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374 lines
10 KiB
Text
Executable file
Building and installing SciPy
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+++++++++++++++++++++++++++++
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See http://www.scipy.org/scipy/scipy/wiki/GetCode
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for updates of this document.
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.. Contents::
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INTRODUCTION
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============
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It is *strongly* recommended that you use the binary packages on your platform
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if they are available, in particular on Windows and Mac OS X. You should not
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attempt to build SciPy if you are not familiar with compiling softwares from
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sources.
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PREREQUISITES
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=============
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SciPy requires the following software installed for your platform:
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1) Python__ 2.4.x or newer
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__ http://www.python.org
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2) NumPy__ 1.4.1 or newer (note: SciPy trunk at times requires latest NumPy
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trunk).
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__ http://www.numpy.org/
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Windows
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-------
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Compilers
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~~~~~~~~~
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It is recommended to use the mingw__ compilers on Windows: you will need gcc
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(C), g++ (C++) and g77 (Fortran) compilers.
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__ http://www.mingw.org
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Blas/Lapack
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~~~~~~~~~~~
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Blas/Lapack are core routines for linear algebra (vector/matrix operations).
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You should use ATLAS__ with a full LAPACK, or simple BLAS/LAPACK built with g77
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from netlib__ sources. Building those libraries on windows may be difficult, as
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they assume a unix-style environment. Please use the binaries if you don't feel
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comfortable with cygwin, make and similar tools.
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__ http://math-atlas.sourceforge.net/
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__ http://www.netlib.org/lapack/
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Mac OS X
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--------
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Compilers
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~~~~~~~~~
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It is recommended to use gcc. gcc is available for free when installing
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Xcode__, the developer toolsuite on Mac OS X. You also need a fortran compiler,
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which is not included with Xcode: you should use gfortran from this page:
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__ http://r.research.att.com/tools/
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Please do NOT use gfortran from hpc.sourceforge.net, it is known to generate
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buggy scipy binaries.
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__Xcode: http://developer.apple.com/TOOLS/xcode
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Blas/Lapack
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~~~~~~~~~~~
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Mac OS X includes the Accelerate framework: it should be detected without any
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intervention when building SciPy.
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Linux
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-----
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Most common distributions include all the dependencies. Here are some
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instructions for the most common ones:
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Ubuntu >= 8.10
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~~~~~~~~~~~~~~
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You can get all the dependencies as follows::
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sudo apt-get install python python-dev libatlas3-base-dev gcc gfortran g++
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Ubuntu < 8.10, Debian
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~~~~~~~~~~~~~~~~~~~~~
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You can get all the dependencies as follows::
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sudo apt-get install python python-dev atlas3-base-dev gcc g77 g++
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OpenSuse >= 10
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~~~~~~~~~~~~~~
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RHEL
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~~~~
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Fedora Core
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~~~~~~~~~~~
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GETTING SCIPY
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=============
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For the latest information, see the web site:
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http://www.scipy.org
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Development version from Subversion (SVN)
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-----------------------------------------
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Use the command::
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svn co http://svn.scipy.org/svn/scipy/trunk scipy
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Before building and installing from SVN, remove the old installation
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(e.g. in /usr/lib/python2.4/site-packages/scipy or
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$HOME/lib/python2.4/site-packages/scipy). Then type::
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cd scipy
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rm -rf build
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python setup.py install
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INSTALLATION
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============
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First make sure that all SciPy prerequisites are installed and working
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properly. Then be sure to remove any old SciPy installations (e.g.
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/usr/lib/python2.4/site-packages/scipy or $HOME/lib/python2.4/
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site-packages/scipy). On windows, if you installed scipy previously from a
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binary, use the remove facility from the add/remove softwares panel, or remote
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the scipy directory by hand if you installed from sources (e.g.
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C:\Python24\Lib\site-packages\scipy for python 2.4).
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From tarballs
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-------------
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Unpack ``SciPy-<version>.tar.gz``, change to the ``SciPy-<version>/``
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directory, and run
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::
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python setup.py install
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This may take several minutes to an hour depending on the speed of your
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computer. To install to a user-specific location instead, run::
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python setup.py install --prefix=$MYDIR
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where $MYDIR is, for example, $HOME or $HOME/usr.
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** Note 1: On Unix, you should avoid installing in /usr, but rather in
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/usr/local or somewhere else. /usr is generally 'owned' by your package
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manager, and you may overwrite a packaged scipy this way.
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TESTING
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=======
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To test SciPy after installation (highly recommended), execute in Python
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>>> import scipy
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>>> scipy.test()
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To run the full test suite use
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>>> scipy.test('full')
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Please note that you must have version 0.10 or later of the 'nose' test
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framework installed in order to run the tests. More information about nose is
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available on the website__.
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__ http://somethingaboutorange.com/mrl/projects/nose/
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COMPILER NOTES
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==============
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Note that SciPy is developed mainly using GNU compilers. Compilers from
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other vendors such as Intel, Absoft, Sun, NAG, Compaq, Vast, Porland,
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Lahey, HP, IBM are supported in the form of community feedback.
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gcc__ compiler is recommended. gcc 3.x and 4.x are known to work.
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If building on OS X, you should use the provided gcc by xcode tools, and the
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gfortran compiler available here:
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http://r.research.att.com/tools/
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You can specify which Fortran compiler to use by using the following
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install command::
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python setup.py config_fc --fcompiler=<Vendor> install
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To see a valid list of <Vendor> names, run::
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python setup.py config_fc --help-fcompiler
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IMPORTANT: It is highly recommended that all libraries that scipy uses (e.g.
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blas and atlas libraries) are built with the same Fortran compiler. In most
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cases, if you mix compilers, you will not be able to import scipy at best, have
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crashes and random results at worse.
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__ http://gcc.gnu.org/
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Using non-GNU Fortran compiler with gcc/g77 compiled Atlas/Lapack libraries
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---------------------------------------------------------------------------
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When Atlas/Lapack libraries are compiled with GNU compilers but
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one wishes to build scipy with some non-GNU Fortran compiler then
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linking extension modules may require -lg2c. You can specify it
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in installation command line as follows::
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python setup.py build build_ext -lg2c install
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If using non-GNU C compiler or linker, the location of g2c library can
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be specified in a similar manner using -L/path/to/libg2c.a after
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build_ext command.
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Intel Fortran Compiler
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----------------------
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Note that code compiled by the Intel Fortran Compiler (IFC) is not
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binary compatible with code compiled by g77. Therefore, when using IFC,
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all Fortran codes used in SciPy must be compiled with IFC. This also
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includes the LAPACK, BLAS, and ATLAS libraries. Using GCC for compiling
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C code is OK. IFC version 5.0 is not supported (because it has bugs that
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cause SciPy's tests to segfault).
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Minimum IFC flags for building LAPACK and ATLAS are
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::
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-FI -w90 -w95 -cm -O3 -unroll
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Also consult 'ifc -help' for additional optimization flags suitable
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for your computers CPU.
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When finishing LAPACK build, you must recompile ?lamch.f, xerbla.f
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with optimization disabled (otherwise infinite loops occur when using
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these routines)::
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make lapacklib # in /path/to/src/LAPACK/
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cd SRC
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ifc -FI -w90 -w95 -cm -O0 -c ?lamch.f xerbla.f
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cd ..
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make lapacklib
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KNOWN INSTALLATION PROBLEMS
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===========================
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BLAS sources shipped with LAPACK are incomplete
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-----------------------------------------------
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Some distributions (e.g. Redhat Linux 7.1) provide BLAS libraries that
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are built from such incomplete sources and therefore cause import
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errors like
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::
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ImportError: .../fblas.so: undefined symbol: srotmg_
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Fix:
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Use ATLAS or the official release of BLAS libraries.
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LAPACK library provided by ATLAS is incomplete
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----------------------------------------------
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You will notice it when getting import errors like
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::
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ImportError: .../flapack.so : undefined symbol: sgesdd_
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To be sure that SciPy is built against a complete LAPACK, check the
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size of the file liblapack.a -- it should be about 6MB. The location
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of liblapack.a is shown by executing
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::
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python /lib/python2.4/site-packages/numpy/distutils/system_info.py
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(or the appropriate installation directory).
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To fix: follow the instructions in
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http://math-atlas.sourceforge.net/errata.html#completelp
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to create a complete liblapack.a. Then copy liblapack.a to the same
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location where libatlas.a is installed and retry with scipy build.
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Using non-GNU Fortran Compiler
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------------------------------
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If import scipy shows a message
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::
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ImportError: undefined symbol: s_wsfe
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and you are using non-GNU Fortran compiler, then it means that any of
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the (may be system provided) Fortran libraries such as LAPACK or BLAS
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were compiled with g77. See also compilers notes above.
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Recommended fix: Recompile all Fortran libraries with the same Fortran
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compiler and rebuild/reinstall scipy.
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Another fix: See `Using non-GNU Fortran compiler with gcc/g77 compiled
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Atlas/Lapack libraries` section above.
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TROUBLESHOOTING
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===============
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If you experience problems when building/installing/testing SciPy, you
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can ask help from scipy-user@scipy.org or scipy-dev@scipy.org mailing
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lists. Please include the following information in your message:
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NOTE: You can generate some of the following information (items 1-5,7)
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in one command::
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python -c 'from numpy.f2py.diagnose import run; run()'
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1) Platform information::
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python -c 'import os,sys;print os.name,sys.platform'
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uname -a
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OS, its distribution name and version information
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etc.
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2) Information about C,C++,Fortran compilers/linkers as reported by
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the compilers when requesting their version information, e.g.,
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the output of
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::
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gcc -v
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g77 --version
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3) Python version::
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python -c 'import sys;print sys.version'
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4) NumPy version::
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python -c 'import numpy;print numpy.__version__'
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5) ATLAS version, the locations of atlas and lapack libraries, building
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information if any. If you have ATLAS version 3.3.6 or newer, then
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give the output of the last command in
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::
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cd scipy/Lib/linalg
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python setup_atlas_version.py build_ext --inplace --force
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python -c 'import atlas_version'
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7) The output of the following commands
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::
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python INSTALLDIR/numpy/distutils/system_info.py
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where INSTALLDIR is, for example, /usr/lib/python2.4/site-packages/.
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8) Feel free to add any other relevant information.
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For example, the full output (both stdout and stderr) of the SciPy
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installation command can be very helpful. Since this output can be
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rather large, ask before sending it into the mailing list (or
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better yet, to one of the developers, if asked).
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9) In case of failing to import extension modules, the output of
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::
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ldd /path/to/ext_module.so
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can be useful.
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You may find the following notes useful:
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http://www.tuxedo.org/~esr/faqs/smart-questions.html
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http://www.chiark.greenend.org.uk/~sgtatham/bugs.html
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