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| Name: hdf5-mvapich2 | Distribution: openSUSE Tumbleweed |
| Version: 1.10.7 | Vendor: openSUSE |
| Release: 3.5 | Build date: Sat Jan 15 08:49:18 2022 |
| Group: Productivity/Scientific/Other | Build host: obs-arm-6 |
| Size: 1432697 | Source RPM: hdf5-mvapich2-1.10.7-3.5.src.rpm |
| Packager: http://bugs.opensuse.org | |
| Url: https://www.hdfgroup.org/HDF5/ | |
| Summary: Command-line programs for the HDF5 scientific data format | |
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes. This package contains the mvapich2 version utility functions for working with HDF5 files.
BSD-3-Clause
* Fri Jan 29 2021 Egbert Eich <eich@suse.com>
- Fix update_so_version.sh, write so versions to file being included.
* Fri Nov 06 2020 Ana Guerrero Lopez <aguerrero@suse.com>
- 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
* Thu Jul 23 2020 Egbert Eich <eich@suse.com>
- Add build support for gcc10 to HPC build (bsc#1174439).
* Mon Jul 20 2020 Egbert Eich <eich@suse.com>
- Add missing openmpi4 flavors.
- Enable build of non-HPC flavors for all non-HPC builds.
* Wed Jun 24 2020 Alin M Elena <alinm.elena@gmail.com>
- add openmpi4 packages to build and disable build for leap
* Fri Apr 17 2020 Egbert Eich <eich@suse.com>
- Fix .so number in baselibs.conf for libhdf5_fortran libs (boo#1169793).
* Thu Apr 02 2020 Egbert Eich <eich@suse.com>
- Fix library link flags on pkg-config file for HPC builds (boo#1134298).
* Mon Jan 20 2020 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- 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
* Tue Dec 10 2019 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- 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
* Thu Nov 28 2019 Egbert Eich <eich@suse.com>
- Add HPC support for gcc8 and gcc9 (jsc#SLE-7766 & jsc#SLE-8604).
* Thu Nov 28 2019 Egbert Eich <eich@suse.com>
- Disable openmpi1 builds for SLE/Leap > 15.1.
- Enable openmpi3 builds for Leap and SLE > 15.1 (jsc#SLE-7773).
* Thu Oct 24 2019 Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
- openmpi has been renamed into openmpi1
* Tue Sep 10 2019 Ana Guerrero Lopez <aguerrero@suse.com>
- Use -ffat-lto-objects to provide a proper static library.
* Tue Sep 03 2019 Ana Guerrero Lopez <aguerrero@suse.com>
- Re-list hdf5-mpi.patch in the spec file for the sake of a avoiding
a script rejecting the package automatically.
* Fri Aug 23 2019 Ana Guerrero Lopez <aguerrero@suse.com>
- 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
* Thu Jul 04 2019 Egbert Eich <eich@suse.com>
- Since build machine size issues do not seem to go way, make
the %check stage optional: enable with '--with check'.
* Thu Apr 25 2019 Christian Goll <cgoll@suse.com>
- set higher constraints for succesfull mpich tests (boo#133222)
* Mon Apr 01 2019 normand@linux.vnet.ibm.com
- Add _constraints to avoid transient build error ppc64le
* Sat Mar 09 2019 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- Update URL: and Source: to use https://.
* Fri Mar 01 2019 Egbert Eich <eich@suse.com>
- Like on PPC ignore transient 'make check' failures on aarch64.
* Fri Mar 01 2019 Egbert Eich <eich@suse.com>
- Remove ringdisabled magic as hdf5 is no longer a ring package.
This should resolve a number of problems in the review channels
for Factory with packages requiring hdf5 libs.
* Wed Feb 13 2019 Egbert Eich <eich@suse.com>
- Consolidate use of openmpi1, openmpi2, openmpi3 for non-HPC builds.
* Fri Jan 25 2019 eich@suse.com
- 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.
* Mon Jan 14 2019 eich@suse.com
- Reenable 'serial' build for SLE: this build creates hdf5-devel-data.
* Thu Jan 03 2019 eich@suse.com
- Do not build non-HPC on SLE: This helps to save some build
cycles.
* Wed Dec 19 2018 Todd R <toddrme2178@gmail.com>
- Use upstream-recommended %{_rpmconfigdir}/macros.d directory
for the rpm macros.
* Wed Dec 12 2018 Todd R <toddrme2178@gmail.com>
- Also build for regular openmpi2 and openmpi3
* Thu Nov 22 2018 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- Build HDF5 C++ bindings also for the MPI variants, there is no reason
not to do it.
- Enable sz2 support also for MPI variants.
* Mon Nov 19 2018 eich@suse.com
- Replace git-archive generated by downloaded tar-ball.
* Sat Nov 17 2018 eich@suse.com
- Update to 1.10.4:
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4-RELEASE.txt
* Update Disable-phdf5-tests.patch
* Replace and update hdf5-buildcompare.patch by
hdf5-Remove-timestamps-from-binaries.patch
* Fri Nov 16 2018 eich@suse.com
- Remove lib*_cpp and lib*_hl_cpp dependencies for MPI for the time
being.
* Sun Nov 11 2018 eich@suse.com
- Create main master package, fix dependencies.
* Fri Sep 21 2018 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- Update to 1.10.3:
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.3/src/hdf5-1.10.3-RELEASE.txt
- Update to 1.10.2:
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt
- Bump soversions (101 -> 103) for libhdf5 and libhdf5_cpp
- Drop Fix-warnings-for-missing-returns.patch, fixed upstream
- Add 0001-Fix-return-value-in-test_libver_bounds_open.patch
- Rebase patches (tab / space conversion):
* PPC64LE-Fix-long-double-handling.patch
* hdf5-buildcompare.patch
* hdf5-mpi.patch
- Rebase Disable-phdf5-tests.patch
- Security bugs fixed:
* CVE-2017-17505: NULL pointer dereference in the function
H5O_pline_decode allowing for DoS via crafted file (bsc#1072087)
* CVE-2017-17506: Out of bounds read in the function
H5Opline_pline_decode (bsc#1072090)
* CVE-2017-17508: divide-by-zero vulnerability in function
H5T_set_loc (bsc#1072108)
* CVE-2017-17509: out of bounds write vulnerability in function
H5G__ent_decode_vec (bsc#1072111)
* CVE-2018-11202: NULL pointer dereference in H5S_hyper_make_spans
in H5Shyper.c allows a remote denial of service attack (bsc#1093641)
* CVE-2018-11203: division by zero in H5D__btree_decode_key in H5Dbtree.c
It could allow a remote denial of service attack (bsc#1093649)
* CVE-2018-11204: A NULL pointer dereference was discovered in
H5O__chunk_deserialize in H5Ocache.c (bsc#1093655)
* CVE-2018-11206: A out of bounds read was discovered
in H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
(bsc#1093657)
* CVE-2018-11207: division by zero was discovered in H5D__chunk_init
in H5Dchunk.c (bsc#1093653)
* Tue Jun 19 2018 eich@suse.com
- Handle license file using %license where applicable.
- Package example package also for HPC build and create
a master file for it.
* Fri Apr 27 2018 eich@suse.com
- Fix HPC library master packages dependency: make it require
the correct flavor (bsc#1091237).
* Sat Apr 07 2018 eich@suse.com
- Only build one examples package for all flavors, do not
include dependencies as these would be flavor specific
(bsc#1088547).
* Sat Mar 31 2018 stefan.bruens@rwth-aachen.de
- Fix some typos, one trivial, two mispelled macros
* Sat Feb 10 2018 jengelh@inai.de
- Trim description for size and drop most of the marketing blurb.
Fix RPM groups.
* Sat Feb 10 2018 eich@suse.com
- Make module files package arch dependent: it
contains arch-dependent paths (boo#1080442).
* Sat Feb 10 2018 eich@suse.com
- Prepend PKG_CONFIG_PATH in modules file (boo#1080426).
* Fri Feb 09 2018 eich@suse.com
- Add support for openmpi2 for HPC (FATE#325089).
* Fri Feb 09 2018 cgoll@suse.com
- Fix summary in module files (bnc#1080259)
* Thu Feb 08 2018 eich@suse.com
- Disable %check stage for mpich builds on s390(x) (bsc#1080022).
* Fri Jan 12 2018 eich@suse.com
- Disable the openmpi3 flavor in some products.
* Fri Jan 05 2018 eich@suse.com
- Switch from gcc6 to gcc7 as additional compiler flavor for HPC on SLES.
- Add support for mpich and openmpi3 for HPC.
/usr/lib/mpi/gcc/mvapich2/bin/gif2h5 /usr/lib/mpi/gcc/mvapich2/bin/h52gif /usr/lib/mpi/gcc/mvapich2/bin/h5clear /usr/lib/mpi/gcc/mvapich2/bin/h5copy /usr/lib/mpi/gcc/mvapich2/bin/h5debug /usr/lib/mpi/gcc/mvapich2/bin/h5diff /usr/lib/mpi/gcc/mvapich2/bin/h5dump /usr/lib/mpi/gcc/mvapich2/bin/h5format_convert /usr/lib/mpi/gcc/mvapich2/bin/h5import /usr/lib/mpi/gcc/mvapich2/bin/h5jam /usr/lib/mpi/gcc/mvapich2/bin/h5ls /usr/lib/mpi/gcc/mvapich2/bin/h5mkgrp /usr/lib/mpi/gcc/mvapich2/bin/h5perf /usr/lib/mpi/gcc/mvapich2/bin/h5perf_serial /usr/lib/mpi/gcc/mvapich2/bin/h5redeploy /usr/lib/mpi/gcc/mvapich2/bin/h5repack /usr/lib/mpi/gcc/mvapich2/bin/h5repart /usr/lib/mpi/gcc/mvapich2/bin/h5stat /usr/lib/mpi/gcc/mvapich2/bin/h5unjam /usr/lib/mpi/gcc/mvapich2/bin/h5watch /usr/lib/mpi/gcc/mvapich2/bin/mirror_server /usr/lib/mpi/gcc/mvapich2/bin/mirror_server_stop /usr/lib/mpi/gcc/mvapich2/bin/ph5diff
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