hdf5_1_10_11-gnu-openmpi2-hpc-1.10.11-150400.3.21.2

- Fix bsc#1224158 - this fixes:
  CVE-2024-29158, CVE-2024-29161, CVE-2024-29166, CVE-2024-32608,
  CVE-2024-32610, CVE-2024-32614, CVE-2024-32619, CVE-2024-32620,
  CVE-2024-33873, CVE-2024-33874, CVE-2024-33875
  Additionally, these fixes resolve crashes triggered by the
  reproducers for CVE-2017-17507, CVE-2018-11205. These crashes
  appear to be unrelated to the original problems.
  Patches added:
  H5O-patches-partial.patch
  Add-H5F-RFIC-boilerplate.patch
  Add-H5T_is_numeric_with_unusual_unused_bits.patch
  Add-H5_RANGE_OVERLAP.patch
  Patch-H5Odtype.c.patch
  Patch-H5Tcommit.c.patch
  Add-unused-bits-checks-and-tools-patches.patch
  Update-overflow-macro.patch
  Update-H5_IS_BUFFER_OVERFLOW-to-account-for-size-of-0.patch
  Fixes-for-file-format-security-issues.patch
  Make-sure-unused-attribute-entries-are-NULLed.patch
  Add-sanity-and-overrun-checks-to-H5HG__cache_heap_deserialize.patch
  Mark-datatype-as-freed-always.patch
  Fix-an-uninitialized-value-warning.patch

- Updated to version 1.10.11
  * Changed the error handling for a not found path in the find
    plugin process.
  * Fixed CVE-2018-11202, a malformed file could result in chunk
    index memory leaks.
  * Fixed a file space allocation bug in the parallel library for
    chunked datasets.
  * Fixed an assertion failure in Parallel HDF5 when a file can't
    be created due to an invalid library version bounds setting.
  * Fixed an assertion in a previous fix for CVE-2016-4332.
  * Fixed segfault on file close in h5debug which fails with a core
    dump on a file that has an illegal file size in its cache image.
    Fixes HDFFV-11052, CVE-2020-10812.
  * Fixed memory leaks that could occur when reading a dataset from
    a malformed file.
  * Fixed a bug in H5Ocopy that could generate invalid HDF5 files
  * Fixed potential heap buffer overflow in decoding of link info
    message.
  * Fixed potential buffer overrun issues in some object header
    decode routines.
  * Fixed a heap buffer overflow that occurs when reading from
    a dataset with a compact layout within a malformed HDF5 file.
  * Fixed CVE-2019-8396, malformed HDF5 files where content does
    not match expected size.
  * Fixed memory leak when running h5dump with proof of
    vulnerability file.
  * Added option --no-compact-subset to h5diff.
  Fixes since 1.10.10:
  * Fixed a memory corruption when reading from dataset using a
    hyperslab selection in file dataspace and a point selection
    memory dataspace.
  * Fix CVE-2021-37501
  * Fixed an issue with variable length attributes.
  * Fixed an issue with hyperslab selections where an incorrect
    combined selection was produced.
  * Fixed an issue with attribute type conversion with compound
    datatypes.
  * Modified H5Fstart_swmr_write() to preserve DAPL properties.
  * Converted an assertion on (possibly corrupt) file contents to
    a normal error check.
  * Fixed memory leak with variable-length fill value in
    H5O_fill_convert().
  * Fix h5repack to only print output when verbose option is
    selected.
  Fixes since 1.10.9:
  * Several improvements to parallel compression feature,
    including:
    + Improved support for collective I/O (for both writes and
    reads).
    + Reduction of copying of application data buffers passed to
    H5Dwrite.
    + Addition of support for incremental file space allocation
    for filtered datasets created in parallel.
    + Addition of support for HDF5's "don't filter partial edge
    chunks" flag
    + Addition of proper support for HDF5 fill values with the
    feature.
    + Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to
    H5pubconf.h
    so HDF5 applications can determine at compile-time whether
    the feature is available.
    + Addition of simple examples
  * h5repack added an optional verbose value for reporting R/W
    timing.
  * Fixed a metadata cache bug when resizing a pinned/protected
    cache entry.
  * Fixed a problem with the H5_VERS_RELEASE check in the
    H5check_version function.
  * Unified handling of collective metadata reads to correctly fix
    old bugs.
  * Fixed several potential MPI deadlocks in library failure
    conditions.
  * Fixed an issue with collective metadata reads being permanently
    disabled after a dataset chunk lookup operation.
- Remove obsolete patch:
  * hdf5-mpi.patch
- Remove upstreamed fixes:
  * hdf5-1.10.8-pr1494-fix-release-check-version.patch
  * Compound-datatypes-may-not-have-members-of-size-0.patch
  * Validate-location-offset-of-the-accumulated-metadata-when-comparing.patch
  * Hot-fix-for-CVE-2020-10812.patch
  * H5O__pline_decode-Make-more-resilient-to-out-of-bounds-read.patch
  * Pass-compact-chunk-size-info-to-ensure-requested-elements-are-within-bounds.patch
  * Report-error-if-dimensions-of-chunked-storage-in-data-layout-2.patch
  * H5O_dtype_decode_helper-Parent-of-enum-needs-to-have-same-size-as-enum-itself.patch
  * Check-for-overflow-when-calculating-on-disk-attribute-data-size-2459.patch
  * Remove-duplicate-code.patch

- Remove timestamp/buildhost/kernel version from libhdf5.settings (boo#1209548).

- Fix CVE-2021-37501 - overflow in calculation of data buffer due to bogus
  input file (bsc#1207973).
  https://github.com/HDFGroup/hdf5/issues/2458
  https://github.com/HDFGroup/hdf5/pull/2459
  Check-for-overflow-when-calculating-on-disk-attribute-data-size-2459.patch
  Remove-duplicate-code.patch

- Fix CVEs:
  * CVE-2021-46244 (bsc#1195215)
    Compound-datatypes-may-not-have-members-of-size-0.patch
  * CVE-2018-13867 (bsc#1101906)
    Validate-location-offset-of-the-accumulated-metadata-when-comparing.patch
  * CVE-2018-16438 (bsc#1107069)
    Make-sure-info-block-for-external-links-has-at-least-3-bytes.patch
  * CVE-2020-10812 (bsc#1167400)
    Hot-fix-for-CVE-2020-10812.patch
  * CVE-2021-45830 (bsc#1194375)
    H5O_fsinfo_decode-Make-more-resilient-to-out-of-bounds-read.patch
  * CVE-2019-8396 (bsc#1125882)
    H5O__pline_decode-Make-more-resilient-to-out-of-bounds-read.patch
  * CVE-2018-11205 (bsc#1093663)
    Pass-compact-chunk-size-info-to-ensure-requested-elements-are-within-bounds.patch
  * CVE-2021-46242 (bsc#1195212)
    When-evicting-driver-info-block-NULL-the-corresponding-entry.patch
  * CVE-2021-45833 (bsc#1194366)
    Report-error-if-dimensions-of-chunked-storage-in-data-layout-2.patch
  * CVE-2018-14031 (bsc#1101475)
    H5O_dtype_decode_helper-Parent-of-enum-needs-to-have-same-size-as-enum-itself.patch
  * CVE-2018-17439 (bsc#1111598)
    H5IMget_image_info-H5Sget_simple_extent_dims-does-not-exceed-array-size.patch
- Fix an error message:
    Fix-error-message-not-the-name-but-the-link-information-is-parsed.patch

- Security Fix:
  Add configure option --disable-hltools to disable GIF tools as
  recommended in the 1.10.8 release:
  CVE-2018-17433 (bsc#1109565),
  CVE-2018-17436 (bsc#1109568),
  CVE-2020-10809 (bsc#1167404).

- add hdf5-wrappers.patch from Fedora, so strip flags from
  wrappers and prefer shared linking
- add missing zlib-devel devel dep

- Add hdf5-1.10.8-pr1494-fix-release-check-version.patch
  * boo#1179521, boo#1196682, gh#HDFGroup/hdf5#1494
  * Avoids package crashes due to an overeager version check.
    Packages depending on the shared libraries are not being
    rebuilt in Factory after a patchlevel version bump of hdf5
    without SONAME changes.

- Update to version 1.10.8:
  * Added new option to control the build of High-Level tools
  * Adds C++ Autotools configuration file for Intel
  * Adds C++ Autotools configuration file for PGI
  * Updates PGI C options
  * CMake will now run the shell script tests in test/ by default
  * Removed unused HDF5_ENABLE_HSIZET option from CMake
  * CMake no longer builds the C++ library by default
  * Removal of pre-VS2015 work-arounds
  * Add CMake variable HDF5_LIB_INFIX
  * Added a configure-time option to control certain compiler
    warnings
  * CMake option to build the HDF filter plugins project as an
    external project
  * Added a configure-time option to consider certain compiler
    warnings
  * Autotools and CMake target added to produce doxygen generated
    documentation
  * CMake option to build the HDF filter plugins project as an
    external project
  * Added CMake option to format source files
  * Change how the release part of version, in major.minor.release
    is checked
  * H5Gcreate1() now rejects size_hint parameters larger than
    UINT32_MAX
  * H5Pset_fapl_log() no longer crashes when passed an invalid
    fapl ID
  * Fixes a segfault when H5Pset_mdc_log_options() is called
    multiple times
  * File locking now works on Windows
  * H5Epush_ret() now requires a trailing semicolon
  * Improved performance of H5Sget_select_elem_pointlist
  * H5Fget_name_f fixed to handle correctly trailing whitespaces
    and newly allocated buffers.
  * Added new H5S functions.
  * Refactored the perform tools and removed dependencies on test
    library.
  * h5repack added help text for user-defined filters.
  * Doxygen documentation is available when configured and
    generated.
  * Fixed CVE-2018-17432 (bsc#1109564)
  * Fixed a segmentation fault
  * Detection of simple data transform function "x"
  * Fixed CVE-2020-10810 - an invalid read and memory leak when
    parsing (bsc#1167401)
  * Fixed CVE-2018-14460 (bsc#1102175)
  * Fixed CVE-2018-11206 (bsc#1093657)
    (same issue as CVE-2018-14032 (bsc#1101474))
  * Fixed CVE-2018-14033 (bsc#1101471)
    (same issue as CVE-2020-10811 (bsc#1167405))
  * Remove underscores on header file guards
  * H5FArray.java class:
  - Convert the entire byte array into a 1-d array of the
    desired type, rather than performing 1 conversion per row;
  - Use the Java Arrays method copyOfRange to grab the section
    of the array from (1) that is desired to be inserted into
    the destination array.
  * Corrected path searched by CMake find_package command
  * Corrected pkg-config compile script
  * Fixed CMake C++ compiler flags
  * Autotools clang debug optimization level change
  * Better support for libaec (open-source Szip library) in CMake
  * Refactor CMake configure for Fortran
  * Remove arbitrary warning flag groups from CMake builds
  * Reclassify CMake messages, to allow new modes and --log-level
    option
  * Fixes Autotools determination of the stat struct having an
    st_blocks field
  * Changed how h5dump and h5ls identify long double.
  * Fixed tools argument parsing.
  * Updated doxygen comments with changes for release
- Minor rebase of patches to apply cleanly.

- Fix update_so_version.sh, write so versions to file being included.

- Update to version 1.10.7
  * Add metadata cache optimization to reduce skip list usage.
  * Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable.
  * Add H5Pset/get_file_locking() API calls.
  * Add Mirror VFD.
    Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote
    machine. Must be used in conjunction with the Splitter VFD.
  * Add Splitter VFD.
    Maintain separate R/W and W/O channels for "concurrent" file writes
    to two files using a single HDF5 file handle.
  * Fixed an assertion failure in the parallel library when collectively
  filling chunks.
  * Fortran/C++ libs: Add wrappers for H5Pset/get_file_locking() API calls.
    h5pget_file_locking_f()
    h5pset_file_locking_f()
  * Added new Fortran parameters:
    H5F_LIBVER_ERROR_F
    H5F_LIBVER_NBOUNDS_F
    H5F_LIBVER_V18_F
    H5F_LIBVER_V110_F
  * Add new Fortran API: h5pget_libver_bounds_f.
  * h5repack added options to control how external links are handled.
  * The tools library was updated by standardizing the error stack process.
  * The H5DSis_scale function was updated to return "not a dimension scale" (0)
    instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
    not written according to Dimension Scales Specification.
  * Bug Fixes:
    + Fix bug and simplify collective metadata write operation when some ranks
    have no entries to contribute.  This fixes parallel regression test
    failures with IBM SpectrumScale MPI on the Summit system at ORNL.
    + Fixed use-of-uninitialized-value error.
    Appropriate initialization of local structs was added to remove the
    use-of-uninitialized-value errors reported by MemorySanitizer.
    + Creation of dataset with optional filter.
    A fix is applied to allow the creation of a dataset in such
    situation, as specified in the user documentation.
    + Explicitly declared dlopen to use RTLD_LOCAL.
    + H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
    causes asserts/errors when passed to other dataspace API calls.
    + Fixed the segmentation fault when reading attributes with multiple threads
    The problem was fixed by setting the file pointer to the current opened
    file pointer when the attribute was accessed.  Similar patch up was done
    before when reading dataset with variable length string datatype.
    + Don't allocate an empty (0-dimensioned) chunked dataset's chunk
    index, until the dataset's dimensions are increased.
    + Fortan: Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in
    h5fget_file_image_f.
    + h5diff fixed a command line parsing error.
    + h5diff added a command line option to ignore attributes.
    + h5diff added another level to the verbose argument to print filenames.
    + h5repack was fixed to repack the reference attributes properly.
  * For details check:
    https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7-RELEASE.txt
- version 1.10.6
  * Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5.
    Instructions to enable them when configuring HDF5 on Linux and Mac
    may be found at.
    https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS.
  * Added new wrappers for H5Pset/get_create_intermediate_group()
    LinkCreatPropList::setCreateIntermediateGroup()
    LinkCreatPropList::getCreateIntermediateGroup()
  * h5repack was fixed to repack datasets with external storage
    to other types of storage.
  * Bug Fixes:
    + Improved performance when creating a large number of small datasets by
    retrieving default property values from the API context instead of doing
    skip list searches. More work is required to achieve parity with HDF5 1.8.
    + Fixed user-created data access properties not existing in the property list
    returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
    reproducer and a patch.
    + Inappropriate linking with deprecated MPI C++ libraries.
    HDF5 does not define *_SKIP_MPICXX in the public headers, so applications
    can inadvertently wind up linking to the deprecated MPI C++ wrappers.
    MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h
    so this should no longer be an issue. HDF5 makes no use of the deprecated
    MPI C++ wrappers.
    + fcntl(2)-based file locking incorrectly passed the lock argument struct
    instead of a pointer to the struct, causing errors on systems where
    flock(2) is not available.
    This bug affects HDF5 1.10.0 through 1.10.5.
    fcntl(2)-based file locking now correctly passes the struct pointer.
    + Fixed a bug caused by a bad tag value when condensing object header
    messages.
    + Fixed an issue when creating a file with non-default file space info
    together with library high bound setting to H5F_LIBVER_V18.
    This was fixed by setting and checking the proper version in the file
    space info message based on the library low and high bounds when creating
    and opening the HDF5 file.
    + Fixed an issue where copying a version 1.8 dataset between files using
    H5Ocopy fails due to an incompatible fill version.
    + Fixed a bug that would cause an error or cause fill values to be
    incorrectly read from a chunked dataset using the "single chunk" index if
    + Fixed a bug that could cause an error or cause fill values to be
    incorrectly read from a dataset that was written to using H5Dwrite_chunk
    if the dataset was not closed after writing.
    + Fixed memory leak in scale offset filter.
  * For details check:
    https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6-RELEASE.txt
- Security bugs fixed:
  * CVE-2018-13870: heap-based buffer over-read in the function
    H5O_link_decode in H5Olink.c  (bsc#1101493)
  * CVE-2018-13869: memcpy parameter overlap in the function
    H5O_link_decode in H5Olink.c (bsc#1101495)
  * CVE-2018-17438:  A SIGFPE signal is raised in the function
    H5D__select_io() of H5Dselect.c in the HDF HDF5 through 1.10.3
    (bsc#1109570)
    library during an attempted parse of a crafted HDF file,
    because of incorrect protection against division
    (bsc#1109570)
  * CVE-2018-17435: A heap-based buffer over-read in H5O_attr_decode()
    in H5Oattr.c in the HDF HDF5 through 1.10.3 library allows
    attackers to cause a denial of service via a crafted HDF5 file.
    (bsc#1109567)
- Refresh patches

- Add build support for gcc10 to HPC build (bsc#1174439).

- Add missing openmpi4 flavors.
- Enable build of non-HPC flavors for all non-HPC builds.

- add openmpi4 packages to build and disable build for leap

- Fix .so number in baselibs.conf for libhdf5_fortran libs (boo#1169793).

- Fix library link flags on pkg-config file for HPC builds (boo#1134298).

- Remove bogus undefines of suffix and mpi_flavor. suffix is the
  name of an RPM built-in (like expand or echo), and since RPM 4.15
  trying to alter a built-in is an error. Fixes built of serial
  flavor on Tumbleweed. See https://rpm.org/user_doc/macros.html

- Add compat provides for renamed hdf5-openmpi{,-devel} package,
  see https://en.opensuse.org/openSUSE:Package_dependencies
- Fix openmpi1 package naming for SLE/Leap <= 15.1

- Add HPC support for gcc8 and gcc9 (jsc#SLE-7766 & jsc#SLE-8604).

- Disable openmpi1 builds for SLE/Leap > 15.1.
- Enable openmpi3 builds for Leap and SLE > 15.1 (jsc#SLE-7773).