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Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)
* 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>
2022-12-13 09:40:59 -08:00
.github Develop fix ubuntu 22.04 openmpi install on github (#2268) 2022-11-28 13:20:24 -06:00
bin Removes MPE instrumentation support. (#2245) 2022-11-09 11:06:26 -08:00
c++ Correct requires setting for pkgconfig files (#2280) 2022-12-07 16:05:51 -06:00
config Add aarch64 toolchain and change dump test to long opt (#2271) 2022-12-01 14:32:34 -08:00
doc Moved the contributing.md document to the project root (#2244) 2022-11-09 09:58:32 -08:00
doxygen Remove hard-coded version text (#2260) 2022-11-16 15:13:46 -06:00
examples Correct the CMake link for MPI (#2198) 2022-11-01 16:03:13 -05:00
fortran fixed unclosed objects in test (#2290) 2022-12-09 21:30:42 -06:00
hl Correct requires setting for pkgconfig files (#2280) 2022-12-07 16:05:51 -06:00
java Develop jni trans (#2266) 2022-12-05 22:29:42 -06:00
m4 Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
release_docs Compound datatypes may not have members of size 0 (#2243) 2022-12-07 16:14:40 -06:00
src Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291) 2022-12-13 09:40:59 -08:00
test Bug Fix: Segfault in H5CX_get_vol_wrap_ctx when H5VLwrap_register is called from an application (#2248) 2022-11-17 16:29:21 -06:00
testpar Removes MPE instrumentation support. (#2245) 2022-11-09 11:06:26 -08:00
tools Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291) 2022-12-13 09:40:59 -08:00
utils Correct the CMake link for MPI (#2198) 2022-11-01 16:03:13 -05:00
.autom4te.cfg Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
.clang-format
.gitattributes
.gitignore
.h5chkright.ini Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
ACKNOWLEDGMENTS
acsite.m4 Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
autogen.sh Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
CMakeFilters.cmake Update CMake code to 3.18 minimum version (#2080) 2022-09-02 17:31:29 -07:00
CMakeInstallation.cmake Implement option for using CMake GNUInstallDirs (#2175) 2022-10-25 08:50:43 -07:00
CMakeLists.txt Removes dmalloc support (#2239) 2022-11-09 09:22:14 -08:00
CMakePlugins.cmake
CODE_OF_CONDUCT.md
configure.ac Simplify & fix check for szlib encoder (#2263) 2022-11-17 16:28:44 -06:00
CONTRIBUTING.md Add text about release notes (#2246) 2022-12-06 06:02:21 -08:00
COPYING
COPYING_LBNL_HDF5
CTestConfig.cmake develop Merge doxygen from 1.12 branch (#2095) 2022-09-14 15:44:24 -05:00
Makefile.am Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
Makefile.dist Update copyright headers (#2184) 2022-11-01 16:02:27 -05:00
README.md Update develop branch version to 1.13.4-1 (#2189) 2022-10-26 11:07:17 -05:00
UserMacros.cmake

HDF5 version 1.13.4-1 currently under development

HDF5 Logo

Build BSD

Please refer to the release_docs/INSTALL file for installation instructions.

This repository contains a high-performance library's source code and a file format specification that implement the HDF5® data model. The model has been adopted across many industries and this implementation has become a de facto data management standard in science, engineering, and research communities worldwide.

The HDF Group is the developer, maintainer, and steward of HDF5 software. Find more information about The HDF Group, the HDF5 Community, and other HDF5 software projects, tools, and services at The HDF Group's website.

https://www.hdfgroup.org/

DOCUMENTATION

This release is fully functional for the API described in the documentation.

https://portal.hdfgroup.org/display/HDF5/The+HDF5+API

Full Documentation and Programming Resources for this release can be found at

https://portal.hdfgroup.org/display/HDF5

See the RELEASE.txt file in the release_docs/ directory for information specific to the features and updates included in this release of the library.

Several more files are located within the release_docs/ directory with specific details for several common platforms and configurations.

INSTALL - Start Here. General instructions for compiling and installing the library
INSTALL_CMAKE  - instructions for building with CMake (Kitware.com)
INSTALL_parallel - instructions for building and configuring Parallel HDF5
INSTALL_Windows and INSTALL_Cygwin - MS Windows installations.

HELP AND SUPPORT

Information regarding Help Desk and Support services is available at

https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk

FORUM and NEWS

The following public forums are provided for public announcements and discussions of interest to the general HDF5 Community.

These forums are provided as an open and public service for searching and reading. Posting requires completing a simple registration and allows one to join in the conversation. Please read the following instructions pertaining to the Forum's use and configuration https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum

RELEASE SCHEDULE

HDF5 release schedule

HDF5 does not release on a regular schedule. Instead, releases are driven by new features and bug fixes, though we try to have at least one release of each maintenance branch per year. Future HDF5 releases indicated on this schedule are tentative.

Release New Features
1.13.2 Onion VFD, Selection I/O, Subfiling
1.13.3 Multi-Dataset I/O
TBD VFD SWMR

This list of feature release versions is also tentative, and the specific release in which a feature is introduced may change.

SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE

Periodically development code snapshots are provided at the following URL:

https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/

Source packages for current and previous releases are located at:

https://portal.hdfgroup.org/display/support/Downloads

Development code is available at our Github location:

https://github.com/HDFGroup/hdf5.git