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Installation from Source: Historical notes on older versions
For installing the latest versions of MDAnalysis see the Install notes.
Older versions of MDAnalysis had different requirements and for historical reasons they are listed here:
up to 0.7.2
A LAPACK library is required (standard LAPACK/BLAS, ATLAS, or the Intel Math Kernel Library (MKL); on Mac OS X we simply use the native fast VecLib framework so you don't have to install anything else).
Fast math libraries
On Mac OS X we use the systems vecLib for fast linear algebra and nothing needs to be configured. On Linux you will probably want to use something such as ATLAS or the Intel Math Kernel Libraries for better performance for the rms fitting.
The fast math library paths are set in
setup.cfg. By default we ship a template file
setup.cfg.template that you can
cp setup.cfg.template setup.cfg
and edit. See the file itself for examples and the ones below.
Linux section of
setup.cfg (your paths are probably different from the
ones in this example)::
[linux] fast_numeric_include = /opt/intel/cmkl/10.0.5.025/include fast_numeric_linkpath = /opt/intel/cmkl/10.0.5.025/lib/em64t fast_numeric_libs = mkl_lapack mkl guide
Example ATLAS LAPACK
If you want to use the ATLAS LAPACK libraries use something such as ::
[linux] fast_numeric_include = /usr/include fast_numeric_linkpath = /usr/lib/atlas fast_numeric_libs = lapack
Your paths could be different. Use a command such as
or your package manager to get an idea of where the files are to be found.
On some versions of Ubuntu we had to use
[linux] # Ubuntu 9.04 i686 fast_numeric_include = /usr/include fast_numeric_linkpath = /usr/lib/sse2/atlas fast_numeric_libs = lapack
Adding lapack packages
sudo apt-get install liblapack-dev # see below for notes on fast_numeric_*