NiPy on Windows

Some work has been done on testing the development version of NiPy on windows. You will need enthon and subversion and MinGW (or some other compiler). For visualization, you will also need a current version of matplotlib.

Enthon

Note that you need enthon for python2.4 -- here is the installer.

Subversion

There is no specific version dependency -- here is a direct link to the installer. Note that the test data downloaded by svn is corrupted -- working on this.

MinGW

Here is a version of the MinGW tool suite installer that is known to work.

Instructions

* After installing all of the above components, checkout the svn repository 

http://neuroimaging.scipy.org/svn/ni/ni/trunk

* In the root nipy directory (wherever you checked out the above to), build the enthought.traits module with 

python setup.py build_ext --inplace --compiler=mingw32

An easy way to do this is to open an IPython shell (which I find easier to use than the standard Windows command prompt) and run 

!python setup.py build_ext --inplace --comipler=mingw32

* The version of scipy that ships with enthon does not have the scipy.sandbox.models package. Here is an installer.

* You should be ready to test. Again in IPython: 

run test

* To build an installer, in the same directory in IPython: 

!python setup.py bdist_wininst

Building Scipy/Numpy on Windows with Optimized Numerical Libraries

This involves compiling several libraries (ATLAS, LAPACK, FFTW and UMFPACK) and then building numpy and scipy from SVN source. But as with most things Windows, this turns out to be a slightly tricky affair.

The following has been tested on Windows Vista Enterprise 32bit only, but should theoretically work on other Windows platforms. It also used Python 2.5.

Ideally, a big chunk of this wiki should move to the scipy/numpy site. And also ideally should become a single script. But it's also good to know exactly how you got there.

Prerequisites

  • You need Windows Vista enterprise/ultimate with SUA enabled and installed or Windows (others, including other Vista variants) with Cygwin installed. You cannot install the SUA package on a non enterprise or ultimate Vista edition.
  • MinGW (installer) with gcc 3.4.5 (choose the candidate option when installing) and the msys environment installed. You will need to download the following packages for msys:
    • bzip2-1.0.3-MSYS-1.0.11-snapshot.tar.bz2
    • coreutils-5.97-MSYS-1.0.11-snapshot.tar.bz2
    • diffutils-2.8.7-MSYS-1.0.11-snapshot.tar.bz2
    • gawk-3.1.5-MSYS-1.0.11-snapshot.tar.bz2
    • make-3.81-MSYS-1.0.11-snapshot.tar.bz2
    • msysCORE-1.0.11-2007.01.19-1.tar.bz2
    • binutils-2.17.50-20070129-1.tar.gz

Just unpack all the package contents in a single directory and copy them over to the MinGW installation directory. You may want to add the following to the system path: 

   set PATH=[PATH TO]\MinGW;[PATH TO]\MinGW\libexec\gcc\mingw32\3.4.5;%PATH%

Installation

  • Create a directory called BUILDS, BUILDS/lib, BUILDS/include
  • Unpack all the numerical library files in BUILDS
  • Create subversion check out directories for scipy and numpy in BUILDS
  • Start SUA c-shell or cygwin shell
  • Start msys.bat 
       PATH=/mingw/libexec/gcc/mingw32/3.4.5:$PATH; export PATH
  • Change directory to location of BUILDS. (/dev/fs/driveletter/... in SUA, /cygdrive/driveletter/... in cygwin, /driveletter/... in msys)

Compiling ATLAS

  • This is done in the SUA/Cygwin shell. In Cygwin you probably want to follow the instructions at Installing Scipy on Windows
  • cd ATLAS; mkdir build; cd build
  • Run ../configure (This will probably fail but will leave you with xconfig)
  • Run ./xconfig --help (to see all options)
  • Run ../configure -O 8 -A 16 -m 3189 -b 32 (replacing the values with your machine configuration)
  • Edit Make.inc to provide correct L2SIZE
  • Run make (leave your computer and go do something else for about an hour)

Compiling LAPACK

  • This is done in the msys shell
  • cd lapack_XX
  • Copy make.inc.example to make.inc
  • Edit the following lines in make.inc 
       PLAT = _NT
   OPTS = -funroll-all-loops -O3 -malign-double -msse2
   BLASLIB      = -L/driveletter/[PATH TO]/BUILDS/ATLAS/build/lib -lf77blas -latlas
  • Run make lib

Combining LAPACK and ATLAS

  • Stay in the msys shell after compiling LAPACK
  • Go to the ATLAS/build/lib directory
  • Execute the following commands: 
       mkdir tmp; cd tmp
   cp ../liblapack.a ../liblapack_ATLAS.a
   ar -x ../liblapack.a
   cp [PATH TO]/lapack_NT.a ../liblapack.a
   ar -r ../liblapack.a *.o
   rm *.o
   ar -x ../liblapack.a xerbla.o
   ar -r ../libf77blas.a xerbla.o
  • Copy liblapack.a, libf77blas.a, libcblas.a, libatlas.a to BUILDS/lib
  • Copy the ATLAS/include to BUILDS/include/ATLAS

Compiling UMFPACK

  • Stay in msys shell
  • Goto UFconfig
  • Edit UFConfig/UFconfig.mk 
       BLAS   = -L/driveletter/[PATH TO]/BUILDS/lib -llapack -lf77blas -lcblas -latlas -lg2c
   LAPACK = -L/driveletter/[PATH TO]/BUILDS/lib -llapack -lf77blas -lcblas -latlas -lg2c
   XERBLA =
  • Run the following commands 
       cd ..\AMD
   make
   cd ..\UMFPACK
   make
  • Copy libamd.a (from AMD), libumfpack.a (from UMFPACK) to BUILDS/lib
  • Copy UMFPACK/include to BUILDS/include/UMFPACK
  • Copy UFconfig/ufconfig.h to BUILDS/include
  • Copy AMD/include/amd.h to BUILDS/include

Compiling fftw

  • Stay in msys shell
  • Goto fftw_XX
  • mkdir build; cd build
  • Run the following command 
       ../configure --prefix=/c/DOWNLOADS/BUILDS/ --enable-sse2 --disable-dependency-tracking --enable-threads --with-our-malloc16 --with-windows-f77-mangling --with-combined-threads
  • Run make OR make -j 4 if you have multiple processors (it'll make things go faster. This build on msys in vista takes a while)
  • Copy .libs/libfftw3.a to BUILDS/lib
  • Copy fftw_XX/api/fftw3.h to BUILDS/include

Compling numpy/scipy

  • Open a Windows cmd window and make sure you can execute python.
  • Make a copy of each of the libs in BUILDS/lib and rename them from libname.a to name.lib
  • Rename lapack.lib to flapack.lib
  • rename site.cfg.example to site.cfg
  • Edit site.cfg in the numpy directory. Replace the blas_opt and lapack_opt section with: 
       [atlas]
   libraries = f77blas, cblas, atlas, g2c
   library_dirs = driveletter:\[PATH TO]\MinGW\lib;driveletter:\[PATH TO]\BUILDS\lib
   include_dirs = driveletter:\[PATH TO]\BUILDS\include\ATLAS

   [lapack]
   libraries = flapack, f77blas, cblas, atlas
   library_dirs = driveletter:\[PATH TO]\MinGW\lib;driveletter:\[PATH TO]\BUILDS\lib

   [amd]
   library_dirs = driveletter:\[PATH TO]\MinGW\lib;driveletter:\[PATH TO]\BUILDS\lib
   include_dirs = driveletter:\[PATH TO]\BUILDS\include
   libraries = amd

   [umfpack]
   library_dirs = driveletter:\[PATH TO]\MinGW\lib;driveletter:\[PATH TO]\BUILDS\lib
   include_dirs = driveletter:\[PATH TO]\BUILDS\include\UMFPACK
   libraries = umfpack
   
   [fftw3]
   library_dirs = driveletter:\[PATH TO]\MinGW\lib;driveletter:\[PATH TO]\BUILDS\lib
   include_dirs = driveletter:\[PATH TO]\BUILDS\include
   libraries = fftw3
  • Edit numpy/distutils/fcompiler/gnu.py. Find the line that says opt.append('gcc') and comment it # opt.append('gcc'). This is probably a Vista SUA thing and perhaps won't be required when using Cygwin to compile ATLAS.
  • Copy site.cfg to ../scipy/site.cfg
  • Compile numpy: 
       cd numpy
   python setup.py config --compiler=mingw32 build --compiler=mingw32 bdist_wininst
  • Install numpy from the numpy/dist folder
  • Create a file called enabled_packages.txt in scipy/Lib/sandbox and insert the following (only models is necessary for NiPy but the others may be useful): 
       models
   rbf
   svm
   timeseries
   wavelet
  • Compile scipy: 
       cd scipy
   python setup.py config --compiler=mingw32 build --compiler=mingw32 bdist_wininst
  • Install scipy from the scipy/dist folder
  • Test installations. In python run: 
       import numpy
   import scipy
   numpy.test()
   scipy.test()
   numpy.show_config()
   scipy.show_config()