Octave for Debian systems: Difference between revisions
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==== HDF5 ==== | ==== HDF5 ==== | ||
On current versions of Debian and Ubuntu, you may get the following warning when building an older version of Octave from source: | |||
HDF5 library not found. Octave will not be able to save or load HDF5 data files. | HDF5 library not found. Octave will not be able to save or load HDF5 data files. | ||
Revision as of 00:39, 6 July 2016
For Debian, and Debian-based distributions such as Ubuntu, specific solutions.
Pre-compiled binaries
Binary packages for Octave and many Octave-Forge packages are provided by all versions of Debian and Ubuntu. These are the most well-tested binaries available and should work best for most users.
sudo apt-get install octave
Aside the octave package that installs GNU Octave, other pieces of it are split over multiple packages. These are octave-doc, octave-info, and octave-htmldoc for the documentation; liboctave-dev for the octave development header files and mkoctfile (required to install Octave Forge packages); and octave-dbg for the debugging symbols.
For Debian stable users, there may also be newer packages available in backports, so don't forget to check there.
Octave packages
Many Octave packages are also distributed by your Linux distribution. These are tested to work the best with your Octave version. For example:
sudo apt-get install octave-control octave-image octave-io octave-optim octave-signal octave-statistics
Octave's Personal Package Archive (PPA) for Ubuntu
For some Ubuntu releases the octave packages are too old (Ubuntu 12.04 only has Octave version 3.2). The GNU Octave Team on Launchpad maintains a PPA providing more up to date packages of Octave for all versions of Ubuntu. These are backported from Debian unstable (the Ubuntu Octave Team needs help testing and preparing the packages so if you can help with this, contact Mike Miller). To set up your system to install these packages:
sudo apt-add-repository ppa:octave/stable sudo apt-get update sudo apt-get install octave
Compiling from source
The only tricky part is to install the dependencies. Once that is solved, installing from source should be as easy as ./configure && make && make install. See the manual for configure options and below for some common examples.
Install dependencies
Note that different Debian and Ubuntu versions may have slightly different package names but their differences should be pretty small, mostly limited to version numbers.
The easy way (but likely incorrect)
This approach is only suitable if you are building from source the same version that your Linux distribution already has packaged.
The easy way to install most of the necessary dependencies is to sudo apt-get build-dep octave. This will install all packages necessary to build and prepare a Debian package for the octave version available on your system repositories. However:
- will install unnecessary packages related to the building of a Debian package;
- may miss some new dependencies;
- may install packages that are no longer octave dependencies.
The even easier way (but experimental)
The MXE-octave package provides a way to compile Octave for different platforms. Dependencies and certain flags are handled automatically.
The right way
The right way is to select and install all the dependencies as listed in the INSTALL.OCTAVE file. The following are their package names in Debian repositories (they will have their own dependencies which your package manager will solve automatically). If you are building development versions, you'll require some more packages as listed on etc/HACKING and INSTALL. Many of them will already be installed on your system. Install the dependencies by typing
sudo apt-get install
followed by the package names of the table below.
- The Debian repositoriy has several libraries for dealing with HDF data files. The recommended is
libhdf5-serial-dev. However, the msh package requires gmsh which is incompatible with it. - The GraphicsMagick++ library (libgraphicsmagick++1-dev) on the Debian repositories was compiled with quantum 8 which limits reading images to 8 bit. The solution is to recompile GraphicsMagick with quantum 16 or 32 before building Octave.
Configuration
As mentioned above, Octave can be compiled with the default settings using ./configure && make && make install. You can also tweak the setup using configure options. Some examples are given below for a Linux system.
64 bit
To get 64-bit requires all linked libraries to support 64-bit variables. You can omit most of these except BLAS which gives a fatal error. This is remedied by compiling OpenBLAS with edits to its Makefile.rule so that BINARY=64 INTERFACE64=1.
./configure LD_LIBRARY_PATH=/opt/OpenBLAS/lib CPPFLAGS=-I/opt/OpenBLAS/include LDFLAGS=-L/opt/OpenBLAS/lib --enable-64
Java
Autodetection for java should work well in Debian systems. It can still be
specified by defining JAVA_HOME
./configure JAVA_HOME="/usr/lib/jvm/java-7-openjdk-amd64"
HDF5
On current versions of Debian and Ubuntu, you may get the following warning when building an older version of Octave from source:
HDF5 library not found. Octave will not be able to save or load HDF5 data files.
The problem is that there are multiple versions of the hdf5 package. Octave was written with the serial version in mind but it is likely to work with the others (OpenMPI and Mpich). Due to the naming scheme done in Debian, it is required to specify the location of the libraries. See bug #38928 for details (starting with comment #19) but basically, use the following when running configure:
./configure --with-hdf5-includedir=/usr/include/hdf5/serial --with-hdf5-libdir=/usr/lib/x86_64-linux-gnu/hdf5/serial