Summary
HDF5 is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I/O.
Versions
v1.12.1 :: 0/1.12.1 :: gentoo
- Modified
- License
- NCSA-HDF
- Keywords
- ~alpha ~amd64 ~amd64-linux ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~x86-linux
- USE flags
- cxx debug doc examples fortran hl mpi szip test threads unsupported zlib
v1.10.5-r1 :: 0/1.10.5 :: gentoo
- Modified
- License
- NCSA-HDF
- Keywords
- amd64 arm arm64 ppc ppc64 x86 ~alpha ~amd64-linux ~hppa ~ia64 ~riscv ~sparc ~x86-linux
- USE flags
- cxx debug examples fortran hl mpi szip threads unsupported zlib
v1.10.5 :: 0/1.10.5 :: gentoo
- Modified
- License
- NCSA-HDF
- Keywords
- amd64 arm64 ppc ppc64 sparc x86 ~alpha ~amd64-linux ~arm ~ia64 ~riscv ~x86-linux
- USE flags
- cxx debug examples fortran hl mpi szip threads zlib
USE flags
General
- cxx
- Build support for C++ (bindings, extra libraries, code generation, ...)
- debug
- Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces
- doc
- Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
- examples
- Install examples, usually source code
- fortran
- Add support for fortran
- hl
- Enable high level API (https://support.hdfgroup.org/HDF5/doc/HL/index.html)
- mpi
- Add MPI (Message Passing Interface) layer to the apps that support it
- szip
- Use the szip compression library
- test
- Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)
- threads
- Add threads support for various packages. Usually pthreads
- unsupported
- Enable unsupported combinations of configuration options
- zlib
- Add support for zlib (de)compression
Dependencies
sys-devel / autoconf : Used to create autoconfiguration files
sys-devel / libtool : A shared library tool for developers
sys-libs / zlib : Standard (de)compression library
virtual / fortran : Virtual for Fortran Compiler
virtual / mpi : Virtual for Message Passing Interface (MPI) v2.0 implementation
virtual / szip : Virtual for szip compression drop-in replacements
Runtime Dependencies
sys-libs / zlib : Standard (de)compression library
virtual / fortran : Virtual for Fortran Compiler
virtual / mpi : Virtual for Message Passing Interface (MPI) v2.0 implementation
virtual / szip : Virtual for szip compression drop-in replacements
Depending packages
dev-lang / gdl : GNU Data Language
dev-libs / starpu : Unified runtime system for heterogeneous multicore architectures
dev-python / h5py : Simple Python interface to HDF5 files
dev-python / netcdf4-python : Python/numpy interface to the netCDF C library
dev-python / pytables : Hierarchical datasets for Python
dev-util / diffoscope : Will try to get to the bottom of what makes files or directories different
media-gfx / alembic : Open framework for storing and sharing scene data
media-gfx / freecad : QT based Computer Aided Design application
media-libs / Field3D : A library for storing voxel data
media-libs / opencv : A collection of algorithms and sample code for various computer vision problems
media-libs / vigra : C++ computer vision library emphasizing customizable algorithms and structures
media-sound / csound : Sound design and signal processing system for composition and performance
sci-biology / kallisto : Near-optimal RNA-Seq quantification
sci-chemistry / avogadro2 : Advanced molecule editor and visualizer 2
sci-chemistry / votca-csg : Votca coarse-graining engine
sci-chemistry / votca-xtp : Votca excitation and charge properties module
sci-electronics / gazebo : A 3D multiple robot simulator with dynamics
sci-geosciences / qgis : User friendly Geographic Information System
sci-libs / armadillo : Streamlined C++ linear algebra library
sci-libs / avogadrolibs : Advanced molecule editor and visualizer 2 - libraries
sci-libs / cgnslib : CFD General Notation System standard library
sci-libs / dealii : Solving partial differential equations with the finite element method
sci-libs / flann : Fast approximate nearest neighbor searches in high dimensional spaces
sci-libs / flann : Fast approximate nearest neighbor searches in high dimensional spaces
sci-libs / gdal : Translator library for raster geospatial data formats (includes OGR support)
sci-libs / h5hut : High-Performance I/O Library for Particle-based Simulations
sci-libs / h5part : Portable High Performance Parallel Data Interface to HDF5
sci-libs / mathgl : Math Graphics Library
sci-libs / matio : Library for reading and writing matlab files
sci-libs / med : A library to store and exchange meshed data or computation results
sci-libs / netcdf : Scientific library and interface for array oriented data access
sci-libs / o2scl : Object-oriented Scientific Computing Library
sci-libs / silo : A mesh and field I/O library and scientific database
sci-libs / trilinos : Scientific library collection for large scale problems
sci-libs / vtk : The Visualization Toolkit
sci-libs / xdmf2 : eXtensible Data Model and Format
sci-mathematics / octave : High-level interactive language for numerical computations
sci-mathematics / petsc : Portable, Extensible Toolkit for Scientific Computation
sci-misc / h5utils : Utilities for visualization and conversion of HDF5 files
sci-physics / espresso : Extensible Simulation Package for Research on Soft matter
sci-physics / geant : Toolkit for simulation of passage of particles through matter
sci-physics / lammps : Large-scale Atomic/Molecular Massively Parallel Simulator
sci-visualization / gwyddion : Framework for Scanning Mode Microscopy data analysis
sci-visualization / labplot : Scientific data analysis and visualisation based on KDE Frameworks
sci-visualization / paraview : Powerful scientific data visualization application
sys-cluster / slurm : A Highly Scalable Resource Manager
Bugs
- 560964
- sci-libs/hdf5 - hdf5-1.8.9-mpicxx.patch causes macro redefinition warnings with clang-3.7
- 661158
- sci-libs/hdf5: Multiple vulnerabilities
- 665378
- sci-libs/hdf5-1.10.1: QA Notice: Pre-stripped files found
- 675606
- sci-libs/hdf5-1.8.21 - pkg-config files are not generated
- 682794
- sci-libs/hdf5-1.10.5 USE="fortran mpi" - FATAL ERROR: Cannot read module file 'mpi.mod' opened at (1), because it was created by a different version of GNU Fortran
- 686620
- sci-libs/hdf5-1.10.5: "unaligned VL strings in compound" fails with SIGBUS on sparc
- 714024
- sci-libs/hdf5: Multiple vulnerabilities (CVE-2020-{10809,10810,10811,10812})
- 716672
- sci-libs/hdf5-1.10.5-r1 fails 8 tests on ppc
- 733578
- sci-libs/hdf5-1.10.5-r1 stable request
- 741438
- sci-libs/hdf5-1.10.5-r1 fails tests
- 808612
- =sci-libs/hdf5-1.12.1[mpi] fails tests
- 808633
- sci-libs/hdf5-1.12.1 - Error: Symbol ‘h5i_invalid_hid_f’ at (1) has no IMPLICIT type.
- 808731
- media-libs/vigra[hdf5] with >=sci-libs/hdf5-1.12: hdf5impex.cxx: too few arguments to function H5Oget_info_by_name3
- 808733
- [TRACKER] sci-libs/hdf5-1.12 support
Change logs
- Repository mirror & CI · gentoo
Merge updates from master - Marek Szuba · gentoo
sci-libs/hdf5: add 1.12.1
Signed-off-by: Marek Szuba <marecki@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Rolf Eike Beer · gentoo
sci-libs/hdf5: keyworded 1.10.5-r1 for hppa, bug #804115
Package-Manager: Portage-3.0.20, Repoman-3.0.3 RepoMan-Options: --include-arches="hppa" Signed-off-by: Rolf Eike Beer <eike@sf-mail.de> Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Alex Fan · gentoo
sci-libs/hdf5: rekeyword 1.10.5{,-r1} for ~riscv
Package-Manager: Portage-3.0.20, Repoman-3.0.2 Signed-off-by: Alex Fan <alexfanqi@yahoo.com> Signed-off-by: Yixun Lan <dlan@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Marek Szuba · gentoo
sci-libs/hdf5: keyword ~1.10.5 for -riscv
Independently observed to fail tests by two arch testers. Bugzilla ticket to follow. Signed-off-by: Marek Szuba <marecki@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-libs/hdf5: eutils--
Signed-off-by: Sam James <sam@gentoo.org> - Sam James · gentoo
sci-libs/hdf5: eutils--
Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-libs/hdf5: fix build with slibtool
It's not completely clear how slibtool should've known to append -fPIC, but let's not worry too much for now. Closes: https://bugs.gentoo.org/775305 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-libs/hdf5: Stabilize 1.10.5-r1 arm, #709830
Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-libs/hdf5: x86 stable wrt bug #733578
Package-Manager: Portage-2.3.99, Repoman-2.3.22 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Repository mirror & CI · gentoo
Merge updates from master - Sergei Trofimovich · gentoo
sci-libs/hdf5: stable 1.10.5-r1 for ppc64
stable wrt bug #733578 Package-Manager: Portage-3.0.1, Repoman-2.3.23 RepoMan-Options: --include-arches="ppc64" Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org> - Sergei Trofimovich · gentoo
sci-libs/hdf5: stable 1.10.5-r1 for ppc
stable wrt bug #733578 Package-Manager: Portage-3.0.1, Repoman-2.3.23 RepoMan-Options: --include-arches="ppc" Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-libs/hdf5: arm64 stable (bug #733578)
Package-Manager: Portage-3.0.0, Repoman-2.3.23 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-libs/hdf5: amd64 stable wrt bug #733578
Package-Manager: Portage-2.3.99, Repoman-2.3.22 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Alexey Sokolov · gentoo
sci-libs/hdf5: update homepage
Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: Alexey Sokolov <alexey+gentoo@asokolov.org> Signed-off-by: Andreas K. Hüttel <dilfridge@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Matt Turner · gentoo
*/*: Drop stable ia64 keywords
Signed-off-by: Matt Turner <mattst88@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Alessandro Barbieri · gentoo
sci-libs/hdf5: add unsupported useflag
this will allow unsupported combinations of useflags such as MPI + CXX. link mpi when using mpi. Closes: https://bugs.gentoo.org/710986 Closes: https://github.com/gentoo/gentoo/pull/14821 Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: Alessandro Barbieri <lssndrbarbieri@gmail.com> Signed-off-by: Benda Xu <heroxbd@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
*/*: Bump copyright on files touched this year
Update the copyright notice on all files that were touched since January 1st but did not have the notice updated. Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Matt Turner · gentoo
*/*: Drop stable alpha keywords
Signed-off-by: Matt Turner <mattst88@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
sci-libs: Remove *-fbsd KEYWORDS
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Alessandro Barbieri · gentoo
sci-libs/hdf5: disable static libraries
Closes: https://bugs.gentoo.org/694128 Closes: https://github.com/gentoo/gentoo/pull/13061 Package-Manager: Portage-2.3.76, Repoman-2.3.17 Signed-off-by: Alessandro Barbieri <lssndrbarbieri@gmail.com> Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-libs/hdf5: Drop 1.8.18 and 1.10.1
Package-Manager: Portage-2.3.67, Repoman-2.3.14 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-libs/hdf5: sparc stable wrt bug #678264
Signed-off-by: Agostino Sarubbo <ago@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.11 RepoMan-Options: --include-arches="sparc" - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-libs/hdf5: ppc stable wrt bug #678264
Signed-off-by: Agostino Sarubbo <ago@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.11 RepoMan-Options: --include-arches="ppc" - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-libs/hdf5: ppc64 stable wrt bug #678264
Signed-off-by: Agostino Sarubbo <ago@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.11 RepoMan-Options: --include-arches="ppc64" - Repository mirror & CI · gentoo
Merge updates from master - Tobias Klausmann · gentoo
sci-libs/hdf5-1.10.5-r0: alpha stable
Bug: http://bugs.gentoo.org/678264 Signed-off-by: Tobias Klausmann <klausman@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sergei Trofimovich · gentoo
sci-libs/hdf5: stable 1.10.5 for ia64, bug #678264
Package-Manager: Portage-2.3.66, Repoman-2.3.12 RepoMan-Options: --include-arches="ia64" Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Mikle Kolyada · gentoo
sci-libs/hdf5: amd64 stable wrt bug #678264
Signed-off-by: Mikle Kolyada <zlogene@gentoo.org> Package-Manager: Portage-2.3.62, Repoman-2.3.11 RepoMan-Options: --include-arches="amd64" - Repository mirror & CI · gentoo
Merge updates from master - Thomas Deutschmann · gentoo
sci-libs/hdf5: x86 stable (bug #678264)
Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Thomas Deutschmann <whissi@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Aaron Bauman · gentoo
sci-libs/hdf5: arm64 stable
Signed-off-by: Aaron Bauman <bman@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.12 RepoMan-Options: --include-arches="arm64" - Repository mirror & CI · gentoo
Merge updates from master - Benda Xu · gentoo
sci-libs/hdf5: bump to 1.10.5 and EAPI 7.
Suggested-By: Fabio Rossi, Bernd Bug: https://bugs.gentoo.org/661158 Closes: https://bugs.gentoo.org/674998 Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Benda Xu <heroxbd@gentoo.org> - Benda Xu · gentoo
sci-libs/hdf5: Add back hl configuration options.
Closes: https://bugs.gentoo.org/640220 Package-Manager: Portage-2.3.16, Repoman-2.3.6 - Benda Xu · gentoo
sci-libs/hdf5: Add back hl USE flag and conditions.
Suggested-by: Nikolaj Šujskij <skrattaren@yandex.ru> Closes: https://bugs.gentoo.org/640220 Package-Manager: Portage-2.3.16, Repoman-2.3.6 - Benda Xu · gentoo
sci-libs/hdf5: drop implicits.patch.
The patch is not needed any more and causes compilation error. Reported-by: Eugene Shalygin <eugene.shalygin@gmail.com> Suggested-by: milan hodoscek <milan@cmm.ki.si> Closes: https://bugs.gentoo.org/639784 Package-Manager: Portage-2.3.16, Repoman-2.3.6 - Benda Xu · gentoo
sci-libs/hdf5: really drop USE fortran2003.
fortran2003 is supported by gfortran-4.9 which is the oldest in the main tree. As of 1.10, hdf5 drops the fortran2003 configuration option. Package-Manager: Portage-2.3.16, Repoman-2.3.6 - Benda Xu · gentoo
sci-libs/hdf5: version bump.
Drop fortran2003 use flag, replace rpath hacks with hprefixify. Reported-by: Erik Quaeghebeur <gentoobugzilla@equaeghe.nospammail.net> Closes: https://bugs.gentoo.org/600656 Package-Manager: Portage-2.3.16, Repoman-2.3.6 - Alexis Ballier · gentoo
sci-libs/hdf5: keyword ~arm64
Package-Manager: Portage-2.3.6, Repoman-2.3.2 - Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> - T. Malfatti · gentoo
media-libs/portaudio: Version bump - Justin Lecher · gentoo
sci-libs/hdf5: Drop vulnerable versions for CVE-2016-4330
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=604386 Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Agostino Sarubbo · gentoo
sci-libs/hdf5: ppc64 stable wrt bug #601404
Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="ppc64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-libs/hdf5: ppc stable wrt bug #601404
Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-libs/hdf5: ia64 stable wrt bug #601404
Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="ia64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-libs/hdf5: sparc stable wrt bug #601404
Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="sparc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-libs/hdf5: x86 stable wrt bug #601404
Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-libs/hdf5: amd64 stable wrt bug #601404
Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Tobias Klausmann · gentoo
sci-libs/hdf5-1.8.18-r0: stable on alpha
Gentoo-Bug: 601404 - Kacper Kowalik · gentoo
sci-libs/hdf5: version bump
Fixes security bugs: #601404, #601408, #601414, #601420 Package-Manager: portage-2.3.2 - Alexis Ballier · gentoo
sci-libs/hdf5: Allow cxx & mpi at the same time.
This allows to install sci-lib/flann-1.9.1[mpi] for example. See: http://hdf-forum.184993.n3.nabble.com/hdf-forum-HDF5-enable-cxx-enable-threadsafe-conflict-ubuntu-debian-packages-td194242.html Package-Manager: portage-2.3.1 - Kacper Kowalik · gentoo
sci-libs/hdf5: add use flag for enabling high level API
Fixes bug #594560 reported by eroen <gentoo@eroen.eu> Package-Manager: portage-2.2.28 - Kacper Kowalik · gentoo
sci-libs/hdf5: update SRC_URI, fixes #594454
Package-Manager: portage-2.2.28 - Kacper Kowalik · gentoo
sci-libs/hdf5: version bump
Package-Manager: portage-2.2.28 - Sébastien Fabbro · gentoo
sci-libs/hdf5: switched to virtual/szip
Package-Manager: portage-2.2.27 - Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed