sci-libs / hdf5

General purpose library and file format for storing scientific data

Official package sites : http://www.hdfgroup.org/HDF5/ ·

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.

v1.10.5 :: 0/1.10.5 :: gentoo

Modified
License
NCSA-HDF
Keywords
alpha amd64 arm64 ia64 ppc ppc64 sparc x86 ~amd64-linux ~arm ~x86-fbsd ~x86-linux
USE flags
cxx debug examples fortran hl mpi static-libs szip threads zlib

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
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
static-libs
Build static versions of dynamic libraries as well
szip
Use the szip compression library
threads
Add threads support for various packages. Usually pthreads
zlib
Add support for zlib (de)compression

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

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

dev-lang / gdl : GNU Data Language

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

media-gfx / alembic : Open framework for storing and sharing scene data

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-video / ffmpeg : Complete solution to record, convert and stream audio and video. Includes libavcodec

sci-astronomy / casacore : Core libraries for the Common Astronomy Software Applications

sci-biology / kallisto : Near-optimal RNA-Seq quantification

sci-chemistry / avogadro2 : Advanced molecule editor and visualizer 2

sci-chemistry / freeon : An experimental suite of programs for linear scaling quantum chemistry

sci-chemistry / votca-csg : Votca coarse-graining engine

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 / cbflib : Library providing a simple mechanism for accessing CBF files and imgCIF files

sci-libs / cgnslib : CFD General Notation System standard library

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 / libmed : A library to store and exchange meshed data or computation results

sci-libs / mathgl : Math Graphics Library

sci-libs / matio : Library for reading and writing matlab files

sci-libs / netcdf : Scientific library and interface for array oriented data access

sci-libs / o2scl : Object-oriented Scientific Computing Library

sci-libs / shogun : Large Scale Machine Learning Toolbox

sci-libs / silo : A mesh and field I/O library and scientific database

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 / xmds : XMDS - The eXtensible Multi-Dimensional Simulator

sci-misc / h5utils : Utilities for visualization and conversion of HDF5 files

sci-physics / espresso : Extensible Simulation Package for Research on Soft matter

sci-physics / lammps : Large-scale Atomic/Molecular Massively Parallel Simulator

sci-physics / meep : Simulation software to model electromagnetic systems

sci-physics / sassena : Software for Calculating Scattering Diagrams on Massively Parallel Computers

sci-visualization / labplot : Scientific data analysis and visualisation based on KDE Frameworks

sci-visualization / paraview : Powerful scientific data visualization application

sci-visualization / visit : A software that delivers parallel interactive visualizations

sys-cluster / slurm : A Highly Scalable Resource Manager

sys-devel / byfl : Compiler-based Application Analysis

560964
sci-libs/hdf5 - hdf5-1.8.9-mpicxx.patch causes macro redefinition warnings with clang-3.7
645692
sci-libs/netcdf-4.3.2-r1 with sci-libs/hdf5-1.10.1 - .../work/netcdf-4.3.2/libsrc4/nc4internal.c:417:1: error: conflicting types for 'nc4_rec_find_nc_type'
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
678264
<sci-libs/hdf5-1.10.5: multiple vulnerabilities
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
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