24f11070aea56331110628d7645332534e4f227':
Add H5_HLDLL prefix for windows link
HDFFV-10805 cleanup examples and test code
Add missing fortran mods
HDFFV-10805 Fix test of library libinfo
Cleanup possible CMake target conflicts
Correct CMake issues
* commit '2e973f7e12301975f9d8dfdd5534682525554e77':
Fix minor typo in H5S_select_iter_release
Fix memory leak in objcopy test after H5Aread of vlen data
* commit '4d20db43bea4bc4588b20abebef5b0d043dcf31d':
Fixed a problem in the ohdr test where hard-coded strings passed to H5Awrite() triggered -fsanitize failures.
* commit '6a1e9a1fbe9606d0dd3452092cab17794e131e64':
Fixed a problem in the ohdr test where hard-coded strings passed to H5Awrite() triggered -fsanitize failures.
* commit 'c6e21cede788790b39af4a46a8bc15e49e382346':
Yanked qsort assert
Switched to HGOTO_DONE() in the links code.
Updated the HDqsort() macro to ensure we don't pass NULL buffers to qsort(3) in the future.
Fixed a bug in the links code where iterating over an empty group would pass a NULL pointer to qsort(3), which is undefined behavior.
* commit '0a75da70a61d41a0bf20a5c617f3eb678ed0b103':
Yanked qsort assert
Switched to HGOTO_DONE() in the links code.
Updated the HDqsort() macro to ensure we don't pass NULL buffers to qsort(3) in the future.
Fixed a bug in the links code where iterating over an empty group would pass a NULL pointer to qsort(3), which is undefined behavior.
* commit '10535e0376d88e218cab782322bfc06f35835f31':
Reset the other convenience pointer because why no
Fixed a memory bug where a pointer is used after it's been freed.
* commit '8d67b440f7d94f1b191ce154a41685bcaa90fd12':
Reset the other convenience pointer because why no
Fixed a memory bug where a pointer is used after it's been freed.
* commit '712a2a13d8add828d053135a172abb2e819d59ad':
Fixed a warning in H5CX.c concerning incorrect use of freeing VOL connector info.
Add H5S_SEL_ITER_SHARE_WITH_DATASPACE selection iterator creation flag, to share dataspace's selection with iterator (and with caution about not modifying or closing the dataspace while the iterator is open).
Fix misc. typos, etc. from code review
New hyperslab selection routines and new public selection iterator routines.
* commit 'd20139399750246f55c902940987e0048a40c268':
Add H5S_SEL_ITER_SHARE_WITH_DATASPACE selection iterator creation flag, to share dataspace's selection with iterator (and with caution about not modifying or closing the dataspace while the iterator is open).
Fix misc. typos, etc. from code review
New hyperslab selection routines and new public selection iterator routines.
* commit 'dfdc27b04b2e8bcd1985ba90ce6553d8b3805fda':
Fix release notes based on feedback from pull request.
Fix for HDFFV-10800 H5Ocopy failure: The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format version bounds array for fill value message, should be version 3 not 2.
* commit '9ef56483f6447b60cf7568e2022aa5d8f193427c':
Added missing DELETE enum value.
Split VOL connector routines into separate headers: * H5VLconnector.h for terminal connector things * H5VLconnector_passthru.h for passthrough connector things
* commit '04dc4ef436b087cfc45030b9183386598d1b4bae':
Moved h5cc.in and h5redeploy.in from tools/misc to bin directory. They should always be built and installed whether tools are enabled or disabled. Also added Makefile.am to bin to build h5redeploy and to install and uninstall them. h5cc is created from h5cc.in by configure.
should always be built and installed whether tools are enabled or
disabled. Also added Makefile.am to bin to build h5redeploy and
to install and uninstall them. h5cc is created from h5cc.in by
configure.
* commit 'bb5e7822f447b8a175e807e2e7bad5e0192394e5':
Fixed an error string typo
Added H5Fdelete call and VOL support (but no VFD/native implementation).
* commit '0742c15fca95965ed4eb87c6d54f41bb07bd4526':
makefile clean-up
move the vol_info to an optional parameter
added H5Pset_vol
added vol connector
added test for vol_connector
removed H5VL constants
removed VOLL NULL connector and replaced it with native VOL
added connector_name test
added missing files
add tests
added more tests
added missing files
Implemented VOL APIs and C constants, no tests
Implemented VOL APIs and C constants, no tests
initial API impl.
* commit '6e1dc507240fba447c79827897b099e91b9dd5c1':
Add release note for enable-tools and enable-tests options.
Modified Makefile.ams for h5repack, h5watch and gif2h5 to allow disabling tests. Moved h5cc.in from tools/src/misc to src directory to always create h5cc whether or not tools are enabled. Added configuration status of tools and tests to libhdf5.settings.
Add options to enable or disable building tools and tests. The default is enabled for each.
disabling tests.
Moved h5cc.in from tools/src/misc to src directory to always create h5cc
whether or not tools are enabled.
Added configuration status of tools and tests to libhdf5.settings.
* commit '0cf52525d5b45cc7cf6f89267da76b46ffa75f90':
H5A__free() was renamed to H5A__shared_free() and now requires attr->shared to not be NULL.
Fixed a memory issue where unfreed shared attribute dataspace memory tripped an assert in our memory sanity checks.
Fixed a memory issue where unfreed shared attribute dataspace memory tripped an assert in our memory sanity checks.
* commit '931abe94244c94e106835250e2f723f634a61c8c':
Move set (MAX_PROC_COUNT 8) back to HPC options files.
Move check for MPI defined to enable parallel from options scripts in HPC to config/cmake/HDF5options.cmake.
* commit '9557087c0ed7811301610155654bf58d6583e38c':
Minor warning fixes: * Fixed an error return value in H5Aint.c (NULL --> FAIL) * Added H5VL_FILE_GET_FILENO to H5trace.c
Complete rework of H5S__hyper_project_intersection. Addresses VDS performance issues raised in HDFFV-10693.
* commit 'd3e242eba1ba98726ed64b14e75f6adee724bea7':
Minor fixes/improvements for VDS performance improvement (HDFFV-10693).
Refactor H5S__hyper_project_intersection to operate directly on span trees, improving performance and removing the conditionn that the extents be equal.
Refactor H5S__hyper_project_intersection to operate directly on span trees, improving performance and removing the conditionn that the extents be equal.
* commit '8a57a683391eed79aca80a7325ef152bb76ad0a6':
Code improvement Description: Fixed potential division by zero occurrences and changed an assert to if statement. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* H5VLconnector.h for terminal connector things
* H5VLconnector_passthru.h for passthrough connector things
Note that these headers are arranged such that they are included in
hdf5.h so VOL connectors only need to include that. The separation into
multiple headers is mainly for readability.
* commit '6eaef5ebd61b8019f66f51d3fe74ec3c1b1d4f0f':
Reorder lines in HDF5config.cmake so that additions to end of $HPC-HDF5options scripts will take precedence.
updated -E option
remove -M option
added -M HPC to ctest command
fixed missing paralle test
Adding cross-compilation for theta (ANL) and qsub (COBALT) batch controls.
* commit '9406278103a7b72d3eacea9fbeaadbf34bf7e43a':
Reorder lines in HDF5config.cmake so that additions to end of $HPC-HDF5options scripts will take precedence.
Description:
Fixed potential division by zero occurrences and changed an assert to
if statement.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit '8a4f679fda20577c4528977d0ee9a7e4c5bee055':
Combine "collective group and dataset write" and "independent group and dataset read" tests into one test. The second test is dependent on the file created by the first test, and will not pass when run by itself.
* commit '08b009cc4ab2a8d8d289697d6d4688c0e5c53c6e':
Clean up if-else chain.
Remove thread-local copy of hyperslab operation generation value.
Core changes to selection code from the hyperslab_updates branch.
* commit '53ffbf4bf89350b5d6b90c11585f39af94209754':
Cast enum to int, for strict varargs handling.
Refactor group creation parameters to take them out of the group creation property list and pass them as normal function parameters.
Warning cleanup
Refactor link creation parameters from being passing as properties in the link creation property list to vararg function parameters.
Minor cleanups
Refactor attribute creation parameters to move parameters out of creation property list and into function parameters.
A few minor cleanups
Refactor dataset creation parameters out of the dataset creation property list and pass them as regular function parameters.
* commit 'e66bf948a7acba0ddc76239f6d02f17c8b10eb0f':
Fix for split VFD and file cleanup when testing H5Fis_hdf5 and H5Fis_accessible in tfile.c.
Improvements to the H5Fis_accessible() and H5Fis_hdf5() tests in tfile.c. * General code tidying. * Expanded tests to work with multi-file VFDs.
* commit '2c9025dcb96e5445ce878fa9e1d05fca738ae328':
HDFFV-10760 Skipping external_env.c and vds_env.c for CMake to do VOL check and VFD check. Temporarily skipping external_env.c and vds_env.c for VFD check and VOL check in CMake following the example of links_env. Leave them for future work.
* commit '62198c2436ac3787afb49fa990d1ba8204264dba':
Add an 'unwrap' VOL callback, so that connectors can unwrap an underlying object without closing it. (Especially needed for pass-through connectors)
Description:
Added wrappers for H5Pset/get_create_intermediate_group:
// Specifies in property list whether to create missing
// intermediate groups
void setCreateIntermediateGroup(bool crt_intmd_group) const;
// Determines whether property is set to enable creating missing
// intermediate groups
bool getCreateIntermediateGroup() const;
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit 'f42b6ace1899bd1e720bbdf4873e6f6e61bee39b':
Changing output file names to avoid possible conflict during parallel build and test, especially on jelly.
* commit '53a5c3be903ce7c24d02a6bd3a8d9b07a3f82404':
Change the checking to H5I_INVALID_HID in test_attr_dense_rename().
Fix for HDFFV-10579 H5Arename fails when creation order of attributes is tracked. The attribute needs to be removed from the creation order index v2 B-tree before re-inserting the renamed attribute via H5A__dense_insert().
* commit 'b5ef82a1786605ae86502bc82086047720b7d4ca': (21 commits)
Moving the handling of null prefix into H5_combine_path.
Changing the prefix of external file and VDS from empty string to null for performance improvement.
Improving the condition checking of empty string.
Replacing string operation strdup with assignment for empty string.
Adding back links_env.out which I accidentally removed in my previous commit.
Taking out two unnecessary diff output files.
Taking out unnecessary diff files for output.
Adding some comments.
Some coding style changes.
Adding the standard output files for the external_env.c and vds_env.c tests.
Small correction for my previous commit.
Forgot to add external_common.c and external_common.h.
Updated CMake for the splitting of external.c and vds.c.
Minor fix: removal of unnecessary enum values.
Minor fixes: updating the test vds_env.c according to the set up of vds.c.
Left out this file in previous commit.
HDFFV-10658 - setting and getting properties in API context: 1. switched to use the existing H5F_prefix_open_t for enum type; 2. put the common private function used by external.c and external_env.c into external_common.c
This commit basically has the following changes: 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get.
HDFFV-10658: I left out this file in my previous commit.
HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work.
...
* commit '659e212e119b4920d2bd41b397cfb0e958817eba':
Correct set extent operation on VDS to iterate over # of used sub-datasets instead of # of allocated sub-datasets.
* commit '9ee3d472113fc3e66ef34e40a0990ed07a2824bc':
Renamed the HDF5_TEST_VOL option to HDF5_TEST_PASSTHROUGH_VOL.
Renamed the autotools check-vol target to check-passthrough-vol.
* commit 'd7e1464058515d07b838741f65a77977224814de':
Add C++, Java, and FORTRAN wrappers and tests for H5Fget_fileno
Add trace macro.
Add H5Fget_fileno() API routine.
* commit '52276f3713eec584044bc72d4724507848cfeba0':
Modifications based on PR feedback: (1) Add H5Sdeprec.c to src/CMakeLists.txt (2) Add test for H5Sencode1.
Modification for num_elem based on PR feedback.
HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change. This also addresses HDFFV-10255: H5Sencode/decode performance issue.
1. switched to use the existing H5F_prefix_open_t for enum type;
2. put the common private function used by external.c and external_env.c into external_common.c
* commit '3ccc98e256587c43f6ba5a31a2cf9d922f4e1773':
Modifications based on PR feedback: (1) Add H5Sdeprec.c to src/CMakeLists.txt (2) Add test for H5Sencode1.
Modification for num_elem based on PR feedback.
HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change. This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* commit '227b7131d1e4b5edce1c3eecc9a7e7f560363093':
Move dataspace selection-specific coding to the callbacks as preparation for the H5Sencode changes.
* commit '4142d8b7d4ac48cffcc2b92af4a54352b329865b':
Move dataspace selection-specific coding to the callbacks as preparation for the H5Sencode changes.
1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties.
2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables.
3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get.
* commit '5774e451dde6410ab2491acda309c43517a49935':
Add help info
Update for namespace
Add namespace option to dependencies
Correct examples for packaging
HDFFV-10741 - add option to skip tool error stack tests
* commit '844f38c6462f42a9a3a6002de6a4acb0520b8fb7':
Correct entry
Snapshot version 1.11 release 4. Update version to 1.11.5.
Allow option to select NAMESPACE
Correct examples for packaging
* commit 'fe104cc38ffbdb39d3e04da107d86ebfc7e8b622':
Test improvement Description Moved the new tests to a more appropriate test function. Platforms tested: Linux/64 (jelly)
Fixed HDFFV-10210 and HDFFV-10587 Description: - Added parameter validation (HDFFV-10210) - Added detection of division by zero (HDFFV-10587 - CVE-2018-17438) - Fixed typos in various tests Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
* commit 'b66df06dbf607741127137ebfda373890cb37649':
Changes that show the right way to iterate over enums.
Changes that show the right way to iterate over enums.
Used the H5_INC_ENUM macro to squash enum value increment warnings.
Description:
- Added parameter validation (HDFFV-10210)
- Added detection of division by zero (HDFFV-10587 - CVE-2018-17438)
- Fixed typos in various tests
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit '0c20c65e2f3abf390ad87c9167daca4cdff2de39':
Added the HDopen work-around on windows to pio_engine.c
Adds _wopen support on Windows so that files with UTF-8 names can be opened.
Fix issues with direct chunk operations and the single chunk index.
* commit 'c812a6c9ec5ff440dc405167c54b86fdb18dcfa4':
Fix issue with direct chunk write not updating the "last chunk" index cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
(Primarily for use in the async VOL connector, which has to schedule API
operations for future execution and then restore the state of the library when
the operation actually executes)
This implicitly adds support for changing the VOL connector for command-line
tools or any application linked with the library.
Also, add 'make check-vol' support for all directories, clearing up necessary
issues in testing scripts, etc.
* commit '6d07eb126e63b025199a5fe68f41a42269b5921b':
Update standard check
Fix typo
HDFFV-10703 Update version match logic
HDFFV-10703 revert pre-3.11 option
HDFFV-10703 macro vars need quotes
HDFFV-10703 Update CMake commands to latest standard
Use correct variable name
* commit '5ad3891d9b861593ebe25d540bed2d913eb83aba':
Remove ' ' (typo).
Code improvement
Removed an extra "using" statement
Adding documentation
More changes to align with incoming selection improvements.
Added C++ wrapper for H5Ovisit2
Adding a C++ wrapper
C++ wrapper for H5Ovisit2
* commit '6c212353c45ef84b5c977c6019e4d72263534aea':
Code improvement
Removed an extra "using" statement
Adding documentation
Added C++ wrapper for H5Ovisit2
Adding a C++ wrapper
Description:
- Added a wrapper for H5Ovisit2 to class H5Object
// Recursively visit elements reachable from this object.
void visit(H5_index_t idx_type, H5_iter_order_t order,
visit_operator_t user_op, void *op_data, unsigned int fields);
- Fixed various typos in documentation
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit 'b5a4f470cdf7113c0691cca6fb201672c4e1d86d':
Use STREQUAL
Add command to build options and check defines
Skip testing of cache_image test
CMake if statement correction
* commit 'edcbc9966f5c742970ad32eb50a7925fcf7ab677':
Refactor parallel test names
Rename parallel tests to start with PAR_
Distinguish parallel performance tests
Set the full generator name
Add new cmake copy file tests to ignore
Use correct values for other file versions
CMake script changes to simplify execution
* commit '36e3d1600a3f9d771cfb9b4475f23c57d4b10280':
Refactor out timeout values
Correct name of variable
Remove F2003 Option and references
Remove obsolete file
Update examples version
Update to example reference version
Switch OFF if compression source is not available
Fail configure if SZIP/ZLIB is requested but not found
* commit '7f5741825db0737db5ac46c43009681508a73002':
Add release notes information.
Modification based on feedback from pull request.
Modification based on feedback from pull request.
There is performance issue when closing an object. The slow down is due to the search of the "tag_list" to find out the "corked" status of an object. The fix: (1) Add a counter "num_objs_corked" in the cache structure to track the number of "corked" objects. (2) Skip the search of "tag_list" if the counter is zero i.e. no "corked" objects.
the "tag_list" to find out the "corked" status of an object.
The fix:
(1) Add a counter "num_objs_corked" in the cache structure to track the number
of "corked" objects.
(2) Skip the search of "tag_list" if the counter is zero i.e. no "corked" objects.
* commit '6c2a4b728f3c8eadb18d4e10d41bdbd7d1c8f3e8':
Add LOCAL_BATCH_SCRIPT_ARG variable for submitting account information and other batch command variations with ctest command.
Add batchscript options that work when running ctest directly.
* commit 'c348d453b583ec9092152e6aef1f7fa9854cf5d9':
Correct H5DIFF to PH5DIFF in *ctestS.sl.in.cmake list of parallel tests reserved for *ctestP.sl.cmake. Revise options to run batch tests and alternative options for cross compile in HPC/*-HDF5options.cmake.
Change examples file to zip for CMake zip file.
Update bin/release for filename changes and HPC-CMake tar file corrections.
Add new files to MANIFEST. Update permissions for raybsub to 755.
* commit '055208b71c573be3d4b1047b840d4d8b255bc25e':
Minor tweak to CMake preadwrite entry.
Updated sec2, log, and core VFDs to use pread/pwrite when available (can be controlled via a configure/CMake option)
* commit '5f1f231310bcb3278f11a51e1ea47782f6ee3235':
Updated H5Dio.c comment.
Fixed a valgrind issue with the unprotect log message. The logging call was placed after the point where the cache entry was freed. The fix was to just use the entry's address directly in the log call instead of the entry itself.
Fixed a bug revealed by the dtransform test. A datatype transform buffer needed to be calloc'd.
* commit 'bae744199b69eb7c3f5eda2441cca30cb8c6175f':
Add more specific batch scripts. Add script raybsub to handle submitting .lsf files on ray with bsub < script.lsf syntax that we couldn't handle with CMake. Add hpc-cmake-tgz option for bin/release.
Account info can be submitted as an argument to run the batch scripts. Special versions for sandia are not needed.
Add HDF5options.cmake files for serial and parallel tests on HPC machines (where tests are to be run as batch jobs. Add README_HPC file with instructions for setting up configuration to use batch scripts for running tests on HPC machines and some pointers for cross compiling.
Remove knl configuration from ctestS.sl.in.cmake. Add sandia batch files with account info.
Add batch files with batch parameters specific to cori and ray. Release.txt entry for skipping long double dt_arith tests on ppc64.
Add script raybsub to handle submitting .lsf files on ray with bsub <
script.lsf syntax that we couldn't handle with CMake.
Add hpc-cmake-tgz option for bin/release.
call was placed after the point where the cache entry was freed.
The fix was to just use the entry's address directly in the log
call instead of the entry itself.
machines (where tests are to be run as batch jobs.
Add README_HPC file with instructions for setting up configuration
to use batch scripts for running tests on HPC machines and some
pointers for cross compiling.
* commit '2fe69e7639198b174da393e47a029d0ac35b31c8':
Added test for HDFFV-10588
Fixed HDFFV-10684
Fixed HDFFV-10586 and HDFFV-10588 Description: HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters Added a check for zero value HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper This is actually an Invalid read issue. It was found that the attribute name length in an attribute message was corrupted, which caused the buffer pointer to be advanced too far and later caused an invalid read. Added a check to detect attribute name and its length mismatch. The fix is not perfect, but it'll reduce the chance of this issue when a name length is corrupted or the attribute name is corrupted. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
HDFFV-10586 and HDFFV-10588
* commit '25cd1ab02b9ddaf58a4f5422f4ab4fde411e050a':
Added test for HDFFV-10588
Fixed HDFFV-10684
Fixed HDFFV-10586 and HDFFV-10588 Description: HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters Added a check for zero value HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper This is actually an Invalid read issue. It was found that the attribute name length in an attribute message was corrupted, which caused the buffer pointer to be advanced too far and later caused an invalid read. Added a check to detect attribute name and its length mismatch. The fix is not perfect, but it'll reduce the chance of this issue when a name length is corrupted or the attribute name is corrupted. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* commit 'f033214796c383a9018dd760e92257dc27d7b852':
Add clear objects to ignore tests
Add clear objects to ignore tests
Add new clear tests to ignore list
Cleanup variable names
HDFFV-10685 Correct syntax
HDFFV-10685 Corrected version
HDFFV-10685 Always set Mac version flags - use soversion
Description:
The test for HDFFV-10588 has revealed a bug in H5Ewalk.
H5Ewalk did not stop midway even when the call back function returns
H5_ITER_STOP. This is because a condition is missing from the for
loops in H5E__walk causing the callback functions unable to stop until
all the errors in the stack are iterated. Quincey advised on the final
fix. In this fix, "status" is switched to "ret_value" and HGOTO_ERROR
to HERROR, and the for loops won't continue when "ret_value" is not 0.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
HDFFV-10586 CVE-2018-17434 Divide by zero inh5repack_filters
Added a check for zero value
HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper
This is actually an Invalid read issue. It was found that the
attribute name length in an attribute message was corrupted,
which caused the buffer pointer to be advanced too far and later
caused an invalid read.
Added a check to detect attribute name and its length mismatch. The
fix is not perfect, but it'll reduce the chance of this issue when a
name length is corrupted or the attribute name is corrupted.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '90d13bef33f9e2e80b23996a0c39f16f7c34ecf8':
Fixed typo Platforms tested: Darwin (osx1010test)
Refixed HDFFV-10578 Description: Applied Neil's fix for this issue after removing previous attempt. The resources are now released in init_objs() when failure occurs there. Neil will fix HDFFV-10676 separately. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Removed previous change in H5O__chunk_deserialize().
Removed the previous change in H5O__chunk_deserialize()
Removed previous change in table_list_add().
Removed the previous change in table_list_add()
Updated per review Description: HDFFV-10676 - CVE-2018-13873 Changed the new assert to if statement, per Dana's comment. Platforms tested: Linux/64 (jelly)
HDFFV-10578 and HDFFV-10676 Description: HDFFV-10578 - CVE-2018-17234 The file has some issue, however, there was a bug in h5dump that caused memory leaks after the problem in the file was encountered. The bug was that an if statement was missing in the function table_list_add() resulting in the memory not being freed at a later time. After the fix had been applied, there were no more leaks after h5dump detected the issue in the file and reported the error.
* commit 'b02de315b93ac29d2483a91d526b110a25073505':
NNSA Tri-LabsTRILAB-98: Another two test cases out.
NNSA Tri-Labs TRILAB-98: Taking out a few more test cases.
NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on sierra.llnl.gov: According to the group decision, simply provide a macro to disable some failing test cases on sierra (IBM power9 cpu). All failing cases involve long double data type.
* commit 'b4d4d371a03158c39f120b1bde6c4bd51f1b2eb6':
HDFFV-10443: Add "field" parameter to H5Oinfo* and H5Ovisit* APIs.
Added chunked dataset, H5S_ALL test
typo
typo
updated defined constants
Documented HDFFV-10652
HDFFV-10652 Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
Removed reason for breaking read-proc0-and-bcast
switched to using CX instead of a global var.
HDFFV-10652 Implemented a process-0 read and then broadcast for collective read of full datasets (H5S_ALL) by all the processes in the file communicator.
* commit 'e27df5a5fe365480b0809ce523b0e9cd1096a43d':
Add variables to set up module switch between configure and build for cross compiling on CrayXC40.
Remove install-exec-hook from hl/fortran/Makefile.am. Add check for existing links in hl/fortran/src/Makefile.am.
Configure build directory in batch scripts.
Add libhdf5_hl_fortran symlinks for libhdf5hl_fortran files. Set ctest*.lsf.in.cmake scripts for sierra. Correct src/CMakelists.txt syntax error.
Correct syntax error in CMakeLists.txt.
Add .lsf batch scripts and insert the build directory into the scripts during configuration.
Description:
Applied Neil's fix for this issue after removing previous
attempt. The resources are now released in init_objs() when
failure occurs there.
Neil will fix HDFFV-10676 separately.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
Avoid potential invalid read when decoding unknown object header message.
* commit '685288beabc4f4383d69ec07be05c067fab78544':
Delay checking if decoded message's "shareable" flag is appropriate for the message type until we've verified we understand the message type. Reduce size of H5O_msg_class_g to *not* include space for H5O_BOGUS_INVALID. Make bogus messages shareable. Add new bogus message test with shareable messages to cover the formerly problematic code. Re-run gen_bogus.c to add this test case and also to fix the bogus_invalid messages that were no longer H5O_BOGUS_INVLAID due to a new message class being added in a previous commit. Added comment to remind developers to run gen_bogus.c when adding a new message class.
* commit 'ab5fe769ab711f736238abc89ef215a6ecff5f7e':
HDFFV-10625 -- Implemented a process-0 read and then broadcast for collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
indent change
changed logic statement in if
Added chunking test, fixed issue with CX set
Correct another git merge failure.
Correct misplaced line from git merge.
Updated and refined version of Scot's "rank 0 bcast" changes.
the message type until we've verified we understand the message type.
Reduce size of H5O_msg_class_g to *not* include space for
H5O_BOGUS_INVALID. Make bogus messages shareable. Add new bogus
message test with shareable messages to cover the formerly problematic
code. Re-run gen_bogus.c to add this test case and also to fix the
bogus_invalid messages that were no longer H5O_BOGUS_INVLAID due to a
new message class being added in a previous commit. Added comment to
remind developers to run gen_bogus.c when adding a new message class.
* commit '7bf6d847ae36940f1b1147820356795c7764dbeb':
Remove incorrect comment.
Updated error stacks for h5dump testing.
Corrected comment in src/H5VLint.c, fixed pass-through info size in src/H5VLpassthru.c, switched to stashing VOL connector ID & info in API context (in src/H5CX.c, src/H5CXprivate.h, src/H5F.c, src/H5Fint.c, and src/H5Fefc.c), patched up all sorts of issues in the tests, to make them work with 'check-vfd' (and 'check-vol' again).
Clean up style issues, make function callbacks static, correct debug statements, etc. No functionality changes at all.
* commit 'f0656a57dc3baf02709e1ad5e496cf63cf820877':
Remove incorrect comment.
Updated error stacks for h5dump testing.
Corrected comment in src/H5VLint.c, fixed pass-through info size in src/H5VLpassthru.c, switched to stashing VOL connector ID & info in API context (in src/H5CX.c, src/H5CXprivate.h, src/H5F.c, src/H5Fint.c, and src/H5Fefc.c), patched up all sorts of issues in the tests, to make them work with 'check-vfd' (and 'check-vol' again).
* commit '8a5d2c130a93a665933cda8db8554d006b7ca093':
Clean up style issues, make function callbacks static, correct debug statements, etc. No functionality changes at all.
Description:
HDFFV-10578 - CVE-2018-17234
The file has some issue, however, there was a bug in h5dump that caused
memory leaks after the problem in the file was encountered. The bug
was that an if statement was missing in the function table_list_add()
resulting in the memory not being freed at a later time.
After the fix had been applied, there were no more leaks after h5dump
detected the issue in the file and reported the error.
In H5O__chunk_deserialize, replaced an assert with an if statement
and reporting error, per Neil's recommendation
HDFFV-10676 - CVE-2018-13873
Also in H5O__chunk_deserialize, added an assertion to detect
out of bound ids
src/H5VLpassthru.c, switched to stashing VOL connector ID & info in
API context (in src/H5CX.c, src/H5CXprivate.h, src/H5F.c, src/H5Fint.c, and
src/H5Fefc.c), patched up all sorts of issues in the tests, to make them work
with 'check-vfd' (and 'check-vol' again).
* commit '0e34f0feaaeb6d2286f87f695f25fae45c070a42': (26 commits)
HDFFV-10664 update reference file
HDFFV-10664 update reference files
HDFFV-10664 add missing function and check for restriction
Remove "bad" statements at end of TEST_ERROR. Formerly arguments to FAIL_PUTS_ERROR
Add RELEASE.txt entry for HDFFV-10596.
Add semicolon at end of TEST_ERROR() invocation for consistency.
Uninstall should remove the libhdf5_hl_fortran links.
Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files.
Change FAIL_PUTS_ERROR to TEST_ERROR.
Cleaned up the parallel flush test and set t_pflush1 to always fail. Also set CMake to handle this.
Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2.
Removed a comment.
Fix comment
Align H5Lcreate_ud behavior with documentation for NULL udata pointer
Update toolchain comment
Use c99 standard cmake variable
Add PGI toolchain
Correction based on code review.
HDFFV-10664 add check for state before set call
HDFFV-10546 refactor variable name
...
* commit 'f4c9ec5d41aa53829617274d3286f1e9a45ae57e':
Add RELEASE.txt entry for HDFFV-10596.
Uninstall should remove the libhdf5_hl_fortran links.
Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files.
* commit 'f7115c31363e80e850c0a228e63a5a035c48b74a':
Remove "bad" statements at end of TEST_ERROR. Formerly arguments to FAIL_PUTS_ERROR
Add semicolon at end of TEST_ERROR() invocation for consistency.
* commit 'd59aa1d75cb6d0ae4f5964d017e275aa53394eb6':
Cleaned up the parallel flush test and set t_pflush1 to always fail. Also set CMake to handle this.
* commit '763db8178e673fdcae4a370fe2e6d345f905d5f1':
Change FAIL_PUTS_ERROR to TEST_ERROR.
Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2.
Merged to catch daily test.
* commit '40c55f24ecbdd322fba527d768689fbdbd268374':
Removed a comment.
Fixed documentation - typo only
Fixed CVE division-by-zero issues Description: Fixed HDFFV-10577 and similar issues found in H5Dchunk.c. All the occurrences are in: H5D__create_chunk_map_single H5D__create_chunk_file_map_hyper H5D__chunk_allocate H5D__chunk_update_old_edge_chunks H5D__chunk_prune_by_extent H5D__chunk_copy_cb H5D__chunk_collective_fill Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* commit 'ed0c468902409ae7fa8fb91c5f5a3a3093846736':
HDFFV-10664 add check for state before set call
HDFFV-10546 refactor variable name
HDFFV-10664 minimized dataset headers for java interface
* commit 'd3dff6efe6f769b219f9dcccebd057afe75ed3c7':
Correction based on code review.
Changes based on feedback from pull request.
Fix for HDFFV-10659: The library abort with "infinite loop closing library" after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
* commit 'af21ce90d9465e805807f17da21f93e64e03492a': (46 commits)
Changed to Unix line endings and chmod -x.
Fix runtest case for data to stdout in tool
Updated the parallel install docs.
Eliminated the need for a separate script variable.
Flipped swapped testing strings.
Specify variable type. Remove unnecessary whitespace.
Added test_vol_plugin.sh to the list of scripts to clean
Fixed a CMake build issue (CMake still doesn't run the VOL plugin tests)
Added more sub-tests to the VOL plugin test.
Added a simple test for registration of VOL connector plugins. Autotools only for right now, but this will be fleshed out in future work.
OHDR tests now accept h5_fileaccess() fapls. Formatting, informative comments, and minor renaming.
Fix some CMake listings
Add error checking to the minimized dset header size calculation. Update printf->HDprintf statements.
Remove `#if 0` block of deprecated code.
Fix mistake with H5E_BEGIN_TRY {...} H5E_END_TRY block containing ERROR-raising macros. Formatting tweaks.
Added a helpful message to the flush script.
Added a shell script so we can run the parallel flush test on OpenMPI.
Add "compact" storage test to relative header size comparisons.
Formatting adjustments.
Formatting adjustments
...
* commit 'b30a1fe44aa804a67f2291005bf8135ac5c2dc99':
Updated the parallel install docs.
Eliminated the need for a separate script variable.
Added a helpful message to the flush script.
Added a shell script so we can run the parallel flush test on OpenMPI.
* commit 'd6c2a96ac2f103d90b96d5b39814810e6a31ef99':
Updated the parallel install docs.
Eliminated the need for a separate script variable.
Added a helpful message to the flush script.
Added a shell script so we can run the parallel flush test on OpenMPI.
* commit '3ca19cca5395d79be69209f8d7d0a2b06834a648':
Flipped swapped testing strings.
Added test_vol_plugin.sh to the list of scripts to clean
Fixed a CMake build issue (CMake still doesn't run the VOL plugin tests)
Added more sub-tests to the VOL plugin test.
Added a simple test for registration of VOL connector plugins. Autotools only for right now, but this will be fleshed out in future work.
Dataset object header minimization
Jira TRILAB-45
* commit 'f54fb420d08ea0a7e7b026150c0ab559803e0acd': (34 commits)
Specify variable type. Remove unnecessary whitespace.
OHDR tests now accept h5_fileaccess() fapls. Formatting, informative comments, and minor renaming.
Fix some CMake listings
Add error checking to the minimized dset header size calculation. Update printf->HDprintf statements.
Remove `#if 0` block of deprecated code.
Fix mistake with H5E_BEGIN_TRY {...} H5E_END_TRY block containing ERROR-raising macros. Formatting tweaks.
Add "compact" storage test to relative header size comparisons.
Formatting adjustments.
Formatting adjustments
Move H5Fset_dset_no_attrs_hint VOL operations to native. Move minimzied object header tests from separate file to test/ohdr.c Some formatting changes.
Re-format test/ohdr_mindset.c Fix a few transcription errors in other test files.
formatting adjustments
Reformat to be more consistent with existing code. Fix a few typos.
add missing paramter - macro seemingly unused, but absence results in compiler complaint
fix reference; move declaration in file
Remove unused debugging print in '#if 0' block
Fix typo. Fix CHECK of wrong ID (dset[2|3]_id).
change test file name and apply 'h5_fixname' to it
Sidestep and hide&flag minor issues causing test failures.
Incorporate minimized dset ohdr tests into extant suite.
...
after deleting attributes in densed storage.
The fix: When deleting attribute nodes from the name index v2 B-tree,
if an attribute is found in the intermediate B-tree nodes, which may be
merged/redistributed in the process, we need to free the dynamically
allocated spaces for the intermediate decoded attribute.
* commit 'b4fe787bb9fe4bfc4709a124df59dd987c9a09d2':
Add test for H5Arename NULL/empty attribute name fix
align H5Arename behavior with H5Arename_by_name
Description:
Fixed HDFFV-10577 and similar issues found in H5Dchunk.c. All
the occurrences are in:
H5D__create_chunk_map_single
H5D__create_chunk_file_map_hyper
H5D__chunk_allocate
H5D__chunk_update_old_edge_chunks
H5D__chunk_prune_by_extent
H5D__chunk_copy_cb
H5D__chunk_collective_fill
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '991996b25122ff010b9af1bbb6cc05be491ce038':
Remove unused CMake files
Update option text
Add reference file to list
HDFFV-10656 remove moved source
HDFFV-10656 Add CHECK_VOL support to CMake
* commit '75a03ea0c36f24a6a3982b75a8c52325879bb569':
Moved private native VOL connector functions to H5VLnative_private.h.
Moved the remainder of the code into separate files.
Split the native VOL connector code into multiple files and moved the attribute code over.
* commit '70c8c629ce1d7b1eb98220135ddcca1bf9c5b7fc':
Added missing H5O calls.
Fixed a missing H5R call.
Made hbool_t processing consistent in va_lists.
Fixed an enums-in-va_list issue in the passthru VOL connector.
Updated enums in VOL va_lists to be passed as ints.
* commit '3597bd469ff0073134b31765d9b87660cd3e0039':
Revert change to MSC_VER, in favor of Dana's
Remove H5VL_FILE_CACHE_VOL_CONN from file specific callbacks, as it turns out not to be necessary.
* commit 'e21c1cf7c6ee6dba5dd5bfd1a525227ac1304b53':
Removed H5I_REFERENCE from the library. It has always been unused and has been marked 'deprecated' since 1.10.0. Fixes HDFFV-10252.
* commit 'a7618f432b671ad041ae63a83bf9b9bb08096dbe':
Updated with extra sanity check and improved comment.
Fixed an issue in the passthru Windows va_copy hack.
* commit '9f175afce8c08bf6193e45ce391e05e4198dd61c':
Updated va_arg-->HDva_arg in the native VOL connector.
Added HD to va_* calls in a couple of library files.
* commit 'b0457117d867d9850d042d7c3f71a747899b932e':
Further va_list improvements.
Added a helpful comment to the va_copy() Windows hack.
Added a work-around for va_copy() on pre-2013 versions of Visual Studio.
* commit '9ae9b3ef513613bb2fca15f96461a156148c2627':
Moved the native VOL connector's optional enums to the public headers and renamed to include native/NATIVE in the name.
* commit '50ca26f3ec428de408040335f2a2999e750d98b3':
Updated the passthru VOL connector: * snprintf --> sprintf (for Windows compat) * tabs --> spaces * removed spurious parens from returns * Changed the logging macro to something less clash-prone
Make sure to free copy of VOL connector's name when H5VL_register_connector fails
* commit '833a4f73fd8dc696f8bf500cd842d88949bb1519':
Fix plugin code from referencing invalid key ID value, and also switch from strtok() to strtok_r() to avoid possible interference with / to application use of strtok().
* commit '76c0d8c434186107176fc83a0ce4e94b584196ae':
Add test for H5Aget_info(_by_name/_by_idx) NULL info pointer
align H5Aget_info behavior with H5Gget_info when null attribute pointer is supplied
* commit 'deb7d2fb9714acc8222815328f71b0aae7e74275':
Use version 2 functions in test file to address compile errors for --with-default-api-version=v16 option.
* commit '139a12d13cda046fd3cd64a4f097eb3485f50173':
HDFFV-10632 correct number
HDFFV-10632 stder/stdout change note
Add stamp files for generated files
HDFFV-10632 update autotools test scripts to match cmake
HDFFV=10632 test cleanup
Fix special macro stdout as empty
Need nonexistent file to skip stdout compare
HDFFV-10632 - split stderr and stdout in cmake
* commit '4643860aa940fb52da251f7023ec2e48d7d10f34':
HDFFV-10635: Some minor changes to the test case and the comments in the library.
HDFFV-10635: add a test case.
HDFFV-10635: Allowing to write the same variable-length element more than once.
* commit '3e8599591504c95d8a97100b9546174f6132dc97':
HDFFV-10635: Some minor changes to the test case and the comments in the library.
HDFFV-10635: add a test case.
HDFFV-10635: Allowing to write the same variable-length element more than once.
* commit '7796cbd4174e85aa211dbffa562ada7413f1dbf7':
Fix build errors VOL changes, when using --disable-deprecated-symbols.
Removed RELEASE.txt entry concerning --enable-debug/production configure flags as those changes were pushed to HDF5 1.10.
Remove reference to h5_vol_external_log_native.
* commit 'dd23dac577c70d7fc0aa3fe21c1ebf52a18975d2':
Removed RELEASE.txt entry concerning --enable-debug/production configure flags as those changes were pushed to HDF5 1.10.
* commit '55e87e5b86aacbb37c57614cd2e869541291caad': (51 commits)
Correct Windows build.
Refactor allocating & releasing pass through wrapper objects.
Fix typo
Remove duplicated comment.
Add a couple of missing prototypes for static routines, along with updating a comment from VOL plugin -> connector.
Switch H5VL_class_value_t from unsigned to int, and add "invalid" ID value.
Correct "make check-vol" regression test target.
Switch H5VL_class_value_t from enum to unsigned integer
Add support for "make check-vol", along with a few minor cleanups, etc.
Refactor infrastructure for setting FAPL information from environment variables during testing, including connecting native, pass-through, and dynamically loaded VOL connectors. Also bring native and pass-through VOL connectors into alignment, removing the "H5VLnative_private.h" header.
Remove example VOL connector, since it's been superceded by the pass-through VOL connector in the src subdirectory.
Add pass-through VOL connector
Update API tracing info for VOL functions and regenerate trace macros for VOL API calls.
Added 'notify' callback for async requests; switched VOL class and info comparison to return comparison value as parameter, so they can return error values; "cancelled" -> "canceled"; switched order of 'wrap_object' and 'free_wrap_ctx' management callbacks.
Add using FAPL from h5_fileaccess() to more tests.
Remove unused test for unimplemented routine.
Switch loc_params to VOL callbacks to pass struct by pointer instead of by value.
Add info_to_str and str_to_info "management" callbacks for serializing and deserializing a connector's info object.
Revert some of the changes to support the original property list value of metadata read attempts.
Add VOL connector info to the flie access property list returned from H5Fget_access_plist(). Also, other misc. cleanups, etc.
...
* commit 'c58d84e721ef9fbda63abc834767a28dc978d121': (50 commits)
Refactor allocating & releasing pass through wrapper objects.
Fix typo
Remove duplicated comment.
Add a couple of missing prototypes for static routines, along with updating a comment from VOL plugin -> connector.
Switch H5VL_class_value_t from unsigned to int, and add "invalid" ID value.
Correct "make check-vol" regression test target.
Switch H5VL_class_value_t from enum to unsigned integer
Add support for "make check-vol", along with a few minor cleanups, etc.
Refactor infrastructure for setting FAPL information from environment variables during testing, including connecting native, pass-through, and dynamically loaded VOL connectors. Also bring native and pass-through VOL connectors into alignment, removing the "H5VLnative_private.h" header.
Remove example VOL connector, since it's been superceded by the pass-through VOL connector in the src subdirectory.
Add pass-through VOL connector
Update API tracing info for VOL functions and regenerate trace macros for VOL API calls.
Added 'notify' callback for async requests; switched VOL class and info comparison to return comparison value as parameter, so they can return error values; "cancelled" -> "canceled"; switched order of 'wrap_object' and 'free_wrap_ctx' management callbacks.
Add using FAPL from h5_fileaccess() to more tests.
Remove unused test for unimplemented routine.
Switch loc_params to VOL callbacks to pass struct by pointer instead of by value.
Add info_to_str and str_to_info "management" callbacks for serializing and deserializing a connector's info object.
Revert some of the changes to support the original property list value of metadata read attempts.
Add VOL connector info to the flie access property list returned from H5Fget_access_plist(). Also, other misc. cleanups, etc.
Switch tool error output to match VOL changes within library
...
variables during testing, including connecting native, pass-through, and
dynamically loaded VOL connectors. Also bring native and pass-through
VOL connectors into alignment, removing the "H5VLnative_private.h" header.
comparison to return comparison value as parameter, so they can return error
values; "cancelled" -> "canceled"; switched order of 'wrap_object' and
'free_wrap_ctx' management callbacks.
* commit '8cf3bfb14bd2a80f13d269a9e84cd99f86f19254':
Yanked all MPI-1 calls
Updated H5S to use the MPI-2 function MPI_Type_get_exten() where available. OpenMPI 4.0 removed the deprecated MPI-1 MPI_type_extent() call by default, so this avoids needing a special OpenMPI build.
* commit 'd517bdf9d36f423e7abad34e109b6ce694fd03c8':
Pulled the RELEASE.txt note concerning HDFFV-10633 since that change was pushed to hdf5_1_10 in case we release the Windows VFD in 1.10.5.
* commit '7bf6e98bd921c4ef1899144ab8a1f0d66a141141':
Move wait_H5init.cmake up to config/cmake.
Changes to CMake code to pause cmake/ctest, waiting for batch jobs to run and finish.
Really don't run parallel tests without option specifying script.
Add script and changes to wait for H5Tinit.c Add more sample batch scripts, specifically for sbatch, not for knl cross compile. Don't run parallel tests when no parallel test script is configured in HDF5options.cmake.
* commit 'c923cdad6e515c842f3795a5b6d754ad94021e09':
HDFFV-10571: Minor format changes.
HDFFV-10571: Minor change - reformatting the error check.
HDFFV-10571: Minor change - adding the error check right after decoding of chunk dimension for safeguard.
HDFFV-10571: Minor change - revised the comment to be clearer.
HDFFV-10571 Divided by Zero vulnerability. Minor fix: I added an error check to make sure the chunk size is not zero.
* commit '4f5a52e595194562644517b7600f3b96d4008c17':
HDFFV-10601: Adding the new hdf5/tools/test/perform/chunk_cache.c to MANIFEST.
HDFFV-10601: Some compiler doesn't support clock_gettime(). So I changed to use gettimeofday (HDgettimeofday in the HDF5 library).
* commit 'cd13d24e5140578a880aebe4e2d8b899179d0870':
HDFFV-10601: I added error checking to the HDF5 functions.
HDFFV10601: Adding performance test to verify the improvement.
HDFFV-10601: I changed to a better way to calculate the number of chunks in a dataset.
HDFFV-10601 Issues with chunk cache hash value calcuation:
Add more sample batch scripts, specifically for sbatch, not for knl
cross compile.
Don't run parallel tests when no parallel test script is configured in
HDF5options.cmake.
* commit '4616c1e863ab756d22af696672ba9bc2fe0eea25':
Add custom target to force wait on generated file
TRILAB-81 fix typo
TRILAB-82 fixed errors found in review
Update windows test machine info
TRILAB-81 Output error if filename length is greater then 255
TRILAB-81 check for func success before using value
TRILAB-81 Coverity fix
Move options to root CMakeLists.txt
TRILAB-34 fix required through testing
TRILAB-34 add batch option (also patch2 from 10633)
TRILAB-81 coverity fixes
* commit '1652a60fcbe9894d7c34a778fb24dce1979fb9a9':
HDFFV-10605 Only test plugins if SHARED enabled
Correct platforms
Correct extlib depends
Commit version changes for additional files for 1.11.3 snapshot release.
* commit 'e6545faa5699aae4d5dca23ed40e3080fa9dc72d':
Update HDF5-Examples version to be included in CMake-* tar/zip files.
Snapshot version 1.11 release 3.
* commit 'e6545faa5699aae4d5dca23ed40e3080fa9dc72d':
Update HDF5-Examples version to be included in CMake-* tar/zip files.
Snapshot version 1.11 release 3.
* commit 'be0d6b206aaa04f7d9cb406a71aeeb458ba67975':
Update HDF5-Examples version to be included in CMake-* tar/zip files.
Snapshot version 1.11 release 3.
* commit '20ad15a1a8e9008103fe7d30401408eaa2aff6e5':
Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
* commit '20ad15a1a8e9008103fe7d30401408eaa2aff6e5':
Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
1. H5D__chunk_hash_val: When the number of chunks in the fastest changing dimension is larger than the number of slots in the hash table, H5D__chunk_hash_val abandons the normal hash value calculation algorithm and simply uses the scaled dimension. This will cause chunks a selection that cuts across chunks in dimensions other than the fastest changing to all have the same hash value, and they will therefore always evict each other from the cache, having an obvious major performance impact. Eliminated the check for the number of slots in this function and always use the full algorithm.
2. H5D__chunk_init: When the scaled dimensions (number of chunks in each dimension) are calculated in H5D__chunk_init, a simple divide ("/") operator is used with the dataset size in elements and the chunk size in elements. While this is fine when the dataset size is an exact multiple of the chunk size, in other cases, since "/" rounds down, it results in a scaled dimension one less than it should (it ignores the partial edge chunk). This has trickle down effects on hash value calculation that can cause excess hash value collisions and therefore performance issues. Changed the calculation to (((dataset_size - 1) / chunk_size) + 1).
Tested the build with Autotool and CMake.
* commit '51076d40617aa6f0236809c2c919cc6921b3bbc1':
Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
* commit '99c1e577da3a2dd45fbfee748220986c42962921':
Removed a couple of extraneous commas from VOL example.
Cleaned up VOL example.
Updated MANIFEST file.
Fixed VOL example to use a platform-independent format specifier for size_t.
* commit '99c1e577da3a2dd45fbfee748220986c42962921':
Removed a couple of extraneous commas from VOL example.
Cleaned up VOL example.
Updated MANIFEST file.
Fixed VOL example to use a platform-independent format specifier for size_t.
* commit 'ee12aff2ca89e92b99590f29096794a84c6bacdc':
Removed a couple of extraneous commas from VOL example.
Cleaned up VOL example.
Updated MANIFEST file.
Fixed VOL example to use a platform-independent format specifier for size_t.
* commit 'ff34cd0a0506ca16f4971cf03bd1b6e33bfa132c':
Updated RELEASE.txt to reflect HDFFV-10609 work (H5Xpkg.h files being incorrectly installed).
Add files and changes to cross compile with CrayLinuxEnvironment and run ctest tests with a batch job on knl compute nodes.
* commit 'b24259ed8cdb273273f82c2b3f3a2dcac60b32ba':
Add files and changes to cross compile with CrayLinuxEnvironment and run ctest tests with a batch job on knl compute nodes.
and CMake.
* CMake will no longer install private generated headers and tools
library headers.
* Several empty public header files (which represent internal packages)
were removed. These were only installed by CMake.
* Autotools installs will install H5FDwindows.h.
Fixes HDFFV-10614.
* commit '47f30b474bdc498c20bd6d2a0ba7e8947ab389f0':
HDFFV-10608 Move toolchain files into a subfolder
TRILAB-36 add option for test script batch command
Fixed warnings in the VOL example and run it from the script.
Split H5VLnative.h into public and private files and updated
* commit '096279caf76a542306b840fb90e1e753e8bbf748':
HDFFV-10608 Move toolchain files into a subfolder
TRILAB-36 add option for test script batch command
* commit 'b33a2e7dfe76a2947c12462adb40c88af9c92e75':
Fixed warnings in the VOL example and run it from the script.
Split H5VLnative.h into public and private files and updated
* commit '5f99891e6dc59524fb6e43ca96a86df22b403c61':
Move options to root cmake file
EED-258 Add modules uses toolchain files
Updates to the VOL ID and object API calls.
This brings the H5VL code in line with the H5I code regarding
naming, parameter order, etc.
Several public API calls were affected by this change.
These changed names to reflect their use with VOL drivers:
H5VLregister() --> H5VLregister_driver()
H5VLregister_by_name() --> H5VLregister_driver_by_name()
H5VLunregister() --> H5VLunregister_driver()
H5VLis_registered() --> H5VLis_driver_registered()
This call was renamed to match H5Iregister(). The order of the first
two parameters also reversed and the object pointer is now const.
H5VLobject_register() --> H5VLregister()
* commit '1e8ef703cdc057211b3587be776a6e9f62e8f76f':
Fixed a C++ style commenting issue and removed an unused field from H5F_trav_obj_ids_t.
Fixed a memory issue in H5Drefresh() where the dataset's H5VL_object_t gets closed but we try to use it to find the driver.
* commit 'c3a813a37fb700d2d1039d6fdc54d8e377412b76':
Fixed a memory issue in H5Drefresh() where the dataset's H5VL_object_t gets closed but we try to use it to find the driver.
* commit '75b84b09bd249b36a063fd51ecd3383801b0118b':
Updated the H5I debug dump to not segfault when types are not initialized or contain zero IDs in the skip list.
The H5I debug ID dump function is now always available instead of hidden behind an H5_DEBUG_OUTPUT ifdef.
* commit '2a95ab5acbe032f58891b653f56b9db8a4938d95':
TRILABS-21 add toolchain related info and files
TRILABS-21 Add intel compiler support
Fix undef for Xl compilers
TRILAB-21 Intel flags
* commit 'd26bb4d26ce5a23804a80c16dcb53e5f3eb957e4':
HDFFV-10594 - mac must be space separated
HDFFV-10594 - Add rpath configuration note
Add extra path option for build location
Use relative RPATH paths
* commit '2618dc314b9e4875e6ece7ee8696846ac2d02183':
Remove extra unneeded
Remove libsettings from pregenerated block
CMake changes for SKIPPED and flush tests
Correct $withval usage in configure
HDFFV-10332 Adjust checks and generation of files
HDFFV-10332 Use pre-generated files
* commit '96d5da7f1ad681573d42d2a4fd9e422fe049442d':
Remove extra unneeded
Remove libsettings from pregenerated block
Correct $withval usage in configure
HDFFV-10332 Adjust checks and generation of files
HDFFV-10332 Use pre-generated files
* commit 'e96bd2d46e208e0eb6c62cfcc4f86141f933884e':
CMake changes for SKIPPED and flush tests
H5S adjust callbacks now return an herr_t instead of void.
Normalization with vol_integration (property lists, file drivers, other misc).
* commit 'bbafe0debae9886988e4b7ec31bb8ef7292e43f9':
Remove extra constant
Fix typo
Add Constants to all ERR STK checks
Use constants for test comparisons
Develop normalization with vol_integration. Mostly peripheral things like the tools and wrappers, with just enough core library code to support that.
* commit '59f36c5cdef1899742feb1c06ee09886e2d0a220':
Remove extra constant
Fix typo
Add Constants to all ERR STK checks
Use constants for test comparisons
* commit 'eb78fd88325d58a95c026129f1e2b4c7c50f621a':
Develop normalization with vol_integration. Mostly peripheral things like the tools and wrappers, with just enough core library code to support that.
* commit 'ec53237fb849042b4a5b276a3e66a98ebb3710ee':
Removed 'VOL' versions of FUNC_ENTER macros as well as empty functions orginally intended to support the full SWMR feature.
* commit '680cf4d946fd10d50e0f7acdc5bc93f91037fb4f':
Removed 'VOL' versions of FUNC_ENTER macros as well as empty functions orginally intended to support the full SWMR feature.
* commit '6c78869c19a88edfd7b6a2a99a8fb8f5febf0b7a':
Fix whitespace and exit status
HDFFV-9059 take file as argument
HDFFV-9059 Allow detect to take a file as an argument
* commit 'fddbbc158d170b4e3a7ffd663f9799fd7e01a6a0':
HDFFV-10568 fix hdf5_java library dependency
Remove another extra path var
Move muti-config dir setting to root process
Fix one more intermediate location
Use different variable
Cleanup and add intermediate dir for java
* commit '763b95c6b0f027025a5a5bfb203b77317ffa2368':
Update RELEASE.txt with suggested changes
Update MANIFEST file for new t_coll_md_read.c file
Remove now-unused local variable
Add fix for HDFFV-10501
* commit 'a02414cc24e01096a239fc774ce94c38655f53ce':
Revert testfile FILE change
change FILE path
Add testfiles to data copy
Same changes needed for examples as test
Correct name of test jar
Only remove test jars
Remove obsolete var
Correct name of osx installer
DT location incorrect
* commit 'd20fd310e42b73e9037fb1a3bcc5e55d5e5c5162':
Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix.
* commit 'a3385675b3cdc2102457a9f91877cc27778ab29a':
Reorder bugfix release notes from latest to earliest, and miscellaneous format cleanup.
Add RELEASE.txt entry for HDFFV-10475
pass the base file first to the comparison callback so the base file's
communicator is used for the broadcast. Modify t_pvds to avoid
situations that won't work with the new scheme for opening source files
independently.
* commit '6e4c036d5dc476396428f4b044e23043a80e8df7':
HDFFV-10544 Correct var name
HDFFV-10544 remove native from class function
HDFFV-10544 correct typo
HDFFV-10544 add release note
HDFFV-10544 add class name to error text
HDFFV-10544 exception variable as local class
Improve error handling of exceptions
* commit '9aa2eaeb9ed9c94f63973cb55f13de256558497c':
Add Autotools and CMake checks for big I/O MPI-3 functions
Add hdf5settings section for parallel compression status in CMake builds
Switch to CheckSymbolExists in CMake
Add configure check for MPI_Mprobe and MPI_Imrecv functions
* commit '272eb4b8bffd2ab732d268c421583587317b8dc2':
RELEASE.txt updates for HDFFV-10467 and HDFFV-10509
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
Add line to libhdf5settings file for status of Parallel writes to
filtered datasets status
Surround Parallel Compression code in MPI_VERSION >= 3 checks
Add disabled message for Parallel Compression built w/ MPI-2
Modify Parallel Compression tests to only run the parallel filtered read
tests when parallel filtered writes are disabled
Update big I/O code to handle being built with MPI-2
Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
* commit 'ac5871c39cd9cd26b4a26041da7f265d5bba64dd':
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
Code improvement
New class for dataset access property list
* commit '3c6a39858fef9e7207cd7c3e3057267ec380be0b':
Fixed typos
Entered entries for HDFFV-10150, HDFFV-10458, HDFFV-1047
Updated for C2Cppfunction_map.htm
Added class DSetAccPropList Description: - Added class DSetAccPropList for the dataset access property list. - Added wrapper for H5Dget_access_plist to class DataSet // Gets the access property list of this dataset. DSetAccPropList getAccessPlist() const;
Code improvement Description: Moved the new H5Object::getInfo member functions to H5Location and made them overloaded with the existing H5Location::getObjinfo. This way is cleaner than the previous approach. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
Description:
- Added class DSetAccPropList for the dataset access property list.
- Added wrapper for H5Dget_access_plist to class DataSet
// Gets the access property list of this dataset.
DSetAccPropList getAccessPlist() const;
- Added wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class
DSetAccPropList
// Sets the raw data chunk cache parameters.
void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0)
// Retrieves the raw data chunk cache parameters.
void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
- Added two more arguments to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
- Added one more argument to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Description:
Moved the new H5Object::getInfo member functions to H5Location and
made them overloaded with the existing H5Location::getObjinfo. This
way is cleaner than the previous approach.
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Fixed HDFFV-10472 and replaced the C2Cpp function mapping table with a more supported format.
* commit 'dd0a040ec807912b80a9f1779fbf46c65d01cd57':
Fixed EED-319 Description: - Fixed doc issue Added an html version for the C++ function mapping table and removed the single web page version. Updated cpp_doc_config to use the html file. - Added a couple more minor tests
Fixed HDFFV-10472 Description: Added operator!= to DataType bool operator!=(const DataType& compared_type) Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* commit '77fa93e07b2b860ca314b2c332ebd440544e3326':
Add cmakehdf5 command line option to turn on shell script testing. Option is on by default but can be disabled with --disable-shell-testing.
* commit '3a8892a0d90edb6c21c91ede18bf6b3cb2895af0':
Adjust error handling
TRILABS-137 Convert tcheck_version script to cmake tests
ifdef around std flag for cygwin
Description:
- Fixed doc issue
Added an html version for the C++ function mapping table and removed
the single web page version.
Updated cpp_doc_config to use the html file.
- Added a couple more minor tests
Fixed part of HDFFV-10458: wrappers for H5Oget_info2, H5Oget_info_by_name2, and H5Oget_info_by_idx2.
* commit '3aa24435180d10aeca6493f7c1b277cfd5c73fad':
Fixed HDFFV-10458 partially Description: Added wrappers for H5Oget_info_by_idx2.
Fixed comments
Fixed HDFFV-10458 partially Description: Added wrappers for H5Oget_info2 and H5Oget_info_by_name2.
* commit '55666ace551369b3d72430c090ab9f1571e1be75':
Combined macro lines as Dana commented Platforms tested: Linux/64 (jelly) (very minor)
Fix evaluation of __has_attribute(no_sanitize_address) on older GCC versions
Fixed division-by-zero issues Description: Fixed HDFFV-10481 and HDFFV-10477, division by 0. Fixed another occurrence beside what were reported. Also, changed a local variable to avoid an unnecessary cast. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
Fixed HDFFV-10481 and HDFFV-10477
* commit '83ca39ba9a2d6852dd7754b533f7839e9d2a0107':
Combined macro lines as Dana commented Platforms tested: Linux/64 (jelly) (very minor)
Fixed division-by-zero issues Description: Fixed HDFFV-10481 and HDFFV-10477, division by 0. Fixed another occurrence beside what were reported. Also, changed a local variable to avoid an unnecessary cast. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* commit 'a8d6f100cdddbfc42d0c4abfeb4ceb8788b1b087':
Add note about single chunk caching and serial library
Add check for actually using the MPI file driver when caching one chunk
Fix error message mentioning wrong MPI function used
Fix for HDFFV-10509
Revise H5D__mpio_array_gatherv() to not allocate memory needlessly
Add test to continually grow and shrink chunks
Changes to test with checksum filter as well as deflate filter
Eliminate warning about signed to unsigned conversion
Remove unused local variable
Fix bug in parallel reads of compressed data
Add data verification to parallel filtered compound write tests
Add seven of fourteen parallel filtered data partial read tests
Description:
Fixed HDFFV-10481 and HDFFV-10477, division by 0.
Fixed another occurrence beside what were reported.
Also, changed a local variable to avoid an unnecessary cast.
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Fixed HDFFV-10404
* commit 'ec31438afdaf575368938e930eb3af0865a342b3':
Fixed HDFFV-10404 Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
* commit '08de02c838c05993fea5febb9c320a679e7f841a':
Changes based on feedback from pull request.
Fix test_misc33() in test/tmisc.c Open the test file read-only so that it can be accessed for testing.
Modifications made based on feedback from pull request.
Fix for HDFFV-10333: 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
Fix daily test failure.
* commit '08a8202eda7a79495a6d48f6be2c0b114e11750f':
Vailin's fix for H5open fail when file doesn't have write permissions for user in test_misc33(). The test file can be opened read-only because the test doesn't write to it.
1) Check for valid object header version for a refcount messge
2) Check for invalid fill value size
3) Check for invalid dimension size in a layout message
4) Add --enable-error-stack option to h5stat
5) Add error checks to h5stat.c
6) Add tests to h5stat and h5dump
* commit 'b1f5c9e9d63e16d67089f08ef2becc5119592a76':
Fix ptr arith
Correct function call
Remove writeVL option
Region reference in compounds need class check
Correct cast formatting
Correct var name
Need to cast from void ptr
Update Java util lib, Refactor H5D write VL to match read
* commit '25f80cbbec3a7d8036325784168b029cb71cc813': (324 commits)
Snapshot version 1.10 release 3 (snap3)
Update document
HDFFV-10433 Updated text to address issues raised.
Snapshot version 1.10 release 3 (snap2)
Updated version to 1.10.3-snap2
Merge corrections from develop
HDFFV-10473 add note for attribute fix
Correct attribute location
HDFFV-9739 and cmake improvements merge from develop
Fix for HDFFV-10469: set to latest format for virtual layout encoding.
Update Windows test machines
Fix soversion
Fixed libver bounds underscore issue
removed extraneous lib. ver. bound, PR comment
temporary fix for HDFFV-10469
Updated version to 1.10.3-snap1
Add new file
Correct number of tests
Whitespace and test reclassify merge from develop
HDFFV-10444 fix so numbers and merge java test changes
...
* commit '87829e06189cd9b29583b5ca8065b52b1f4cd523': (30 commits)
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
Cleaned up H5Fmount/unmount code.
Normalization with vol_integration branch.
Add fortran MPI to test and example
Add mpi include folders for fortran C objects
Normalization with the vol_integration branch.
Fixed MANIFEST
Fix usage of compression lib in shared tests
Fix jni function call version
Fix the error found after earlier checkin.
H5O_info fixes for java and examples
Added a RELASE.txt entry for HDFFV-10505.
Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags.
(1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463.
Normalize with vol_integration.
Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c.
Restored some unused #defines to the deprecated section of H5Dpublic.h.
Changes made based on feedback from pull request #1039.
...
* commit '57f64b92d19fed2879ee9bafe1d29bfac865d54c': (30 commits)
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
Cleaned up H5Fmount/unmount code.
Normalization with vol_integration branch.
Add fortran MPI to test and example
Add mpi include folders for fortran C objects
Normalization with the vol_integration branch.
Fixed MANIFEST
Fix usage of compression lib in shared tests
Fix jni function call version
Fix the error found after earlier checkin.
H5O_info fixes for java and examples
Added a RELASE.txt entry for HDFFV-10505.
Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags.
(1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463.
Normalize with vol_integration.
Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c.
Restored some unused #defines to the deprecated section of H5Dpublic.h.
Changes made based on feedback from pull request #1039.
...
* commit '18fbdebb977d7a4dbaa99ec6b153a49e3b4883d5':
Cleaned up H5Fmount/unmount code.
Normalization with vol_integration branch.
Normalization with the vol_integration branch.
* commit 'fe325fb554eddceccfa1674d804d5c7aed846bde':
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly
h5fget_obj_count_f with H5F_OBJ_ALL_F counted objects created in h5open_f, which should not be included in the count. The function now returns the correct number of objects (i.e., objects created in h5open are not included in the total).
* commit '1da9c5545c013ebc540ba3044810889d4acfa5be':
Restored some unused #defines to the deprecated section of H5Dpublic.h.
Added deprecated symbol wrappers for the H5DOwrite/read_chunk wrappers.
Updated commenting in the H5DO compat test.
Stripped out most of the duplicated functionality in the H5DO compat test.
* Added H5DO compatibility functions. * Changed the offset copy to use an array on the stack. * Yanked some unused #defines.
* Fixed the error tests * Moved common functionality into helper functions
Normalize with trunk prior to update merge
Fixed a warning.
Finished move of H5DOread/write_chunk calls to H5D.
First stage of moving H5DOread/write_chunk() to src/ and making them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform and renamed to direct_write_perf. * Updated autotools and CMake files.
* commit '931bd3aa6a7aa742d3a302b49eb20233b021f1bf':
Added a RELASE.txt entry for HDFFV-10505.
Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags.
* commit '796dc16e3409b9f3746cfa4127adb6dd334ee8c9':
(1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463.
Changes made based on feedback from pull request #1039.
Fix for HDFFV-10180 Performance issues with H5Oget_info.
* commit 'd184e6db94163dcc8761182744a6c524a4850887':
Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c.
Correct script names
Fix typo
Minor H5FS tweaks.
Put back CTRL-L chars
Update support link
Update text
Valgrind fixed by checking for prefix_len of 0
* commit 'e8eb130ce6f031a3b8ea50dae491b101d92e9c80': (117 commits)
Put back CTRL-L chars
Update support link
Update text
Valgrind fixed by checking for prefix_len of 0
HDFFV-9739 only executes H5E tests in production
Remove link flag from compile command
fix typo
Add release note
Correct attribute location
HDFFV-9739 fix copy testfiles command
HDFFV-9739 remove obsolete test files
HDFFV-9739 dup test file for concurrent tests
HDFFV-9739 Fix autotools script
HDFFV-9739 Change autotools test scripts
Fix for HDFFV-10469: set to latest format for virtual layout encoding.
Fix typo
HDFFV-9739 Update test reference
Update current windows test machines
HDFFV-9739 Grab err number before API call
HDFFV-9739 Add release note
...
* commit 'bcd8b31f3c9ace931df4483b855fae371c27a3dc':
Put back CTRL-L chars
Update support link
Update text
Valgrind fixed by checking for prefix_len of 0
* commit '2b0fb7e3f1f7da5b23d430702493ed4fb7f87166': (21 commits)
HDFFV-9739 only executes H5E tests in production
Remove link flag from compile command
fix typo
Add release note
Correct attribute location
HDFFV-9739 fix copy testfiles command
HDFFV-9739 remove obsolete test files
HDFFV-9739 dup test file for concurrent tests
HDFFV-9739 Fix autotools script
HDFFV-9739 Change autotools test scripts
Fix typo
HDFFV-9739 Update test reference
Update current windows test machines
HDFFV-9739 Grab err number before API call
HDFFV-9739 Add release note
Adjust test names for concurrent tests
Fix soversion
HDFFV-9739 Fix copy name
HDFFV-9739 factor out tests into separate JUnit
Updated the threadsafety test to use error macros instead of asserts.
...
* commit 'ab8a7235c3892ac0427f37661aa0d821993dae9b':
HDFFV-10473 add note for attribute fix
Correct attribute location
HDFFV-9739 and cmake improvements merge from develop
Update Windows test machines
Fix soversion
* commit '926260763940c77cf8f94807823765a3624fa29d':
HDFFV-9739 fix copy testfiles command
HDFFV-9739 remove obsolete test files
HDFFV-9739 dup test file for concurrent tests
HDFFV-9739 Fix autotools script
HDFFV-9739 Change autotools test scripts
Fix typo
HDFFV-9739 Update test reference
Update current windows test machines
HDFFV-9739 Grab err number before API call
HDFFV-9739 Add release note
Adjust test names for concurrent tests
Fix soversion
HDFFV-9739 Fix copy name
HDFFV-9739 factor out tests into separate JUnit
Fix MPI on Windows by adding MPI include folder
* commit 'dcc66a4f157ace0858b788228550f3e104df3242': (35 commits)
GGC requires attribute before function
Correct COMPILE defs usage
Add missing module_dir property
Text cleanup
Correct sentence punctuation.
Add release note.
Use set_property for MT flag
Correct command usage
Remove APPEND
Fix typo
Add missing test lib
add missing folder to path
Fix another command revert
Missed a command revert
Revert to old style for LINK_FLAGS gen expr not working
LINK_FLAGS must be separate property sets
Fix link flags syntax
Revert refactor link flags
refactor link flags to interface
Refactor link flags
...
* commit '0344785872020c4ef1de90cf57f286f1cf4ad2fc': (28 commits)
Text cleanup
Correct sentence punctuation.
Add release note.
Use set_property for MT flag
Correct command usage
Remove APPEND
Fix typo
Add missing test lib
add missing folder to path
Fix another command revert
Missed a command revert
Revert to old style for LINK_FLAGS gen expr not working
LINK_FLAGS must be separate property sets
Fix link flags syntax
Revert refactor link flags
refactor link flags to interface
Refactor link flags
Fix defs and additional MSVC items
TRILABS-19 fix syntax for windows
TRILABS-19 Link flags need - character
...
* commit '1f8cb03e11a46f853881f45dac18eff2dd68401e':
Fix errors in Makefile.am files that cause "make check" to repeat test, even when there are no changes to source files. (Also add a ggenerated script to the list of files cleaned up on 'make distclean')
Further minor cleanups
Checkpoint normalization against incoming hyperslab / selection / dataspace improvements.
them H5D calls.
* Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*.
* Moved the hl/test/test_dset_opt test to test/ and renamed to
direct_chunk.
* Moved the hl/test/dectris_hl_perf test to tools/test/perform
and renamed to direct_write_perf.
* Updated autotools and CMake files.
* commit '83e2ea681dd73e65c9b153385279b528cfdfe9df':
Fix errors in Makefile.am files that cause "make check" to repeat test, even when there are no changes to source files. (Also add a ggenerated script to the list of files cleaned up on 'make distclean')
* commit 'f435ed67fa53ca35462a60f4025464465d7dc9d0':
TRILABS-20 set a compiler name on all project commands
TRILABS-19 All c code INCLUDE_DIRECTORIES converted
TRILABS-19 Initial conversion of include_directories to targets
* commit 'e217bd113db96b96b485de82395688ca2313918a':
Resolve memory leak of last API context, by freeing it in H5CX terminate routine.
Revert "Close memory leak of last API context when shutting library down."
* commit 'bcab84db9f291920ed0fe321116405f73eaddfa5':
Resolve memory leak of last API context, by freeing it in H5CX terminate routine.
Revert "Close memory leak of last API context when shutting library down."
* commit '34e3e3ef17f29b721780941866a3ad4c261b7c05':
Whitespace changes
Whitespace and test reclassify
Move two more functions from unit tests
Reorder of tests for debug APIs option
HDFFV-10444 fix soversion numbers for libraries
Fix Java test for DEBUG_APIS
Use var instead of absolute number
* commit '3211e907f4f9349ba7510d70cfbcc6ee36d99c58':
Remove vestiges of H5_DEBUG_BUILD macro, switching it to the more standard H5CX_DEBUG form.
Minor warning cleanup while working on VOL issues.
* commit '048ae59d2970dd21810577c999f756c028b6faaf':
Correct errors with non-"instrumented library" builds (production & parallel, generally speaking).
Update java error stack tests
Revert using H5MF_sect_small_can_shrink and H5MF_sect_small_shrink for the file's free space manager (and add a comment about them).
Add comment for the file flush when the file low / high bounds are changed after a file is open.
Expanded comments abuot H5CX_t fields.
Add an assert to verify that we don't write when between MPI_Barrier() calls during a flush.
Add comments for internal structs.
Remove redundant 'is_collective' parameter from H5CX_set_loc.
Correct typo in comment.
Revert some tangential code cleanups.
Add API context source files to CMake configuration file.
Corrections for parallel I/O & tests.
Update handling of reporting for breaking collective I/O when the default DXPL is used.
Update encoded DXPLs to reflect changes in properties.
Correct typo for error checking malloc return value.
Refactor H5CX code to reduce duplication.
Cleanup API context function usage.
Add API context interface and use it throughout the library.
Commit API context and related changes
* commit '01a783dbee8160641a5a682f2116ffbd1ac123fe':
Correct errors with non-"instrumented library" builds (production & parallel, generally speaking).
Update java error stack tests
Revert using H5MF_sect_small_can_shrink and H5MF_sect_small_shrink for the file's free space manager (and add a comment about them).
Add comment for the file flush when the file low / high bounds are changed after a file is open.
Expanded comments abuot H5CX_t fields.
Add an assert to verify that we don't write when between MPI_Barrier() calls during a flush.
Add comments for internal structs.
Remove redundant 'is_collective' parameter from H5CX_set_loc.
Correct typo in comment.
Revert some tangential code cleanups.
Add API context source files to CMake configuration file.
Corrections for parallel I/O & tests.
Update handling of reporting for breaking collective I/O when the default DXPL is used.
Update encoded DXPLs to reflect changes in properties.
Correct typo for error checking malloc return value.
Refactor H5CX code to reduce duplication.
Cleanup API context function usage.
Add API context interface and use it throughout the library.
message(FATAL_ERROR" **** Fortran high-level routines are not supported when the default REAL is DOUBLE PRECISION, use HDF5_BUILD_HL_LIB:BOOL=OFF **** ")
} elsif($warning =~ /duplicate declaration of '[A-Za-z_0-9]*' is invalid in.*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
} elsif($warning =~ /Variable '[A-Za-z_0-9]*' at \([0-9]*\) is a dummy argument of the BIND\(C\) procedure '[A-Za-z_0-9]*' but may not be C interoperable.*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
$warning =~ s/at \([0-9]*\)/at \(-\)/g;
} elsif($warning =~ /Variable '[A-Za-z_0-9]*' at \([0-9]*\) may not be a C interoperable kind but it is BIND\(C\).*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
$warning =~ s/at \([0-9]*\)/at \(-\)/g;
} elsif($warning =~ /Component '[A-Za-z_0-9]*' in derived type '[A-Za-z_0-9]*' at \([0-9]*\) may not be C interoperable, even though derived type '[A-Za-z_0-9]*' is BIND\(C\).*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
$warning =~ s/at \([0-9]*\)/at \(-\)/g;
} elsif($warning =~ /function might be candidate for attribute '[A-Za-z_0-9]*' if it is known to return normally \[-Wsuggest-attribute=[A-Za-z_0-9]*\].*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
$warning =~ s/=[A-Za-z_0-9]*\]/=-\]/g;
} elsif($warning =~ /function might be candidate for attribute '[A-Za-z_0-9]*' \[-Wsuggest-attribute=[A-Za-z_0-9]*\].*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
$warning =~ s/=[A-Za-z_0-9]*\]/=-\]/g;
} elsif($warning =~ /passing argument [0-9]+ of '[A-Za-z_0-9]*' makes integer from pointer without a cast \[-Wint-conversion\].*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
$warning =~ s/[0-9]+/-/g;
} elsif($warning =~ /function '[A-Za-z_0-9]*' might be a candidate for '[A-Za-z_0-9]*' format attribute \[-Wsuggest-attribute=format\].*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
} elsif($warning =~ /inlining failed in call to '[A-Za-z_0-9]*': call is unlikely and code size would grow \[-Winline\].*/) {
$warning =~ s/'[A-Za-z_0-9]*'/'-'/g;
} elsif($warning =~ /'%[0-9]*[\.\*]*[0-9]*[dfsu]' directive writing between [0-9]+ and [0-9]+ bytes into a region of size [0-9]+ \[-Wformat-overflow=\].*/) {
$warning =~ s/'%[0-9]*[\.\*]*[0-9]*[dfsu]'/'-'/g;
$warning =~ s/[0-9]+/-/g;
} elsif($warning =~ /'%[0-9]*[\.\*]*[0-9]*[dfsu]' directive writing between [0-9]+ and [0-9]+ bytes into a region of size between [0-9]+ and [0-9]+ \[-Wformat-overflow=\].*/) {
$warning =~ s/'%[0-9]*[\.\*]*[0-9]*[dfsu]'/'-'/g;
$warning =~ s/[0-9]+/-/g;
} elsif($warning =~ /'%[0-9]*[\.\*]*[0-9]*[dfsu]' directive output may be truncated writing between [0-9]+ and [0-9]+ bytes into a region of size [0-9]+ \[-Wformat-truncation=\].*/) {
$warning =~ s/'%[0-9]*[\.\*]*[0-9]*[dfsu]'/'-'/g;
$warning =~ s/[0-9]+/-/g;
} elsif($warning =~ /'%[0-9]*[\.\*]*[0-9]*[dfsu]' directive output may be truncated writing up to [0-9]+ bytes into a region of size [0-9]+ \[-Wformat-truncation=\].*/) {
$warning =~ s/'%[0-9]*[\.\*]*[0-9]*[dfsu]'/'-'/g;
$warning =~ s/[0-9]+/-/g;
} elsif($warning =~ /'%[0-9]*[\.\*]*[0-9]*[dfsu]' directive output may be truncated writing between [0-9]+ and [0-9]+ bytes into a region of size between [0-9]+ and [0-9]+ \[-Wformat-truncation=\].*/) {
# The machine's conversion gets the correct value. We define the macro and disable
# this kind of test until we figure out what algorithm they use.
#
H5ConversionTests(H5_LDOUBLE_TO_LONG_SPECIAL"Checking IF your system converts long double to (unsigned) long values with special algorithm")
H5ConversionTests(${HDF_PREFIX}_LDOUBLE_TO_LONG_SPECIAL"Checking IF your system converts long double to (unsigned) long values with special algorithm")
# Set the flag to indicate that the machine is using a special algorithm
# to convert some values of '(unsigned) long' to 'long double' values.
@@ -231,7 +227,7 @@ H5ConversionTests (H5_LDOUBLE_TO_LONG_SPECIAL "Checking IF your system converts
# ..., 7fffff..., the compiler uses a unknown algorithm. We define a
# macro and skip the test for now until we know about the algorithm.
#
H5ConversionTests(H5_LONG_TO_LDOUBLE_SPECIAL"Checking IF your system can convert (unsigned) long to long double values with special algorithm")
H5ConversionTests(${HDF_PREFIX}_LONG_TO_LDOUBLE_SPECIAL"Checking IF your system can convert (unsigned) long to long double values with special algorithm")
H5ConversionTests(${HDF_PREFIX}_NO_ALIGNMENT_RESTRICTIONS"Checking IF alignment restrictions are strictly enforced")
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