hdf5-openmpi3-1.10.7-bp153.3.62

- 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
    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).

- openmpi has been renamed into openmpi1

- Use -ffat-lto-objects to provide a proper static library.

- Re-list hdf5-mpi.patch in the spec file for the sake of a avoiding
  a script rejecting the package automatically.

- Update to version 1.10.5: (jsc#SLE-8501)
  * https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5-RELEASE.txt
- Security bugs fixed:
  * CVE-2018-17233: A SIGFPE signal is raised in the function
  H5D__create_chunk_file_map_hyper. (bsc#1109166)
  * CVE-2018-17434: Memory leak in the H5O__chunk_deserialize()
  function in H5Ocache.c (bsc#1109167)
  * CVE-2018-17437: A SIGFPE signal is raised in the function
  H5D__chunk_set_info_real. (bsc#1109168)
- Bump fortran library soname, sonum_F from 100 to 102.
- Adjust library installation path, use %hpc_prefix/lib64 in x86_64
  and %hpc_libdir in all other cases
- Patches refreshed:
  * hdf5-LD_LIBRARY_PATH.patch
  * hdf5-1.8.11-abort_unknown_host_config.patch
  * PPC64LE-Fix-long-double-handling.patch
  * hdf5-Remove-timestamps-from-binaries.patch
  * Disable-phdf5-tests.patch
- Patch disabled, upstream have changed the file that was being patched,
  while it could be ported, it's unknown if this patch is still needed.
  * hdf5-mpi.patch
- Patch removed, merged upstream
  * 0001-Fix-return-value-in-test_libver_bounds_open.patch

- Since build machine size issues do not seem to go way, make
  the %check stage optional: enable with '--with check'.

- set higher constraints for succesfull mpich tests (boo#133222)

- Add _constraints to avoid transient build error ppc64le

- Update URL: and Source: to use https://.

- Like on PPC ignore transient 'make check' failures on aarch64.

- Like on PPC ignore transient 'make check' failures on aarch64.

- Consolidate use of openmpi1, openmpi2, openmpi3 for non-HPC builds.

- Remove dependency to the hdf5-devel-data file for HPC:
  Currently, there are no macro files for HPC - these files
  will have to be handled differently.
- Re-disable all non-HPC builds for SLE.

- Reenable 'serial' build for SLE: this build creates hdf5-devel-data.

- Do not build non-HPC on SLE: This helps to save some build
  cycles.