Compiling EMAN2 on Linux System

Required Libraries / Programs

The following libraries are required for EMAN2 installation (the libraries should be installed as shared-object libraries where applicable):

1. fftw (version 2.1.3+) (http://www.fftw.org/) To install fftw from source use either configure option:

   % ./configure --enable-static=no --enable-shared=yes --enable-float --enable-type-prefix

   OR

   % ./configure --enable-shared=yes --enable-float

   Followed by:

   % make

2. gsl (version 1.3+) (http://www.gnu.org/software/gsl/)

   % ./configure
   % make

3. Boost (version 1.32+) (http://www.boost.org) 3.1 Installing Boost requires Boost.Jam. Executables and source code for jam can be found at the Boost website.

   Installing Boost requires the user to identify a particular toolset to use during compilation. Most UNIX systems will probably use the "gcc" toolset; visit http://www.boost.org/more/getting_started.html#Tools for a complete listing.

   % bjam "-sTOOLS=gcc" install

   Header files from the Boost installation (located in the "boost" subdirectory of the Boost installation (eg. /boost_1_32_0/boost)) must now either be added to the compilers path or copied into an existing location on the path in a subdirectory /boost. One possibility for this might be:

   % cp -r boost /usr/include/boost

4. CMake (version 2.0.6+) (http://www.cmake.org) Executables for several platforms are available; source code can also be used for custom installations.

Optional Libraries / Programs

• To read/write HDF5 image, use hdf5 (http://hdf.ncsa.uiuc.edu/HDF5).

• To read TIFF image, use libtiff (http://www.libtiff.org)

• To read PNG image, use PNG (http://www.libpng.org) For development the following libraries/programs are required (see Appendix A for installation help):

• Python (version 2.2+) (http://www.python.org)

• Boost Python (version 1.32+) (http://www.boost.org)

• numpy (http://www.scipy.org)

Quick Installation

Suppose you have source code eman2.tar.gz

1. % cd $HOME
   % mkdir -p EMAN2/src
   % cd EMAN2/src
   % gunzip eman2.tar.gz
   % tar xf eman2.tar

2. % mkdir build
   % cd build

3. % cmake ../eman2
   % make
   % make install

4. Set up login shell for csh/tcsh, put the following to your .cshrc or .tcshrc file:

   setenv EMAN2DIR $home/username/EMAN2
   setenv PATH $EMAN2DIR/bin:${PATH}
   setenv LD_LIBRARY_PATH  $EMAN2DIR/lib
   setenv PYTHONPATH .:$HOME/EMAN2/lib

   For bash in .bashrc add:

   export EMAN2DIR=/home/username/EMAN2
   export PATH=$PATH:$EMAN2DIR/bin
   export LD_LIBRARY_PATH=$EMAN2DIR/lib
   export PYTHONPATH=$PYTHONPATH:$HOME/EMAN2/lib

Advanced Installation

If your libraries (fftw, gsl, hdf, etc) are not found by Quick Installation, or if you want to change the compilation options, the following steps help:

1. Follow the first 2 steps in Quick Installation.
2. If your libraries are not installed at the default places, set up the related environment variables:

   • fftw -> FFTWDIR

   • gsl -> GSLDIR

   • tiff -> TIFFDIR

   • png -> PNGDIR

   • hdf5 -> HDF5DIR

   • python -> PYTHON_ROOT and PYTHON_VERSION

3. % ccmake ../eman2

4. Type 'c' if it asks about "CMAKE_BACKWARDS_COMPATIBILITY".
5. Make necessary changes for compilation flags.
   • Developers will probably want to set BOOST-LIBRARY to a Boost.Python object file (ex. libboost_python-gcc-1_32.so)
6. Then type 'c', and type 'g'.

7. % make
   % make install

Platform Dependent Optimization

In CMake Configuration, enable the following option for your platform:

• Athlon:                         ENABLE_ATHLON
  Opteron(AMD64):                 ENABLE_OPTERON
  Mac G5:                         ENABLE_G5

How to Generate Latest Documentation

1. Install doxygen (version 1.4.3+, http://www.doxygen.org)

2. Install graphviz (http://www.graphviz.org/)

3. install latex (http://www.latex-project.org/)

4. After you have a successful EMAN2 install, i.e., you can import EMAN2 in Python,

   cd EMAN2/src/build
   ccmake ../eman2

   Type 't' toggle to advanced mode,

   check ENABLE_AUTODOC to ON
   make 
   make install

   All documents will be in your EMAN2/doc directory.

Notes For Developers

1. For Emacs users, please add the following line to your $HOME/.emacs:

   (setq default-tab-width 4)

2. Ensure the Boost.Python
3. To generate new boost python wrapper, run

   % cd eman2/libpyEM
   % ./create_boost_python

4. Windows Installer

   EMAN uses "Nullsoft Scriptable Install System" (http://nsis.sourceforge.net/) to generate the windows installer. It also uses "HM NIS Edit" (http://hmne.sourceforge.net/) as the editor.

Appendix A

A.1. How to Install Boost Python

1. Download 'bjam' for your platform.

2. Download boost source from http://www.boost.org. Assume the version is boost_1_32_0.

   % cd /usr/local/src; tar zxf boost_1_32_0.tar.gz; cd boost_1_32_0.

3. Set up environment variables "PYTHON_ROOT" and "PYTHON_VERSION". For example, if your python is at /usr/bin/python then PYTHON_ROOT is

• "/usr". If your python version is 2.2.X, PYTHON_VERSION is '2.2'.
  • a) Check your shell:

    % echo $SHELL

    b) If you are using bash/zsh, do

    % export PYTHON_VERSION=2.2
    % export PYTHON_ROOT=/usr

    If you are using csh/tcsh, do

    % setenv PYTHON_VERSION 2.2
    % setenv PYTHON_ROOT /usr

  1. cd libs/python/build [didn't do this]
  2. run 'bjam' with your options:
     • a) linux-x86: % bjam b) SGI Irix: % bjam "-sTOOLS=mipspro" c) Mac OS X: % bjam "-sTOOLS=darwin"
  3. login as root

  4. cp -df bin-stage/libboost_python.so* /usr/local/lib
     cd ../../..; cp -rf boost /usr/local/include

A.2. How to use your own python version

• If the python you want to use in your computer is not found by CMake, you may set up environment variables "PYTHON_ROOT" and "PYTHON_VERSION". For example, if your python is at /usr/local/python2.4/bin/python. PYTHON_ROOT is "/usr/local/python2.4". if your python is 2.4.X, PYTHON_VERSION is '2.4'.

A.3. How to Install numpy

• From the website http://sourceforge.net/projects/numpy download source package. For windows, run the binary installer and the installation is complete. Other users must download the source code and install manually as follows: - get source code numpy-1.0.1.tar.gz - % gunzip numpy-1.0.1.tar.gz

  • % tar xf numpy-1.0.1.tar
  - login as root - % cd numpy-1.0.1;
  • % python setup.py install